Starting phenix.real_space_refine on Fri Sep 27 15:36:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/09_2024/6hxx_0297_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/09_2024/6hxx_0297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/09_2024/6hxx_0297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/09_2024/6hxx_0297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/09_2024/6hxx_0297_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/09_2024/6hxx_0297_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 175 5.49 5 S 490 5.16 5 C 40600 2.51 5 N 11235 2.21 5 O 13265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 65765 Number of models: 1 Model: "" Number of chains: 2 Chain: "BD" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Bd" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Restraints were copied for chains: BE, BF, BG, BA, BB, BC, BH, BI, AA, AC, AB, AE, AD, AG, AF, AI, AH, AK, AJ, AM, AL, AO, AN, AQ, AP, AS, AR, AU, AT, AW, AV, AY, AX, AZ, Be, Bf, Bg, Ba, Bb, Bc, Bh, Bi, Aa, Ac, Ab, Ae, Ad, Ag, Af, Ai, Ah, Ak, Aj, Am, Al, Ao, An, Aq, Ap, As, Ar, Au, At, Aw, Av, Ay, Ax, Az Time building chain proxies: 11.11, per 1000 atoms: 0.17 Number of scatterers: 65765 At special positions: 0 Unit cell: (143.235, 143.235, 253.579, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 490 16.00 P 175 15.00 O 13265 8.00 N 11235 7.00 C 40600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.51 Conformation dependent library (CDL) restraints added in 6.4 seconds 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14840 Finding SS restraints... Secondary structure from input PDB file: 315 helices and 70 sheets defined 44.6% alpha, 5.4% beta 0 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 15.70 Creating SS restraints... Processing helix chain 'AA' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAA 72 " --> pdb=" O GLUAA 68 " (cutoff:3.500A) Processing helix chain 'AA' and resid 86 through 100 Processing helix chain 'AA' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAA 111 " --> pdb=" O GLUAA 107 " (cutoff:3.500A) Processing helix chain 'AA' and resid 145 through 152 Processing helix chain 'AA' and resid 155 through 161 removed outlier: 3.604A pdb=" N ILEAA 159 " --> pdb=" O THRAA 155 " (cutoff:3.500A) Processing helix chain 'AA' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAA 177 " --> pdb=" O METAA 173 " (cutoff:3.500A) Processing helix chain 'AA' and resid 182 through 189 Processing helix chain 'AA' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAA 197 " --> pdb=" O SERAA 194 " (cutoff:3.500A) Processing helix chain 'AA' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAA 226 " --> pdb=" O ALAAA 222 " (cutoff:3.500A) Processing helix chain 'AB' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAB 72 " --> pdb=" O GLUAB 68 " (cutoff:3.500A) Processing helix chain 'AB' and resid 86 through 100 Processing helix chain 'AB' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAB 111 " --> pdb=" O GLUAB 107 " (cutoff:3.500A) Processing helix chain 'AB' and resid 145 through 152 Processing helix chain 'AB' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAB 159 " --> pdb=" O THRAB 155 " (cutoff:3.500A) Processing helix chain 'AB' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAB 177 " --> pdb=" O METAB 173 " (cutoff:3.500A) Processing helix chain 'AB' and resid 182 through 189 Processing helix chain 'AB' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAB 197 " --> pdb=" O SERAB 194 " (cutoff:3.500A) Processing helix chain 'AB' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAB 226 " --> pdb=" O ALAAB 222 " (cutoff:3.500A) Processing helix chain 'AC' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAC 72 " --> pdb=" O GLUAC 68 " (cutoff:3.500A) Processing helix chain 'AC' and resid 86 through 100 Processing helix chain 'AC' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAC 111 " --> pdb=" O GLUAC 107 " (cutoff:3.500A) Processing helix chain 'AC' and resid 145 through 152 Processing helix chain 'AC' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAC 159 " --> pdb=" O THRAC 155 " (cutoff:3.500A) Processing helix chain 'AC' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAC 177 " --> pdb=" O METAC 173 " (cutoff:3.500A) Processing helix chain 'AC' and resid 182 through 189 Processing helix chain 'AC' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAC 197 " --> pdb=" O SERAC 194 " (cutoff:3.500A) Processing helix chain 'AC' and resid 210 through 226 removed outlier: 3.725A pdb=" N LYSAC 226 " --> pdb=" O ALAAC 222 " (cutoff:3.500A) Processing helix chain 'AD' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAD 72 " --> pdb=" O GLUAD 68 " (cutoff:3.500A) Processing helix chain 'AD' and resid 86 through 100 Processing helix chain 'AD' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAD 111 " --> pdb=" O GLUAD 107 " (cutoff:3.500A) Processing helix chain 'AD' and resid 145 through 152 Processing helix chain 'AD' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAD 159 " --> pdb=" O THRAD 155 " (cutoff:3.500A) Processing helix chain 'AD' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAD 177 " --> pdb=" O METAD 173 " (cutoff:3.500A) Processing helix chain 'AD' and resid 182 through 189 Processing helix chain 'AD' and resid 193 through 198 removed outlier: 4.043A pdb=" N ARGAD 197 " --> pdb=" O SERAD 194 " (cutoff:3.500A) Processing helix chain 'AD' and resid 210 through 226 removed outlier: 3.726A pdb=" N LYSAD 226 " --> pdb=" O ALAAD 222 " (cutoff:3.500A) Processing helix chain 'AE' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAE 72 " --> pdb=" O GLUAE 68 " (cutoff:3.500A) Processing helix chain 'AE' and resid 86 through 100 Processing helix chain 'AE' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAE 111 " --> pdb=" O GLUAE 107 " (cutoff:3.500A) Processing helix chain 'AE' and resid 145 through 152 Processing helix chain 'AE' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAE 159 " --> pdb=" O THRAE 155 " (cutoff:3.500A) Processing helix chain 'AE' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAE 177 " --> pdb=" O METAE 173 " (cutoff:3.500A) Processing helix chain 'AE' and resid 182 through 189 Processing helix chain 'AE' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAE 197 " --> pdb=" O SERAE 194 " (cutoff:3.500A) Processing helix chain 'AE' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAE 226 " --> pdb=" O ALAAE 222 " (cutoff:3.500A) Processing helix chain 'AF' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAF 72 " --> pdb=" O GLUAF 68 " (cutoff:3.500A) Processing helix chain 'AF' and resid 86 through 100 Processing helix chain 'AF' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAF 111 " --> pdb=" O GLUAF 107 " (cutoff:3.500A) Processing helix chain 'AF' and resid 145 through 152 Processing helix chain 'AF' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAF 159 " --> pdb=" O THRAF 155 " (cutoff:3.500A) Processing helix chain 'AF' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAF 177 " --> pdb=" O METAF 173 " (cutoff:3.500A) Processing helix chain 'AF' and resid 182 through 189 Processing helix chain 'AF' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAF 197 " --> pdb=" O SERAF 194 " (cutoff:3.500A) Processing helix chain 'AF' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAF 226 " --> pdb=" O ALAAF 222 " (cutoff:3.500A) Processing helix chain 'AG' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAG 72 " --> pdb=" O GLUAG 68 " (cutoff:3.500A) Processing helix chain 'AG' and resid 86 through 100 Processing helix chain 'AG' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAG 111 " --> pdb=" O GLUAG 107 " (cutoff:3.500A) Processing helix chain 'AG' and resid 145 through 152 Processing helix chain 'AG' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAG 159 " --> pdb=" O THRAG 155 " (cutoff:3.500A) Processing helix chain 'AG' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAG 177 " --> pdb=" O METAG 173 " (cutoff:3.500A) Processing helix chain 'AG' and resid 182 through 189 Processing helix chain 'AG' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAG 197 " --> pdb=" O SERAG 194 " (cutoff:3.500A) Processing helix chain 'AG' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAG 226 " --> pdb=" O ALAAG 222 " (cutoff:3.500A) Processing helix chain 'AH' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAH 72 " --> pdb=" O GLUAH 68 " (cutoff:3.500A) Processing helix chain 'AH' and resid 86 through 100 Processing helix chain 'AH' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAH 111 " --> pdb=" O GLUAH 107 " (cutoff:3.500A) Processing helix chain 'AH' and resid 145 through 152 Processing helix chain 'AH' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAH 159 " --> pdb=" O THRAH 155 " (cutoff:3.500A) Processing helix chain 'AH' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAH 177 " --> pdb=" O METAH 173 " (cutoff:3.500A) Processing helix chain 'AH' and resid 182 through 189 Processing helix chain 'AH' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAH 197 " --> pdb=" O SERAH 194 " (cutoff:3.500A) Processing helix chain 'AH' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAH 226 " --> pdb=" O ALAAH 222 " (cutoff:3.500A) Processing helix chain 'AI' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAI 72 " --> pdb=" O GLUAI 68 " (cutoff:3.500A) Processing helix chain 'AI' and resid 86 through 100 Processing helix chain 'AI' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAI 111 " --> pdb=" O GLUAI 107 " (cutoff:3.500A) Processing helix chain 'AI' and resid 145 through 152 Processing helix chain 'AI' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAI 159 " --> pdb=" O THRAI 155 " (cutoff:3.500A) Processing helix chain 'AI' and resid 163 through 178 removed outlier: 3.985A pdb=" N LYSAI 177 " --> pdb=" O METAI 173 " (cutoff:3.500A) Processing helix chain 'AI' and resid 182 through 189 Processing helix chain 'AI' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAI 197 " --> pdb=" O SERAI 194 " (cutoff:3.500A) Processing helix chain 'AI' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAI 226 " --> pdb=" O ALAAI 222 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAJ 72 " --> pdb=" O GLUAJ 68 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 86 through 100 Processing helix chain 'AJ' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAJ 111 " --> pdb=" O GLUAJ 107 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 145 through 152 Processing helix chain 'AJ' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAJ 159 " --> pdb=" O THRAJ 155 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAJ 177 " --> pdb=" O METAJ 173 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 182 through 189 Processing helix chain 'AJ' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAJ 197 " --> pdb=" O SERAJ 194 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAJ 226 " --> pdb=" O ALAAJ 222 " (cutoff:3.500A) Processing helix chain 'AK' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAK 72 " --> pdb=" O GLUAK 68 " (cutoff:3.500A) Processing helix chain 'AK' and resid 86 through 100 Processing helix chain 'AK' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAK 111 " --> pdb=" O GLUAK 107 " (cutoff:3.500A) Processing helix chain 'AK' and resid 145 through 152 Processing helix chain 'AK' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAK 159 " --> pdb=" O THRAK 155 " (cutoff:3.500A) Processing helix chain 'AK' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAK 177 " --> pdb=" O METAK 173 " (cutoff:3.500A) Processing helix chain 'AK' and resid 182 through 189 Processing helix chain 'AK' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAK 197 " --> pdb=" O SERAK 194 " (cutoff:3.500A) Processing helix chain 'AK' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAK 226 " --> pdb=" O ALAAK 222 " (cutoff:3.500A) Processing helix chain 'AL' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAL 72 " --> pdb=" O GLUAL 68 " (cutoff:3.500A) Processing helix chain 'AL' and resid 86 through 100 Processing helix chain 'AL' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAL 111 " --> pdb=" O GLUAL 107 " (cutoff:3.500A) Processing helix chain 'AL' and resid 145 through 152 Processing helix chain 'AL' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAL 159 " --> pdb=" O THRAL 155 " (cutoff:3.500A) Processing helix chain 'AL' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAL 177 " --> pdb=" O METAL 173 " (cutoff:3.500A) Processing helix chain 'AL' and resid 182 through 189 Processing helix chain 'AL' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAL 197 " --> pdb=" O SERAL 194 " (cutoff:3.500A) Processing helix chain 'AL' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAL 226 " --> pdb=" O ALAAL 222 " (cutoff:3.500A) Processing helix chain 'AM' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAM 72 " --> pdb=" O GLUAM 68 " (cutoff:3.500A) Processing helix chain 'AM' and resid 86 through 100 Processing helix chain 'AM' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAM 111 " --> pdb=" O GLUAM 107 " (cutoff:3.500A) Processing helix chain 'AM' and resid 145 through 152 Processing helix chain 'AM' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAM 159 " --> pdb=" O THRAM 155 " (cutoff:3.500A) Processing helix chain 'AM' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAM 177 " --> pdb=" O METAM 173 " (cutoff:3.500A) Processing helix chain 'AM' and resid 182 through 189 Processing helix chain 'AM' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAM 197 " --> pdb=" O SERAM 194 " (cutoff:3.500A) Processing helix chain 'AM' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAM 226 " --> pdb=" O ALAAM 222 " (cutoff:3.500A) Processing helix chain 'AN' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAN 72 " --> pdb=" O GLUAN 68 " (cutoff:3.500A) Processing helix chain 'AN' and resid 86 through 100 Processing helix chain 'AN' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAN 111 " --> pdb=" O GLUAN 107 " (cutoff:3.500A) Processing helix chain 'AN' and resid 145 through 152 Processing helix chain 'AN' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAN 159 " --> pdb=" O THRAN 155 " (cutoff:3.500A) Processing helix chain 'AN' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAN 177 " --> pdb=" O METAN 173 " (cutoff:3.500A) Processing helix chain 'AN' and resid 182 through 189 Processing helix chain 'AN' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAN 197 " --> pdb=" O SERAN 194 " (cutoff:3.500A) Processing helix chain 'AN' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAN 226 " --> pdb=" O ALAAN 222 " (cutoff:3.500A) Processing helix chain 'AO' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAO 72 " --> pdb=" O GLUAO 68 " (cutoff:3.500A) Processing helix chain 'AO' and resid 86 through 100 Processing helix chain 'AO' and resid 107 through 122 removed outlier: 3.717A pdb=" N VALAO 111 " --> pdb=" O GLUAO 107 " (cutoff:3.500A) Processing helix chain 'AO' and resid 145 through 152 Processing helix chain 'AO' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAO 159 " --> pdb=" O THRAO 155 " (cutoff:3.500A) Processing helix chain 'AO' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAO 177 " --> pdb=" O METAO 173 " (cutoff:3.500A) Processing helix chain 'AO' and resid 182 through 189 Processing helix chain 'AO' and resid 193 through 198 removed outlier: 4.043A pdb=" N ARGAO 197 " --> pdb=" O SERAO 194 " (cutoff:3.500A) Processing helix chain 'AO' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAO 226 " --> pdb=" O ALAAO 222 " (cutoff:3.500A) Processing helix chain 'AP' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAP 72 " --> pdb=" O GLUAP 68 " (cutoff:3.500A) Processing helix chain 'AP' and resid 86 through 100 Processing helix chain 'AP' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAP 111 " --> pdb=" O GLUAP 107 " (cutoff:3.500A) Processing helix chain 'AP' and resid 145 through 152 Processing helix chain 'AP' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAP 159 " --> pdb=" O THRAP 155 " (cutoff:3.500A) Processing helix chain 'AP' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAP 177 " --> pdb=" O METAP 173 " (cutoff:3.500A) Processing helix chain 'AP' and resid 182 through 189 Processing helix chain 'AP' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAP 197 " --> pdb=" O SERAP 194 " (cutoff:3.500A) Processing helix chain 'AP' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAP 226 " --> pdb=" O ALAAP 222 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUAQ 72 " --> pdb=" O GLUAQ 68 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 86 through 100 Processing helix chain 'AQ' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAQ 111 " --> pdb=" O GLUAQ 107 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 145 through 152 Processing helix chain 'AQ' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAQ 159 " --> pdb=" O THRAQ 155 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAQ 177 " --> pdb=" O METAQ 173 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 182 through 189 Processing helix chain 'AQ' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAQ 197 " --> pdb=" O SERAQ 194 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAQ 226 " --> pdb=" O ALAAQ 222 " (cutoff:3.500A) Processing helix chain 'AR' and resid 66 through 72 removed outlier: 3.893A pdb=" N GLUAR 72 " --> pdb=" O GLUAR 68 " (cutoff:3.500A) Processing helix chain 'AR' and resid 86 through 100 Processing helix chain 'AR' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAR 111 " --> pdb=" O GLUAR 107 " (cutoff:3.500A) Processing helix chain 'AR' and resid 145 through 152 Processing helix chain 'AR' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAR 159 " --> pdb=" O THRAR 155 " (cutoff:3.500A) Processing helix chain 'AR' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAR 177 " --> pdb=" O METAR 173 " (cutoff:3.500A) Processing helix chain 'AR' and resid 182 through 189 Processing helix chain 'AR' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAR 197 " --> pdb=" O SERAR 194 " (cutoff:3.500A) Processing helix chain 'AR' and resid 210 through 226 removed outlier: 3.726A pdb=" N LYSAR 226 " --> pdb=" O ALAAR 222 " (cutoff:3.500A) Processing helix chain 'AS' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAS 72 " --> pdb=" O GLUAS 68 " (cutoff:3.500A) Processing helix chain 'AS' and resid 86 through 100 Processing helix chain 'AS' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAS 111 " --> pdb=" O GLUAS 107 " (cutoff:3.500A) Processing helix chain 'AS' and resid 145 through 152 Processing helix chain 'AS' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAS 159 " --> pdb=" O THRAS 155 " (cutoff:3.500A) Processing helix chain 'AS' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAS 177 " --> pdb=" O METAS 173 " (cutoff:3.500A) Processing helix chain 'AS' and resid 182 through 189 Processing helix chain 'AS' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAS 197 " --> pdb=" O SERAS 194 " (cutoff:3.500A) Processing helix chain 'AS' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAS 226 " --> pdb=" O ALAAS 222 " (cutoff:3.500A) Processing helix chain 'AT' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAT 72 " --> pdb=" O GLUAT 68 " (cutoff:3.500A) Processing helix chain 'AT' and resid 86 through 100 Processing helix chain 'AT' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAT 111 " --> pdb=" O GLUAT 107 " (cutoff:3.500A) Processing helix chain 'AT' and resid 145 through 152 Processing helix chain 'AT' and resid 155 through 161 removed outlier: 3.604A pdb=" N ILEAT 159 " --> pdb=" O THRAT 155 " (cutoff:3.500A) Processing helix chain 'AT' and resid 163 through 178 removed outlier: 3.985A pdb=" N LYSAT 177 " --> pdb=" O METAT 173 " (cutoff:3.500A) Processing helix chain 'AT' and resid 182 through 189 Processing helix chain 'AT' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAT 197 " --> pdb=" O SERAT 194 " (cutoff:3.500A) Processing helix chain 'AT' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAT 226 " --> pdb=" O ALAAT 222 " (cutoff:3.500A) Processing helix chain 'AU' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUAU 72 " --> pdb=" O GLUAU 68 " (cutoff:3.500A) Processing helix chain 'AU' and resid 86 through 100 Processing helix chain 'AU' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAU 111 " --> pdb=" O GLUAU 107 " (cutoff:3.500A) Processing helix chain 'AU' and resid 145 through 152 Processing helix chain 'AU' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAU 159 " --> pdb=" O THRAU 155 " (cutoff:3.500A) Processing helix chain 'AU' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAU 177 " --> pdb=" O METAU 173 " (cutoff:3.500A) Processing helix chain 'AU' and resid 182 through 189 Processing helix chain 'AU' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAU 197 " --> pdb=" O SERAU 194 " (cutoff:3.500A) Processing helix chain 'AU' and resid 210 through 226 removed outlier: 3.728A pdb=" N LYSAU 226 " --> pdb=" O ALAAU 222 " (cutoff:3.500A) Processing helix chain 'AV' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAV 72 " --> pdb=" O GLUAV 68 " (cutoff:3.500A) Processing helix chain 'AV' and resid 86 through 100 Processing helix chain 'AV' and resid 107 through 122 removed outlier: 3.717A pdb=" N VALAV 111 " --> pdb=" O GLUAV 107 " (cutoff:3.500A) Processing helix chain 'AV' and resid 145 through 152 Processing helix chain 'AV' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAV 159 " --> pdb=" O THRAV 155 " (cutoff:3.500A) Processing helix chain 'AV' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAV 177 " --> pdb=" O METAV 173 " (cutoff:3.500A) Processing helix chain 'AV' and resid 182 through 189 Processing helix chain 'AV' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAV 197 " --> pdb=" O SERAV 194 " (cutoff:3.500A) Processing helix chain 'AV' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAV 226 " --> pdb=" O ALAAV 222 " (cutoff:3.500A) Processing helix chain 'AW' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAW 72 " --> pdb=" O GLUAW 68 " (cutoff:3.500A) Processing helix chain 'AW' and resid 86 through 100 Processing helix chain 'AW' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAW 111 " --> pdb=" O GLUAW 107 " (cutoff:3.500A) Processing helix chain 'AW' and resid 145 through 152 Processing helix chain 'AW' and resid 155 through 161 removed outlier: 3.601A pdb=" N ILEAW 159 " --> pdb=" O THRAW 155 " (cutoff:3.500A) Processing helix chain 'AW' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAW 177 " --> pdb=" O METAW 173 " (cutoff:3.500A) Processing helix chain 'AW' and resid 182 through 189 Processing helix chain 'AW' and resid 193 through 198 removed outlier: 4.043A pdb=" N ARGAW 197 " --> pdb=" O SERAW 194 " (cutoff:3.500A) Processing helix chain 'AW' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAW 226 " --> pdb=" O ALAAW 222 " (cutoff:3.500A) Processing helix chain 'AX' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAX 72 " --> pdb=" O GLUAX 68 " (cutoff:3.500A) Processing helix chain 'AX' and resid 86 through 100 Processing helix chain 'AX' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAX 111 " --> pdb=" O GLUAX 107 " (cutoff:3.500A) Processing helix chain 'AX' and resid 145 through 152 Processing helix chain 'AX' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAX 159 " --> pdb=" O THRAX 155 " (cutoff:3.500A) Processing helix chain 'AX' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAX 177 " --> pdb=" O METAX 173 " (cutoff:3.500A) Processing helix chain 'AX' and resid 182 through 189 Processing helix chain 'AX' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAX 197 " --> pdb=" O SERAX 194 " (cutoff:3.500A) Processing helix chain 'AX' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAX 226 " --> pdb=" O ALAAX 222 " (cutoff:3.500A) Processing helix chain 'AY' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAY 72 " --> pdb=" O GLUAY 68 " (cutoff:3.500A) Processing helix chain 'AY' and resid 86 through 100 Processing helix chain 'AY' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAY 111 " --> pdb=" O GLUAY 107 " (cutoff:3.500A) Processing helix chain 'AY' and resid 145 through 152 Processing helix chain 'AY' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAY 159 " --> pdb=" O THRAY 155 " (cutoff:3.500A) Processing helix chain 'AY' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAY 177 " --> pdb=" O METAY 173 " (cutoff:3.500A) Processing helix chain 'AY' and resid 182 through 189 Processing helix chain 'AY' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAY 197 " --> pdb=" O SERAY 194 " (cutoff:3.500A) Processing helix chain 'AY' and resid 210 through 226 removed outlier: 3.726A pdb=" N LYSAY 226 " --> pdb=" O ALAAY 222 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAZ 72 " --> pdb=" O GLUAZ 68 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 86 through 100 Processing helix chain 'AZ' and resid 107 through 122 removed outlier: 3.717A pdb=" N VALAZ 111 " --> pdb=" O GLUAZ 107 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 145 through 152 Processing helix chain 'AZ' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAZ 159 " --> pdb=" O THRAZ 155 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAZ 177 " --> pdb=" O METAZ 173 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 182 through 189 Processing helix chain 'AZ' and resid 193 through 198 removed outlier: 4.043A pdb=" N ARGAZ 197 " --> pdb=" O SERAZ 194 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAZ 226 " --> pdb=" O ALAAZ 222 " (cutoff:3.500A) Processing helix chain 'BA' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUBA 72 " --> pdb=" O GLUBA 68 " (cutoff:3.500A) Processing helix chain 'BA' and resid 86 through 100 Processing helix chain 'BA' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALBA 111 " --> pdb=" O GLUBA 107 " (cutoff:3.500A) Processing helix chain 'BA' and resid 145 through 152 Processing helix chain 'BA' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEBA 159 " --> pdb=" O THRBA 155 " (cutoff:3.500A) Processing helix chain 'BA' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBA 177 " --> pdb=" O METBA 173 " (cutoff:3.500A) Processing helix chain 'BA' and resid 182 through 189 Processing helix chain 'BA' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGBA 197 " --> pdb=" O SERBA 194 " (cutoff:3.500A) Processing helix chain 'BA' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBA 226 " --> pdb=" O ALABA 222 " (cutoff:3.500A) Processing helix chain 'BB' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUBB 72 " --> pdb=" O GLUBB 68 " (cutoff:3.500A) Processing helix chain 'BB' and resid 86 through 100 Processing helix chain 'BB' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALBB 111 " --> pdb=" O GLUBB 107 " (cutoff:3.500A) Processing helix chain 'BB' and resid 145 through 152 Processing helix chain 'BB' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEBB 159 " --> pdb=" O THRBB 155 " (cutoff:3.500A) Processing helix chain 'BB' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBB 177 " --> pdb=" O METBB 173 " (cutoff:3.500A) Processing helix chain 'BB' and resid 182 through 189 Processing helix chain 'BB' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGBB 197 " --> pdb=" O SERBB 194 " (cutoff:3.500A) Processing helix chain 'BB' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBB 226 " --> pdb=" O ALABB 222 " (cutoff:3.500A) Processing helix chain 'BC' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUBC 72 " --> pdb=" O GLUBC 68 " (cutoff:3.500A) Processing helix chain 'BC' and resid 86 through 100 Processing helix chain 'BC' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALBC 111 " --> pdb=" O GLUBC 107 " (cutoff:3.500A) Processing helix chain 'BC' and resid 145 through 152 Processing helix chain 'BC' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEBC 159 " --> pdb=" O THRBC 155 " (cutoff:3.500A) Processing helix chain 'BC' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBC 177 " --> pdb=" O METBC 173 " (cutoff:3.500A) Processing helix chain 'BC' and resid 182 through 189 Processing helix chain 'BC' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGBC 197 " --> pdb=" O SERBC 194 " (cutoff:3.500A) Processing helix chain 'BC' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBC 226 " --> pdb=" O ALABC 222 " (cutoff:3.500A) Processing helix chain 'BD' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUBD 72 " --> pdb=" O GLUBD 68 " (cutoff:3.500A) Processing helix chain 'BD' and resid 86 through 100 Processing helix chain 'BD' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALBD 111 " --> pdb=" O GLUBD 107 " (cutoff:3.500A) Processing helix chain 'BD' and resid 145 through 152 Processing helix chain 'BD' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEBD 159 " --> pdb=" O THRBD 155 " (cutoff:3.500A) Processing helix chain 'BD' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBD 177 " --> pdb=" O METBD 173 " (cutoff:3.500A) Processing helix chain 'BD' and resid 182 through 189 Processing helix chain 'BD' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGBD 197 " --> pdb=" O SERBD 194 " (cutoff:3.500A) Processing helix chain 'BD' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBD 226 " --> pdb=" O ALABD 222 " (cutoff:3.500A) Processing helix chain 'BE' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUBE 72 " --> pdb=" O GLUBE 68 " (cutoff:3.500A) Processing helix chain 'BE' and resid 86 through 100 Processing helix chain 'BE' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALBE 111 " --> pdb=" O GLUBE 107 " (cutoff:3.500A) Processing helix chain 'BE' and resid 145 through 152 Processing helix chain 'BE' and resid 155 through 161 removed outlier: 3.604A pdb=" N ILEBE 159 " --> pdb=" O THRBE 155 " (cutoff:3.500A) Processing helix chain 'BE' and resid 163 through 178 removed outlier: 3.982A pdb=" N LYSBE 177 " --> pdb=" O METBE 173 " (cutoff:3.500A) Processing helix chain 'BE' and resid 182 through 189 Processing helix chain 'BE' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGBE 197 " --> pdb=" O SERBE 194 " (cutoff:3.500A) Processing helix chain 'BE' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBE 226 " --> pdb=" O ALABE 222 " (cutoff:3.500A) Processing helix chain 'BF' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUBF 72 " --> pdb=" O GLUBF 68 " (cutoff:3.500A) Processing helix chain 'BF' and resid 86 through 100 Processing helix chain 'BF' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALBF 111 " --> pdb=" O GLUBF 107 " (cutoff:3.500A) Processing helix chain 'BF' and resid 145 through 152 Processing helix chain 'BF' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEBF 159 " --> pdb=" O THRBF 155 " (cutoff:3.500A) Processing helix chain 'BF' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBF 177 " --> pdb=" O METBF 173 " (cutoff:3.500A) Processing helix chain 'BF' and resid 182 through 189 Processing helix chain 'BF' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGBF 197 " --> pdb=" O SERBF 194 " (cutoff:3.500A) Processing helix chain 'BF' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBF 226 " --> pdb=" O ALABF 222 " (cutoff:3.500A) Processing helix chain 'BG' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUBG 72 " --> pdb=" O GLUBG 68 " (cutoff:3.500A) Processing helix chain 'BG' and resid 86 through 100 Processing helix chain 'BG' and resid 107 through 122 removed outlier: 3.717A pdb=" N VALBG 111 " --> pdb=" O GLUBG 107 " (cutoff:3.500A) Processing helix chain 'BG' and resid 145 through 152 Processing helix chain 'BG' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEBG 159 " --> pdb=" O THRBG 155 " (cutoff:3.500A) Processing helix chain 'BG' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBG 177 " --> pdb=" O METBG 173 " (cutoff:3.500A) Processing helix chain 'BG' and resid 182 through 189 Processing helix chain 'BG' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGBG 197 " --> pdb=" O SERBG 194 " (cutoff:3.500A) Processing helix chain 'BG' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBG 226 " --> pdb=" O ALABG 222 " (cutoff:3.500A) Processing helix chain 'BH' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUBH 72 " --> pdb=" O GLUBH 68 " (cutoff:3.500A) Processing helix chain 'BH' and resid 86 through 100 Processing helix chain 'BH' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALBH 111 " --> pdb=" O GLUBH 107 " (cutoff:3.500A) Processing helix chain 'BH' and resid 145 through 152 Processing helix chain 'BH' and resid 155 through 161 removed outlier: 3.604A pdb=" N ILEBH 159 " --> pdb=" O THRBH 155 " (cutoff:3.500A) Processing helix chain 'BH' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBH 177 " --> pdb=" O METBH 173 " (cutoff:3.500A) Processing helix chain 'BH' and resid 182 through 189 Processing helix chain 'BH' and resid 193 through 198 removed outlier: 4.043A pdb=" N ARGBH 197 " --> pdb=" O SERBH 194 " (cutoff:3.500A) Processing helix chain 'BH' and resid 210 through 226 removed outlier: 3.726A pdb=" N LYSBH 226 " --> pdb=" O ALABH 222 " (cutoff:3.500A) Processing helix chain 'BI' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUBI 72 " --> pdb=" O GLUBI 68 " (cutoff:3.500A) Processing helix chain 'BI' and resid 86 through 100 Processing helix chain 'BI' and resid 107 through 122 removed outlier: 3.717A pdb=" N VALBI 111 " --> pdb=" O GLUBI 107 " (cutoff:3.500A) Processing helix chain 'BI' and resid 145 through 152 Processing helix chain 'BI' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEBI 159 " --> pdb=" O THRBI 155 " (cutoff:3.500A) Processing helix chain 'BI' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBI 177 " --> pdb=" O METBI 173 " (cutoff:3.500A) Processing helix chain 'BI' and resid 182 through 189 Processing helix chain 'BI' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGBI 197 " --> pdb=" O SERBI 194 " (cutoff:3.500A) Processing helix chain 'BI' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBI 226 " --> pdb=" O ALABI 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AA' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'AA' and resid 131 through 136 Processing sheet with id=AA3, first strand: chain 'AB' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'AB' and resid 131 through 136 Processing sheet with id=AA5, first strand: chain 'AC' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'AC' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'AD' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'AD' and resid 131 through 136 Processing sheet with id=AA9, first strand: chain 'AE' and resid 58 through 59 Processing sheet with id=AB1, first strand: chain 'AE' and resid 131 through 136 Processing sheet with id=AB2, first strand: chain 'AF' and resid 58 through 59 Processing sheet with id=AB3, first strand: chain 'AF' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'AG' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'AG' and resid 131 through 136 Processing sheet with id=AB6, first strand: chain 'AH' and resid 58 through 59 Processing sheet with id=AB7, first strand: chain 'AH' and resid 131 through 136 Processing sheet with id=AB8, first strand: chain 'AI' and resid 58 through 59 Processing sheet with id=AB9, first strand: chain 'AI' and resid 131 through 136 Processing sheet with id=AC1, first strand: chain 'AJ' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'AJ' and resid 131 through 136 Processing sheet with id=AC3, first strand: chain 'AK' and resid 58 through 59 Processing sheet with id=AC4, first strand: chain 'AK' and resid 131 through 136 Processing sheet with id=AC5, first strand: chain 'AL' and resid 58 through 59 Processing sheet with id=AC6, first strand: chain 'AL' and resid 131 through 136 Processing sheet with id=AC7, first strand: chain 'AM' and resid 58 through 59 Processing sheet with id=AC8, first strand: chain 'AM' and resid 131 through 136 Processing sheet with id=AC9, first strand: chain 'AN' and resid 58 through 59 Processing sheet with id=AD1, first strand: chain 'AN' and resid 131 through 136 Processing sheet with id=AD2, first strand: chain 'AO' and resid 58 through 59 Processing sheet with id=AD3, first strand: chain 'AO' and resid 131 through 136 Processing sheet with id=AD4, first strand: chain 'AP' and resid 58 through 59 Processing sheet with id=AD5, first strand: chain 'AP' and resid 131 through 136 Processing sheet with id=AD6, first strand: chain 'AQ' and resid 58 through 59 Processing sheet with id=AD7, first strand: chain 'AQ' and resid 131 through 136 Processing sheet with id=AD8, first strand: chain 'AR' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'AR' and resid 131 through 136 Processing sheet with id=AE1, first strand: chain 'AS' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'AS' and resid 131 through 136 Processing sheet with id=AE3, first strand: chain 'AT' and resid 58 through 59 Processing sheet with id=AE4, first strand: chain 'AT' and resid 131 through 136 Processing sheet with id=AE5, first strand: chain 'AU' and resid 58 through 59 Processing sheet with id=AE6, first strand: chain 'AU' and resid 131 through 136 Processing sheet with id=AE7, first strand: chain 'AV' and resid 58 through 59 Processing sheet with id=AE8, first strand: chain 'AV' and resid 131 through 136 Processing sheet with id=AE9, first strand: chain 'AW' and resid 58 through 59 Processing sheet with id=AF1, first strand: chain 'AW' and resid 131 through 136 Processing sheet with id=AF2, first strand: chain 'AX' and resid 58 through 59 Processing sheet with id=AF3, first strand: chain 'AX' and resid 131 through 136 Processing sheet with id=AF4, first strand: chain 'AY' and resid 58 through 59 Processing sheet with id=AF5, first strand: chain 'AY' and resid 131 through 136 Processing sheet with id=AF6, first strand: chain 'AZ' and resid 58 through 59 Processing sheet with id=AF7, first strand: chain 'AZ' and resid 131 through 136 Processing sheet with id=AF8, first strand: chain 'BA' and resid 58 through 59 Processing sheet with id=AF9, first strand: chain 'BA' and resid 131 through 136 Processing sheet with id=AG1, first strand: chain 'BB' and resid 58 through 59 Processing sheet with id=AG2, first strand: chain 'BB' and resid 131 through 136 Processing sheet with id=AG3, first strand: chain 'BC' and resid 58 through 59 Processing sheet with id=AG4, first strand: chain 'BC' and resid 131 through 136 Processing sheet with id=AG5, first strand: chain 'BD' and resid 58 through 59 Processing sheet with id=AG6, first strand: chain 'BD' and resid 131 through 136 Processing sheet with id=AG7, first strand: chain 'BE' and resid 58 through 59 Processing sheet with id=AG8, first strand: chain 'BE' and resid 131 through 136 Processing sheet with id=AG9, first strand: chain 'BF' and resid 58 through 59 Processing sheet with id=AH1, first strand: chain 'BF' and resid 131 through 136 Processing sheet with id=AH2, first strand: chain 'BG' and resid 58 through 59 Processing sheet with id=AH3, first strand: chain 'BG' and resid 131 through 136 Processing sheet with id=AH4, first strand: chain 'BH' and resid 58 through 59 Processing sheet with id=AH5, first strand: chain 'BH' and resid 131 through 136 Processing sheet with id=AH6, first strand: chain 'BI' and resid 58 through 59 Processing sheet with id=AH7, first strand: chain 'BI' and resid 131 through 136 2345 hydrogen bonds defined for protein. 6615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 18.65 Time building geometry restraints manager: 14.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 20036 1.34 - 1.45: 10672 1.45 - 1.57: 35372 1.57 - 1.69: 315 1.69 - 1.81: 945 Bond restraints: 67340 Sorted by residual: bond pdb=" N PROAS 57 " pdb=" CD PROAS 57 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" N PROAO 57 " pdb=" CD PROAO 57 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" N PROBB 57 " pdb=" CD PROBB 57 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.11e+01 bond pdb=" N PROAH 57 " pdb=" CD PROAH 57 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.10e+01 bond pdb=" N PROAG 57 " pdb=" CD PROAG 57 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.10e+01 ... (remaining 67335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 83106 1.67 - 3.34: 6425 3.34 - 5.01: 1633 5.01 - 6.68: 415 6.68 - 8.35: 226 Bond angle restraints: 91805 Sorted by residual: angle pdb=" N LEUAK 261 " pdb=" CA LEUAK 261 " pdb=" C LEUAK 261 " ideal model delta sigma weight residual 110.42 102.89 7.53 1.46e+00 4.69e-01 2.66e+01 angle pdb=" N LEUAJ 261 " pdb=" CA LEUAJ 261 " pdb=" C LEUAJ 261 " ideal model delta sigma weight residual 110.42 102.90 7.52 1.46e+00 4.69e-01 2.66e+01 angle pdb=" N LEUAF 261 " pdb=" CA LEUAF 261 " pdb=" C LEUAF 261 " ideal model delta sigma weight residual 110.42 102.90 7.52 1.46e+00 4.69e-01 2.65e+01 angle pdb=" N LEUBE 261 " pdb=" CA LEUBE 261 " pdb=" C LEUBE 261 " ideal model delta sigma weight residual 110.42 102.91 7.51 1.46e+00 4.69e-01 2.65e+01 angle pdb=" N LEUAM 261 " pdb=" CA LEUAM 261 " pdb=" C LEUAM 261 " ideal model delta sigma weight residual 110.42 102.91 7.51 1.46e+00 4.69e-01 2.65e+01 ... (remaining 91800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.55: 37259 13.55 - 27.09: 2606 27.09 - 40.64: 1155 40.64 - 54.18: 350 54.18 - 67.73: 385 Dihedral angle restraints: 41755 sinusoidal: 18795 harmonic: 22960 Sorted by residual: dihedral pdb=" CA GLNAF 76 " pdb=" C GLNAF 76 " pdb=" N GLNAF 77 " pdb=" CA GLNAF 77 " ideal model delta harmonic sigma weight residual 180.00 159.41 20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLNAH 76 " pdb=" C GLNAH 76 " pdb=" N GLNAH 77 " pdb=" CA GLNAH 77 " ideal model delta harmonic sigma weight residual 180.00 159.41 20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLNAQ 76 " pdb=" C GLNAQ 76 " pdb=" N GLNAQ 77 " pdb=" CA GLNAQ 77 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 41752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 8008 0.070 - 0.141: 1721 0.141 - 0.211: 526 0.211 - 0.282: 35 0.282 - 0.352: 70 Chirality restraints: 10360 Sorted by residual: chirality pdb=" CB ILEAI 50 " pdb=" CA ILEAI 50 " pdb=" CG1 ILEAI 50 " pdb=" CG2 ILEAI 50 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB ILEBF 50 " pdb=" CA ILEBF 50 " pdb=" CG1 ILEBF 50 " pdb=" CG2 ILEBF 50 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB ILEAJ 50 " pdb=" CA ILEAJ 50 " pdb=" CG1 ILEAJ 50 " pdb=" CG2 ILEAJ 50 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 10357 not shown) Planarity restraints: 11375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLYAU 263 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C GLYAU 263 " 0.055 2.00e-02 2.50e+03 pdb=" O GLYAU 263 " -0.021 2.00e-02 2.50e+03 pdb=" N VALAU 264 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYAW 263 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C GLYAW 263 " 0.054 2.00e-02 2.50e+03 pdb=" O GLYAW 263 " -0.020 2.00e-02 2.50e+03 pdb=" N VALAW 264 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYBD 263 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.74e+00 pdb=" C GLYBD 263 " 0.054 2.00e-02 2.50e+03 pdb=" O GLYBD 263 " -0.020 2.00e-02 2.50e+03 pdb=" N VALBD 264 " -0.018 2.00e-02 2.50e+03 ... (remaining 11372 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 34 2.25 - 2.91: 25891 2.91 - 3.57: 93809 3.57 - 4.24: 156400 4.24 - 4.90: 263166 Nonbonded interactions: 539300 Sorted by model distance: nonbonded pdb=" O3' UAp 11 " pdb=" P UAq 7 " model vdw 1.586 3.400 nonbonded pdb=" O3' UAg 11 " pdb=" P UAh 7 " model vdw 1.587 3.400 nonbonded pdb=" O3' UAi 11 " pdb=" P UAj 7 " model vdw 1.589 3.400 nonbonded pdb=" O3' UAl 11 " pdb=" P UAm 7 " model vdw 1.590 3.400 nonbonded pdb=" O3' UAt 11 " pdb=" P UAu 7 " model vdw 1.592 3.400 ... (remaining 539295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AI' selection = chain 'AJ' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AR' selection = chain 'AS' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'BA' selection = chain 'BB' selection = chain 'BC' selection = chain 'BD' selection = chain 'BE' selection = chain 'BF' selection = chain 'BG' selection = chain 'BH' selection = chain 'BI' } ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' selection = chain 'Ay' selection = chain 'Az' selection = chain 'Ba' selection = chain 'Bb' selection = chain 'Bc' selection = chain 'Bd' selection = chain 'Be' selection = chain 'Bf' selection = chain 'Bg' selection = chain 'Bh' selection = chain 'Bi' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.140 Check model and map are aligned: 0.380 Set scattering table: 0.480 Process input model: 99.120 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 67340 Z= 0.511 Angle : 1.137 8.353 91805 Z= 0.679 Chirality : 0.071 0.352 10360 Planarity : 0.008 0.070 11375 Dihedral : 13.789 67.726 26915 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.28 % Allowed : 6.94 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.08), residues: 7770 helix: -2.50 (0.07), residues: 2870 sheet: -1.45 (0.22), residues: 350 loop : -2.72 (0.08), residues: 4550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRPBA 118 HIS 0.004 0.001 HISAQ 69 PHE 0.021 0.003 PHEAS 200 TYR 0.011 0.002 TYRAH 101 ARG 0.007 0.001 ARGBG 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2371 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 2352 time to evaluate : 5.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8057 (mm-40) REVERT: AA 83 THR cc_start: 0.9111 (m) cc_final: 0.8594 (p) REVERT: AA 94 TYR cc_start: 0.9021 (t80) cc_final: 0.8608 (t80) REVERT: AA 136 ASP cc_start: 0.8498 (t70) cc_final: 0.7459 (t0) REVERT: AA 168 GLU cc_start: 0.8520 (tt0) cc_final: 0.8263 (tt0) REVERT: AA 184 TYR cc_start: 0.9157 (t80) cc_final: 0.8905 (t80) REVERT: AA 191 ARG cc_start: 0.8292 (mtt90) cc_final: 0.6372 (mpt180) REVERT: AA 231 ARG cc_start: 0.7844 (ttt90) cc_final: 0.7577 (tpm170) REVERT: AB 59 SER cc_start: 0.6250 (p) cc_final: 0.5883 (p) REVERT: AB 82 ASN cc_start: 0.8257 (t0) cc_final: 0.8032 (t0) REVERT: AB 94 TYR cc_start: 0.9053 (t80) cc_final: 0.8697 (t80) REVERT: AB 173 MET cc_start: 0.8903 (tmm) cc_final: 0.8603 (tmm) REVERT: AB 191 ARG cc_start: 0.8131 (mtt90) cc_final: 0.6729 (mpt180) REVERT: AB 231 ARG cc_start: 0.7666 (ttt90) cc_final: 0.7385 (tpm170) REVERT: AB 236 ASP cc_start: 0.8056 (p0) cc_final: 0.7655 (p0) REVERT: AB 266 ASN cc_start: 0.8386 (t0) cc_final: 0.7875 (t0) REVERT: AC 59 SER cc_start: 0.6309 (p) cc_final: 0.5935 (p) REVERT: AC 87 GLN cc_start: 0.9154 (tp40) cc_final: 0.8846 (tp40) REVERT: AC 94 TYR cc_start: 0.9031 (t80) cc_final: 0.8596 (t80) REVERT: AC 108 MET cc_start: 0.8401 (tpt) cc_final: 0.7958 (tpt) REVERT: AC 158 GLN cc_start: 0.8873 (mt0) cc_final: 0.8665 (mt0) REVERT: AC 176 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8529 (mptt) REVERT: AC 191 ARG cc_start: 0.8184 (mtt90) cc_final: 0.6634 (mpt180) REVERT: AC 215 GLU cc_start: 0.8430 (tp30) cc_final: 0.8155 (tp30) REVERT: AC 231 ARG cc_start: 0.7694 (ttt90) cc_final: 0.7375 (tpm170) REVERT: AD 94 TYR cc_start: 0.8961 (t80) cc_final: 0.8704 (t80) REVERT: AD 170 TYR cc_start: 0.9140 (t80) cc_final: 0.8880 (t80) REVERT: AD 173 MET cc_start: 0.8814 (tmm) cc_final: 0.8593 (tmm) REVERT: AD 191 ARG cc_start: 0.8200 (mtt90) cc_final: 0.6574 (mpt180) REVERT: AE 94 TYR cc_start: 0.9023 (t80) cc_final: 0.8628 (t80) REVERT: AE 136 ASP cc_start: 0.8640 (t70) cc_final: 0.7727 (t0) REVERT: AE 173 MET cc_start: 0.8916 (tmm) cc_final: 0.8608 (tmm) REVERT: AE 191 ARG cc_start: 0.8227 (mtt90) cc_final: 0.6576 (mpt180) REVERT: AE 231 ARG cc_start: 0.7734 (ttt90) cc_final: 0.7406 (tpm170) REVERT: AF 87 GLN cc_start: 0.9267 (tp40) cc_final: 0.8804 (tp40) REVERT: AF 94 TYR cc_start: 0.9058 (t80) cc_final: 0.8734 (t80) REVERT: AF 136 ASP cc_start: 0.8586 (t70) cc_final: 0.8381 (t0) REVERT: AF 158 GLN cc_start: 0.8924 (mt0) cc_final: 0.8448 (mt0) REVERT: AF 176 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8464 (mmtm) REVERT: AF 191 ARG cc_start: 0.8199 (mtt90) cc_final: 0.6317 (mpt180) REVERT: AF 215 GLU cc_start: 0.8454 (tp30) cc_final: 0.8238 (tp30) REVERT: AF 231 ARG cc_start: 0.7563 (ttt90) cc_final: 0.7343 (tpm170) REVERT: AF 246 THR cc_start: 0.8703 (p) cc_final: 0.8297 (t) REVERT: AG 87 GLN cc_start: 0.9222 (tp40) cc_final: 0.8958 (tp40) REVERT: AG 94 TYR cc_start: 0.8989 (t80) cc_final: 0.8622 (t80) REVERT: AG 136 ASP cc_start: 0.8421 (t70) cc_final: 0.8114 (t0) REVERT: AG 191 ARG cc_start: 0.8287 (mtt90) cc_final: 0.7006 (mpp-170) REVERT: AG 231 ARG cc_start: 0.7856 (ttt90) cc_final: 0.7501 (tpm170) REVERT: AG 255 SER cc_start: 0.9080 (m) cc_final: 0.8798 (t) REVERT: AH 94 TYR cc_start: 0.9079 (t80) cc_final: 0.8615 (t80) REVERT: AH 136 ASP cc_start: 0.8405 (t70) cc_final: 0.7574 (t0) REVERT: AH 191 ARG cc_start: 0.8068 (mtt90) cc_final: 0.6484 (mpt180) REVERT: AH 231 ARG cc_start: 0.7832 (ttt90) cc_final: 0.7629 (tpm170) REVERT: AI 83 THR cc_start: 0.9103 (m) cc_final: 0.8732 (p) REVERT: AI 94 TYR cc_start: 0.9067 (t80) cc_final: 0.8806 (t80) REVERT: AI 173 MET cc_start: 0.8894 (tmm) cc_final: 0.8508 (tmm) REVERT: AI 246 THR cc_start: 0.8830 (p) cc_final: 0.8405 (t) REVERT: AJ 94 TYR cc_start: 0.9027 (t80) cc_final: 0.8106 (t80) REVERT: AJ 98 GLN cc_start: 0.8654 (tt0) cc_final: 0.8386 (tt0) REVERT: AJ 108 MET cc_start: 0.8424 (tpt) cc_final: 0.7860 (tpt) REVERT: AJ 266 ASN cc_start: 0.8399 (t0) cc_final: 0.8133 (t0) REVERT: AK 59 SER cc_start: 0.6792 (p) cc_final: 0.6192 (p) REVERT: AK 94 TYR cc_start: 0.8960 (t80) cc_final: 0.7960 (t80) REVERT: AK 146 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8054 (tptm) REVERT: AK 158 GLN cc_start: 0.8859 (mt0) cc_final: 0.8658 (mt0) REVERT: AK 236 ASP cc_start: 0.8137 (p0) cc_final: 0.7733 (p0) REVERT: AL 94 TYR cc_start: 0.9025 (t80) cc_final: 0.8597 (t80) REVERT: AL 168 GLU cc_start: 0.8602 (tt0) cc_final: 0.8381 (tt0) REVERT: AL 236 ASP cc_start: 0.8064 (p0) cc_final: 0.7771 (p0) REVERT: AM 94 TYR cc_start: 0.9053 (t80) cc_final: 0.8761 (t80) REVERT: AM 151 ASN cc_start: 0.8926 (m-40) cc_final: 0.8414 (m110) REVERT: AM 236 ASP cc_start: 0.8024 (p0) cc_final: 0.7571 (p0) REVERT: AM 266 ASN cc_start: 0.8392 (t0) cc_final: 0.8061 (t0) REVERT: AN 94 TYR cc_start: 0.8951 (t80) cc_final: 0.8587 (t80) REVERT: AN 136 ASP cc_start: 0.8626 (t70) cc_final: 0.8320 (t0) REVERT: AN 158 GLN cc_start: 0.8845 (mt0) cc_final: 0.8636 (mt0) REVERT: AO 59 SER cc_start: 0.6656 (p) cc_final: 0.5887 (p) REVERT: AO 94 TYR cc_start: 0.9029 (t80) cc_final: 0.8670 (t80) REVERT: AP 83 THR cc_start: 0.9041 (m) cc_final: 0.8543 (p) REVERT: AP 94 TYR cc_start: 0.9088 (t80) cc_final: 0.8713 (t80) REVERT: AQ 94 TYR cc_start: 0.9077 (t80) cc_final: 0.8689 (t80) REVERT: AQ 246 THR cc_start: 0.8703 (p) cc_final: 0.8198 (t) REVERT: AR 94 TYR cc_start: 0.8978 (t80) cc_final: 0.8639 (t80) REVERT: AS 94 TYR cc_start: 0.9005 (t80) cc_final: 0.8589 (t80) REVERT: AS 178 GLU cc_start: 0.7913 (pt0) cc_final: 0.7670 (pm20) REVERT: AS 226 LYS cc_start: 0.8127 (mttt) cc_final: 0.7885 (mttt) REVERT: AS 246 THR cc_start: 0.8848 (p) cc_final: 0.8541 (t) REVERT: AT 94 TYR cc_start: 0.9062 (t80) cc_final: 0.8764 (t80) REVERT: AT 127 ASN cc_start: 0.8929 (m110) cc_final: 0.8661 (m-40) REVERT: AT 173 MET cc_start: 0.8885 (tmm) cc_final: 0.8604 (tmm) REVERT: AT 246 THR cc_start: 0.8718 (p) cc_final: 0.8438 (t) REVERT: AT 266 ASN cc_start: 0.8245 (t0) cc_final: 0.7934 (t0) REVERT: AU 94 TYR cc_start: 0.9106 (t80) cc_final: 0.8692 (t80) REVERT: AU 116 MET cc_start: 0.8463 (ttp) cc_final: 0.8135 (ttp) REVERT: AU 136 ASP cc_start: 0.8589 (t70) cc_final: 0.8389 (t0) REVERT: AU 151 ASN cc_start: 0.8949 (m-40) cc_final: 0.8383 (m110) REVERT: AU 246 THR cc_start: 0.8806 (p) cc_final: 0.8494 (t) REVERT: AU 266 ASN cc_start: 0.8327 (t0) cc_final: 0.8049 (t0) REVERT: AV 87 GLN cc_start: 0.9295 (tp40) cc_final: 0.8044 (tp40) REVERT: AV 94 TYR cc_start: 0.9016 (t80) cc_final: 0.8364 (t80) REVERT: AV 108 MET cc_start: 0.8449 (tpt) cc_final: 0.8247 (tpt) REVERT: AV 220 MET cc_start: 0.9010 (mtm) cc_final: 0.8751 (mtm) REVERT: AV 236 ASP cc_start: 0.8109 (p0) cc_final: 0.7644 (p0) REVERT: AW 83 THR cc_start: 0.9073 (m) cc_final: 0.8748 (p) REVERT: AW 94 TYR cc_start: 0.8998 (t80) cc_final: 0.8673 (t80) REVERT: AW 136 ASP cc_start: 0.8661 (t70) cc_final: 0.8351 (t0) REVERT: AW 236 ASP cc_start: 0.8086 (p0) cc_final: 0.7793 (p0) REVERT: AX 59 SER cc_start: 0.6361 (p) cc_final: 0.6061 (p) REVERT: AX 83 THR cc_start: 0.9055 (m) cc_final: 0.8655 (p) REVERT: AX 94 TYR cc_start: 0.9037 (t80) cc_final: 0.8676 (t80) REVERT: AX 136 ASP cc_start: 0.8502 (t70) cc_final: 0.7750 (t0) REVERT: AX 151 ASN cc_start: 0.9003 (m-40) cc_final: 0.8513 (m110) REVERT: AX 173 MET cc_start: 0.8886 (tmm) cc_final: 0.8600 (tmm) REVERT: AX 236 ASP cc_start: 0.8050 (p0) cc_final: 0.7650 (p0) REVERT: AX 266 ASN cc_start: 0.8369 (t0) cc_final: 0.7969 (t0) REVERT: AY 59 SER cc_start: 0.6092 (p) cc_final: 0.5834 (p) REVERT: AY 94 TYR cc_start: 0.8945 (t80) cc_final: 0.8573 (t80) REVERT: AY 158 GLN cc_start: 0.8851 (mt0) cc_final: 0.8606 (mt0) REVERT: AY 176 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8420 (mptt) REVERT: AY 215 GLU cc_start: 0.8477 (tp30) cc_final: 0.8209 (tp30) REVERT: AY 236 ASP cc_start: 0.8045 (p0) cc_final: 0.7601 (p0) REVERT: AY 246 THR cc_start: 0.8787 (p) cc_final: 0.8498 (t) REVERT: AZ 94 TYR cc_start: 0.8976 (t80) cc_final: 0.8143 (t80) REVERT: AZ 136 ASP cc_start: 0.8533 (t70) cc_final: 0.8120 (m-30) REVERT: AZ 168 GLU cc_start: 0.8693 (tt0) cc_final: 0.8472 (tt0) REVERT: AZ 236 ASP cc_start: 0.8067 (p0) cc_final: 0.7808 (p0) REVERT: BA 83 THR cc_start: 0.9135 (m) cc_final: 0.8761 (p) REVERT: BA 94 TYR cc_start: 0.9034 (t80) cc_final: 0.8644 (t80) REVERT: BA 136 ASP cc_start: 0.8438 (t70) cc_final: 0.8171 (m-30) REVERT: BA 146 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8109 (tptm) REVERT: BA 150 GLU cc_start: 0.7750 (tt0) cc_final: 0.7498 (tm-30) REVERT: BA 151 ASN cc_start: 0.9041 (m-40) cc_final: 0.8642 (m110) REVERT: BA 173 MET cc_start: 0.8915 (tmm) cc_final: 0.8610 (tmm) REVERT: BA 266 ASN cc_start: 0.8189 (t0) cc_final: 0.7735 (t0) REVERT: BB 59 SER cc_start: 0.6507 (p) cc_final: 0.6027 (p) REVERT: BB 87 GLN cc_start: 0.9304 (tp40) cc_final: 0.9095 (tp-100) REVERT: BB 94 TYR cc_start: 0.9026 (t80) cc_final: 0.8734 (t80) REVERT: BB 136 ASP cc_start: 0.8379 (t70) cc_final: 0.8000 (m-30) REVERT: BB 146 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8348 (tptm) REVERT: BB 176 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8547 (mmtm) REVERT: BB 220 MET cc_start: 0.8982 (mtm) cc_final: 0.8735 (mtp) REVERT: BC 87 GLN cc_start: 0.9163 (tp40) cc_final: 0.8596 (tp40) REVERT: BC 94 TYR cc_start: 0.9028 (t80) cc_final: 0.8460 (t80) REVERT: BC 108 MET cc_start: 0.8548 (tpt) cc_final: 0.8252 (tpt) REVERT: BC 146 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8126 (tptm) REVERT: BC 150 GLU cc_start: 0.7773 (tt0) cc_final: 0.7565 (tm-30) REVERT: BC 176 LYS cc_start: 0.8755 (mmtp) cc_final: 0.8521 (mptt) REVERT: BC 236 ASP cc_start: 0.7891 (p0) cc_final: 0.7551 (p0) REVERT: BD 136 ASP cc_start: 0.8510 (t70) cc_final: 0.8176 (m-30) REVERT: BD 146 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8268 (tptm) REVERT: BD 150 GLU cc_start: 0.7685 (tt0) cc_final: 0.7455 (tm-30) REVERT: BD 246 THR cc_start: 0.8866 (p) cc_final: 0.8588 (t) REVERT: BE 94 TYR cc_start: 0.9036 (t80) cc_final: 0.8770 (t80) REVERT: BE 136 ASP cc_start: 0.8334 (t70) cc_final: 0.7964 (m-30) REVERT: BE 151 ASN cc_start: 0.8997 (m-40) cc_final: 0.8179 (m110) REVERT: BE 173 MET cc_start: 0.8999 (tmm) cc_final: 0.8394 (tmm) REVERT: BE 266 ASN cc_start: 0.8290 (t0) cc_final: 0.7912 (t0) REVERT: BF 94 TYR cc_start: 0.9015 (t80) cc_final: 0.8414 (t80) REVERT: BF 98 GLN cc_start: 0.8666 (tt0) cc_final: 0.8428 (tt0) REVERT: BF 134 MET cc_start: 0.9059 (ttt) cc_final: 0.8801 (ttp) REVERT: BF 136 ASP cc_start: 0.8333 (t70) cc_final: 0.7887 (m-30) REVERT: BF 146 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8095 (tptm) REVERT: BF 151 ASN cc_start: 0.8999 (m-40) cc_final: 0.8453 (m110) REVERT: BF 158 GLN cc_start: 0.8925 (mt0) cc_final: 0.8594 (mt0) REVERT: BF 176 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8376 (mptt) REVERT: BF 266 ASN cc_start: 0.8351 (t0) cc_final: 0.8115 (t0) REVERT: BG 59 SER cc_start: 0.6430 (p) cc_final: 0.5860 (p) REVERT: BG 136 ASP cc_start: 0.8399 (t70) cc_final: 0.8075 (m-30) REVERT: BG 146 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8361 (tptm) REVERT: BG 150 GLU cc_start: 0.7846 (tt0) cc_final: 0.7635 (tm-30) REVERT: BH 83 THR cc_start: 0.9156 (m) cc_final: 0.8686 (p) REVERT: BH 94 TYR cc_start: 0.8992 (t80) cc_final: 0.8610 (t80) REVERT: BH 116 MET cc_start: 0.8519 (ttp) cc_final: 0.8279 (ttp) REVERT: BH 143 TYR cc_start: 0.8998 (m-80) cc_final: 0.8790 (m-80) REVERT: BH 146 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8227 (tptm) REVERT: BH 150 GLU cc_start: 0.7798 (tt0) cc_final: 0.7522 (tm-30) REVERT: BH 236 ASP cc_start: 0.8088 (p0) cc_final: 0.7869 (p0) REVERT: BI 94 TYR cc_start: 0.8863 (t80) cc_final: 0.8186 (t80) REVERT: BI 108 MET cc_start: 0.8522 (tpt) cc_final: 0.8095 (tpt) REVERT: BI 136 ASP cc_start: 0.8371 (t70) cc_final: 0.8032 (m-30) REVERT: BI 173 MET cc_start: 0.8989 (tmm) cc_final: 0.8731 (tmm) REVERT: BI 191 ARG cc_start: 0.8370 (mtt90) cc_final: 0.6563 (mmt180) REVERT: BI 198 TYR cc_start: 0.9106 (m-80) cc_final: 0.8622 (m-80) outliers start: 19 outliers final: 1 residues processed: 2352 average time/residue: 0.6721 time to fit residues: 2687.6656 Evaluate side-chains 1435 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1433 time to evaluate : 5.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 176 LYS Chi-restraints excluded: chain AO residue 176 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 650 optimal weight: 0.9980 chunk 583 optimal weight: 0.7980 chunk 323 optimal weight: 0.8980 chunk 199 optimal weight: 5.9990 chunk 393 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 603 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 366 optimal weight: 6.9990 chunk 449 optimal weight: 5.9990 chunk 699 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 140 GLN AB 151 ASN AE 69 HIS AJ 127 ASN AJ 229 GLN AK 229 GLN AL 69 HIS AL 140 GLN AL 229 GLN AM 98 GLN AM 229 GLN AN 69 HIS AN 229 GLN AO 229 GLN AP 229 GLN AQ 229 GLN AR 229 GLN AS 229 GLN AT 151 ASN AT 229 GLN AU 69 HIS AU 127 ASN AU 229 GLN AV 229 GLN AW 229 GLN AX 229 GLN ** AY 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 229 GLN AZ 229 GLN BA 229 GLN BB 229 GLN BC 69 HIS BC 229 GLN BD 229 GLN BE 98 GLN BE 229 GLN BF 69 HIS BF 127 ASN BF 229 GLN BG 229 GLN BH 229 GLN BI 229 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 67340 Z= 0.185 Angle : 0.646 10.923 91805 Z= 0.331 Chirality : 0.041 0.164 10360 Planarity : 0.004 0.037 11375 Dihedral : 11.528 59.324 11313 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.59 % Allowed : 12.39 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.09), residues: 7770 helix: -0.23 (0.09), residues: 3150 sheet: -1.34 (0.20), residues: 350 loop : -2.21 (0.09), residues: 4270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAT 132 HIS 0.004 0.001 HISBD 162 PHE 0.014 0.001 PHEAQ 200 TYR 0.018 0.002 TYRAK 198 ARG 0.005 0.000 ARGBH 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1836 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1660 time to evaluate : 5.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 GLN cc_start: 0.8481 (tm-30) cc_final: 0.7975 (mm-40) REVERT: AA 83 THR cc_start: 0.9209 (m) cc_final: 0.8924 (p) REVERT: AA 94 TYR cc_start: 0.8919 (t80) cc_final: 0.8684 (t80) REVERT: AA 172 GLU cc_start: 0.8347 (tp30) cc_final: 0.7930 (tp30) REVERT: AA 191 ARG cc_start: 0.8161 (mtt90) cc_final: 0.6325 (mpt180) REVERT: AA 231 ARG cc_start: 0.8030 (ttt90) cc_final: 0.7637 (tpm170) REVERT: AB 82 ASN cc_start: 0.8332 (t0) cc_final: 0.8056 (t0) REVERT: AB 83 THR cc_start: 0.9195 (m) cc_final: 0.8977 (p) REVERT: AB 94 TYR cc_start: 0.8860 (t80) cc_final: 0.8608 (t80) REVERT: AB 191 ARG cc_start: 0.8076 (mtt90) cc_final: 0.6541 (mpt180) REVERT: AB 219 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8612 (mm110) REVERT: AB 231 ARG cc_start: 0.7772 (ttt90) cc_final: 0.7480 (tpm170) REVERT: AB 246 THR cc_start: 0.8732 (p) cc_final: 0.8364 (t) REVERT: AB 266 ASN cc_start: 0.8310 (t0) cc_final: 0.7970 (t0) REVERT: AC 83 THR cc_start: 0.9074 (m) cc_final: 0.8817 (p) REVERT: AC 87 GLN cc_start: 0.8811 (tp40) cc_final: 0.8578 (tp40) REVERT: AC 94 TYR cc_start: 0.8805 (t80) cc_final: 0.8332 (t80) REVERT: AC 158 GLN cc_start: 0.8907 (mt0) cc_final: 0.8598 (mt0) REVERT: AC 191 ARG cc_start: 0.8141 (mtt90) cc_final: 0.6547 (mpt180) REVERT: AC 219 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8526 (mm110) REVERT: AC 231 ARG cc_start: 0.7822 (ttt90) cc_final: 0.7320 (mmp-170) REVERT: AC 246 THR cc_start: 0.8830 (p) cc_final: 0.8433 (t) REVERT: AC 267 MET cc_start: 0.7799 (mmm) cc_final: 0.7598 (mmm) REVERT: AD 83 THR cc_start: 0.9108 (m) cc_final: 0.8780 (p) REVERT: AD 94 TYR cc_start: 0.8879 (t80) cc_final: 0.8558 (t80) REVERT: AD 136 ASP cc_start: 0.8464 (t0) cc_final: 0.8229 (t0) REVERT: AD 173 MET cc_start: 0.8687 (tmm) cc_final: 0.8459 (tmm) REVERT: AD 191 ARG cc_start: 0.8169 (mtt90) cc_final: 0.6721 (mpt180) REVERT: AD 246 THR cc_start: 0.8736 (p) cc_final: 0.8403 (t) REVERT: AE 83 THR cc_start: 0.9086 (m) cc_final: 0.8748 (p) REVERT: AE 94 TYR cc_start: 0.8932 (t80) cc_final: 0.8600 (t80) REVERT: AE 160 MET cc_start: 0.9156 (mmm) cc_final: 0.8892 (mmm) REVERT: AE 191 ARG cc_start: 0.8047 (mtt90) cc_final: 0.6494 (mpt180) REVERT: AE 231 ARG cc_start: 0.7904 (ttt90) cc_final: 0.7483 (tpm170) REVERT: AE 249 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.7670 (t70) REVERT: AE 267 MET cc_start: 0.7803 (mmm) cc_final: 0.7587 (mmm) REVERT: AF 94 TYR cc_start: 0.8978 (t80) cc_final: 0.8643 (t80) REVERT: AF 135 MET cc_start: 0.8947 (mmm) cc_final: 0.8725 (mmm) REVERT: AF 136 ASP cc_start: 0.8402 (t70) cc_final: 0.8175 (t0) REVERT: AF 170 TYR cc_start: 0.9161 (t80) cc_final: 0.8900 (t80) REVERT: AF 191 ARG cc_start: 0.8147 (mtt90) cc_final: 0.6241 (mpt180) REVERT: AF 231 ARG cc_start: 0.7698 (ttt90) cc_final: 0.7311 (mmp-170) REVERT: AF 246 THR cc_start: 0.8813 (p) cc_final: 0.8416 (t) REVERT: AF 249 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.8365 (t70) REVERT: AG 83 THR cc_start: 0.9289 (m) cc_final: 0.8948 (p) REVERT: AG 94 TYR cc_start: 0.8805 (t80) cc_final: 0.8216 (t80) REVERT: AG 116 MET cc_start: 0.8935 (ttp) cc_final: 0.8555 (ttp) REVERT: AG 136 ASP cc_start: 0.8393 (t70) cc_final: 0.8071 (t0) REVERT: AG 143 TYR cc_start: 0.8929 (m-80) cc_final: 0.8694 (m-80) REVERT: AG 158 GLN cc_start: 0.8900 (mt0) cc_final: 0.8594 (mt0) REVERT: AG 191 ARG cc_start: 0.8218 (mtt90) cc_final: 0.6502 (mpt180) REVERT: AG 231 ARG cc_start: 0.7978 (ttt90) cc_final: 0.7340 (mmp-170) REVERT: AG 246 THR cc_start: 0.8850 (p) cc_final: 0.8498 (t) REVERT: AH 94 TYR cc_start: 0.8925 (t80) cc_final: 0.8701 (t80) REVERT: AH 191 ARG cc_start: 0.8027 (mtt90) cc_final: 0.6482 (mpt180) REVERT: AH 219 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8548 (mm110) REVERT: AH 231 ARG cc_start: 0.7994 (ttt90) cc_final: 0.7618 (tpm170) REVERT: AH 267 MET cc_start: 0.7814 (mmm) cc_final: 0.7476 (mmm) REVERT: AI 83 THR cc_start: 0.9098 (m) cc_final: 0.8833 (p) REVERT: AI 94 TYR cc_start: 0.8838 (t80) cc_final: 0.8575 (t80) REVERT: AI 136 ASP cc_start: 0.8447 (t0) cc_final: 0.8225 (t0) REVERT: AI 173 MET cc_start: 0.8816 (tmm) cc_final: 0.8263 (tmm) REVERT: AJ 94 TYR cc_start: 0.8801 (t80) cc_final: 0.8153 (t80) REVERT: AJ 98 GLN cc_start: 0.8411 (tt0) cc_final: 0.8187 (tt0) REVERT: AJ 108 MET cc_start: 0.8313 (tpt) cc_final: 0.7981 (tpt) REVERT: AJ 136 ASP cc_start: 0.8434 (t0) cc_final: 0.8234 (t0) REVERT: AJ 246 THR cc_start: 0.8822 (p) cc_final: 0.8445 (t) REVERT: AK 87 GLN cc_start: 0.8871 (tp40) cc_final: 0.8442 (tp40) REVERT: AK 94 TYR cc_start: 0.8926 (t80) cc_final: 0.8363 (t80) REVERT: AK 134 MET cc_start: 0.8830 (ttt) cc_final: 0.8527 (ttt) REVERT: AK 136 ASP cc_start: 0.8483 (t0) cc_final: 0.8226 (t0) REVERT: AK 246 THR cc_start: 0.8831 (p) cc_final: 0.8409 (t) REVERT: AK 267 MET cc_start: 0.7517 (mmm) cc_final: 0.7192 (mmm) REVERT: AL 83 THR cc_start: 0.9228 (m) cc_final: 0.8895 (p) REVERT: AL 136 ASP cc_start: 0.8643 (t0) cc_final: 0.8379 (t0) REVERT: AL 173 MET cc_start: 0.8731 (tmm) cc_final: 0.8341 (tmm) REVERT: AL 267 MET cc_start: 0.7964 (mmm) cc_final: 0.7743 (mmm) REVERT: AM 94 TYR cc_start: 0.8905 (t80) cc_final: 0.8674 (t80) REVERT: AM 136 ASP cc_start: 0.8453 (t0) cc_final: 0.8186 (t0) REVERT: AM 184 TYR cc_start: 0.9132 (t80) cc_final: 0.8774 (t80) REVERT: AM 249 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.8159 (t-170) REVERT: AM 267 MET cc_start: 0.7451 (mmm) cc_final: 0.7220 (mmm) REVERT: AN 83 THR cc_start: 0.9035 (m) cc_final: 0.8811 (p) REVERT: AN 94 TYR cc_start: 0.8900 (t80) cc_final: 0.8662 (t80) REVERT: AN 136 ASP cc_start: 0.8613 (t70) cc_final: 0.8305 (t0) REVERT: AN 181 MET cc_start: 0.9046 (tpp) cc_final: 0.8712 (tpp) REVERT: AN 246 THR cc_start: 0.8847 (p) cc_final: 0.8470 (t) REVERT: AN 267 MET cc_start: 0.7713 (mmm) cc_final: 0.7496 (mmm) REVERT: AO 83 THR cc_start: 0.9186 (m) cc_final: 0.8953 (p) REVERT: AO 94 TYR cc_start: 0.8890 (t80) cc_final: 0.8540 (t80) REVERT: AO 170 TYR cc_start: 0.9213 (t80) cc_final: 0.8793 (t80) REVERT: AO 246 THR cc_start: 0.8697 (p) cc_final: 0.8325 (t) REVERT: AO 249 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.8358 (t70) REVERT: AP 83 THR cc_start: 0.9090 (m) cc_final: 0.8755 (p) REVERT: AP 94 TYR cc_start: 0.8893 (t80) cc_final: 0.8632 (t80) REVERT: AP 136 ASP cc_start: 0.8316 (t0) cc_final: 0.8052 (t0) REVERT: AP 143 TYR cc_start: 0.9002 (m-80) cc_final: 0.8602 (m-80) REVERT: AP 160 MET cc_start: 0.9071 (mmm) cc_final: 0.8863 (mmm) REVERT: AP 249 HIS cc_start: 0.8668 (OUTLIER) cc_final: 0.7600 (t-90) REVERT: AQ 83 THR cc_start: 0.9212 (m) cc_final: 0.8928 (p) REVERT: AQ 146 LYS cc_start: 0.8553 (tptm) cc_final: 0.8318 (tptm) REVERT: AQ 246 THR cc_start: 0.8768 (p) cc_final: 0.8284 (t) REVERT: AR 136 ASP cc_start: 0.8451 (t0) cc_final: 0.7994 (t0) REVERT: AR 172 GLU cc_start: 0.8105 (tp30) cc_final: 0.7811 (mm-30) REVERT: AR 246 THR cc_start: 0.8863 (p) cc_final: 0.8563 (t) REVERT: AS 83 THR cc_start: 0.9160 (m) cc_final: 0.8879 (p) REVERT: AS 87 GLN cc_start: 0.9134 (tp40) cc_final: 0.8475 (tp-100) REVERT: AS 116 MET cc_start: 0.8769 (ttp) cc_final: 0.8422 (ptm) REVERT: AS 143 TYR cc_start: 0.9004 (m-80) cc_final: 0.8653 (m-80) REVERT: AS 267 MET cc_start: 0.7707 (mmm) cc_final: 0.7461 (mmm) REVERT: AT 83 THR cc_start: 0.8973 (m) cc_final: 0.8736 (p) REVERT: AT 94 TYR cc_start: 0.8920 (t80) cc_final: 0.8626 (t80) REVERT: AT 136 ASP cc_start: 0.8501 (t0) cc_final: 0.8292 (t0) REVERT: AT 170 TYR cc_start: 0.9205 (t80) cc_final: 0.8887 (t80) REVERT: AT 173 MET cc_start: 0.8673 (tmm) cc_final: 0.8339 (tmm) REVERT: AT 249 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.8010 (t70) REVERT: AT 266 ASN cc_start: 0.7888 (t0) cc_final: 0.7661 (t0) REVERT: AU 83 THR cc_start: 0.9276 (m) cc_final: 0.9020 (p) REVERT: AU 94 TYR cc_start: 0.8926 (t80) cc_final: 0.8666 (t80) REVERT: AU 108 MET cc_start: 0.8475 (tpt) cc_final: 0.8233 (tpp) REVERT: AU 116 MET cc_start: 0.8550 (ttp) cc_final: 0.8280 (ttp) REVERT: AU 136 ASP cc_start: 0.8538 (t70) cc_final: 0.8286 (t0) REVERT: AU 173 MET cc_start: 0.8721 (tmm) cc_final: 0.8478 (tmm) REVERT: AU 246 THR cc_start: 0.8789 (p) cc_final: 0.8507 (t) REVERT: AV 83 THR cc_start: 0.9234 (m) cc_final: 0.9004 (p) REVERT: AV 94 TYR cc_start: 0.8850 (t80) cc_final: 0.8450 (t80) REVERT: AV 267 MET cc_start: 0.7597 (mmm) cc_final: 0.7265 (mmm) REVERT: AW 94 TYR cc_start: 0.8865 (t80) cc_final: 0.8573 (t80) REVERT: AW 172 GLU cc_start: 0.8401 (tp30) cc_final: 0.8097 (tp30) REVERT: AX 83 THR cc_start: 0.9176 (m) cc_final: 0.8968 (p) REVERT: AX 94 TYR cc_start: 0.8954 (t80) cc_final: 0.8651 (t80) REVERT: AX 184 TYR cc_start: 0.9301 (t80) cc_final: 0.9063 (t80) REVERT: AX 267 MET cc_start: 0.7712 (mmm) cc_final: 0.7378 (mmm) REVERT: AY 77 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8142 (tp40) REVERT: AY 94 TYR cc_start: 0.8836 (t80) cc_final: 0.8534 (t80) REVERT: AY 158 GLN cc_start: 0.8852 (mt0) cc_final: 0.8625 (mt0) REVERT: AY 181 MET cc_start: 0.9116 (tpp) cc_final: 0.8860 (tpp) REVERT: AY 215 GLU cc_start: 0.8498 (tp30) cc_final: 0.8218 (tp30) REVERT: AY 246 THR cc_start: 0.8819 (p) cc_final: 0.8577 (t) REVERT: AY 267 MET cc_start: 0.7701 (mmm) cc_final: 0.7472 (mmm) REVERT: AZ 83 THR cc_start: 0.9238 (m) cc_final: 0.8967 (p) REVERT: AZ 94 TYR cc_start: 0.8821 (t80) cc_final: 0.8534 (t80) REVERT: AZ 136 ASP cc_start: 0.8810 (t70) cc_final: 0.8150 (m-30) REVERT: AZ 267 MET cc_start: 0.7632 (mmm) cc_final: 0.7409 (mmm) REVERT: BA 83 THR cc_start: 0.9207 (m) cc_final: 0.8932 (p) REVERT: BA 94 TYR cc_start: 0.8883 (t80) cc_final: 0.8599 (t80) REVERT: BA 136 ASP cc_start: 0.8659 (t70) cc_final: 0.8131 (m-30) REVERT: BA 146 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8089 (tptm) REVERT: BA 173 MET cc_start: 0.8820 (tmm) cc_final: 0.8512 (tmm) REVERT: BA 249 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.8220 (t70) REVERT: BA 267 MET cc_start: 0.7829 (mmm) cc_final: 0.7617 (mmm) REVERT: BB 94 TYR cc_start: 0.8933 (t80) cc_final: 0.8646 (t80) REVERT: BB 136 ASP cc_start: 0.8576 (t70) cc_final: 0.7905 (m-30) REVERT: BB 146 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8326 (tptm) REVERT: BB 173 MET cc_start: 0.8851 (tmm) cc_final: 0.8548 (tmm) REVERT: BB 184 TYR cc_start: 0.9176 (t80) cc_final: 0.8961 (t80) REVERT: BB 236 ASP cc_start: 0.8226 (p0) cc_final: 0.7887 (m-30) REVERT: BC 83 THR cc_start: 0.9133 (m) cc_final: 0.8827 (p) REVERT: BC 87 GLN cc_start: 0.8711 (tp40) cc_final: 0.8320 (mm-40) REVERT: BC 94 TYR cc_start: 0.8851 (t80) cc_final: 0.8321 (t80) REVERT: BC 146 LYS cc_start: 0.8497 (ttmt) cc_final: 0.8244 (tptm) REVERT: BC 184 TYR cc_start: 0.9120 (t80) cc_final: 0.8903 (t80) REVERT: BD 136 ASP cc_start: 0.8695 (t70) cc_final: 0.8419 (t0) REVERT: BD 173 MET cc_start: 0.8749 (tmm) cc_final: 0.8486 (tmm) REVERT: BD 246 THR cc_start: 0.8794 (p) cc_final: 0.8571 (t) REVERT: BD 267 MET cc_start: 0.7751 (mmm) cc_final: 0.7447 (mmm) REVERT: BE 83 THR cc_start: 0.9231 (m) cc_final: 0.9008 (p) REVERT: BE 94 TYR cc_start: 0.8951 (t80) cc_final: 0.8661 (t80) REVERT: BE 136 ASP cc_start: 0.8583 (t70) cc_final: 0.7883 (m-30) REVERT: BE 180 TYR cc_start: 0.8353 (t80) cc_final: 0.8073 (t80) REVERT: BE 267 MET cc_start: 0.7823 (mmm) cc_final: 0.7561 (mmm) REVERT: BF 87 GLN cc_start: 0.8983 (tp40) cc_final: 0.8040 (tp40) REVERT: BF 94 TYR cc_start: 0.8835 (t80) cc_final: 0.8535 (t80) REVERT: BF 134 MET cc_start: 0.9040 (ttt) cc_final: 0.8775 (ttp) REVERT: BF 136 ASP cc_start: 0.8257 (t70) cc_final: 0.7915 (m-30) REVERT: BF 146 LYS cc_start: 0.8234 (ttmt) cc_final: 0.8017 (tptm) REVERT: BF 158 GLN cc_start: 0.8876 (mt0) cc_final: 0.8536 (mt0) REVERT: BG 112 MET cc_start: 0.8776 (mmp) cc_final: 0.8483 (mpp) REVERT: BG 136 ASP cc_start: 0.8627 (t70) cc_final: 0.8118 (m-30) REVERT: BG 146 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8199 (tptm) REVERT: BG 180 TYR cc_start: 0.8199 (t80) cc_final: 0.7648 (t80) REVERT: BG 267 MET cc_start: 0.7490 (mmm) cc_final: 0.7174 (mmm) REVERT: BH 83 THR cc_start: 0.9207 (m) cc_final: 0.8919 (p) REVERT: BH 94 TYR cc_start: 0.8859 (t80) cc_final: 0.8622 (t80) REVERT: BH 136 ASP cc_start: 0.8618 (t0) cc_final: 0.8179 (m-30) REVERT: BH 173 MET cc_start: 0.8738 (tmm) cc_final: 0.8467 (tmm) REVERT: BI 78 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8799 (tp) REVERT: BI 83 THR cc_start: 0.9037 (m) cc_final: 0.8742 (p) REVERT: BI 91 ASP cc_start: 0.8233 (m-30) cc_final: 0.7992 (m-30) REVERT: BI 94 TYR cc_start: 0.8659 (t80) cc_final: 0.8026 (t80) REVERT: BI 108 MET cc_start: 0.8294 (tpt) cc_final: 0.8052 (tpt) REVERT: BI 121 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7926 (tt0) REVERT: BI 136 ASP cc_start: 0.8273 (t70) cc_final: 0.7998 (m-30) REVERT: BI 173 MET cc_start: 0.8826 (tmm) cc_final: 0.8479 (tmm) REVERT: BI 191 ARG cc_start: 0.8278 (mtt90) cc_final: 0.6567 (mmt180) REVERT: BI 266 ASN cc_start: 0.8253 (t0) cc_final: 0.8000 (t0) outliers start: 176 outliers final: 67 residues processed: 1779 average time/residue: 0.6659 time to fit residues: 1989.0538 Evaluate side-chains 1457 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1382 time to evaluate : 5.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 88 SER Chi-restraints excluded: chain AB residue 88 SER Chi-restraints excluded: chain AB residue 249 HIS Chi-restraints excluded: chain AB residue 261 LEU Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AD residue 81 SER Chi-restraints excluded: chain AD residue 88 SER Chi-restraints excluded: chain AD residue 106 THR Chi-restraints excluded: chain AE residue 88 SER Chi-restraints excluded: chain AE residue 249 HIS Chi-restraints excluded: chain AF residue 88 SER Chi-restraints excluded: chain AF residue 249 HIS Chi-restraints excluded: chain AG residue 88 SER Chi-restraints excluded: chain AH residue 56 MET Chi-restraints excluded: chain AH residue 88 SER Chi-restraints excluded: chain AH residue 252 GLU Chi-restraints excluded: chain AI residue 88 SER Chi-restraints excluded: chain AJ residue 88 SER Chi-restraints excluded: chain AK residue 88 SER Chi-restraints excluded: chain AK residue 230 SER Chi-restraints excluded: chain AK residue 261 LEU Chi-restraints excluded: chain AL residue 56 MET Chi-restraints excluded: chain AL residue 88 SER Chi-restraints excluded: chain AL residue 249 HIS Chi-restraints excluded: chain AM residue 88 SER Chi-restraints excluded: chain AM residue 249 HIS Chi-restraints excluded: chain AM residue 261 LEU Chi-restraints excluded: chain AN residue 88 SER Chi-restraints excluded: chain AN residue 230 SER Chi-restraints excluded: chain AO residue 88 SER Chi-restraints excluded: chain AO residue 230 SER Chi-restraints excluded: chain AO residue 249 HIS Chi-restraints excluded: chain AP residue 56 MET Chi-restraints excluded: chain AP residue 88 SER Chi-restraints excluded: chain AP residue 249 HIS Chi-restraints excluded: chain AP residue 261 LEU Chi-restraints excluded: chain AQ residue 88 SER Chi-restraints excluded: chain AQ residue 261 LEU Chi-restraints excluded: chain AR residue 88 SER Chi-restraints excluded: chain AR residue 230 SER Chi-restraints excluded: chain AS residue 88 SER Chi-restraints excluded: chain AS residue 230 SER Chi-restraints excluded: chain AS residue 252 GLU Chi-restraints excluded: chain AT residue 88 SER Chi-restraints excluded: chain AT residue 249 HIS Chi-restraints excluded: chain AT residue 261 LEU Chi-restraints excluded: chain AU residue 88 SER Chi-restraints excluded: chain AV residue 78 ILE Chi-restraints excluded: chain AV residue 88 SER Chi-restraints excluded: chain AV residue 106 THR Chi-restraints excluded: chain AV residue 261 LEU Chi-restraints excluded: chain AW residue 88 SER Chi-restraints excluded: chain AW residue 230 SER Chi-restraints excluded: chain AX residue 249 HIS Chi-restraints excluded: chain AX residue 261 LEU Chi-restraints excluded: chain AY residue 78 ILE Chi-restraints excluded: chain AY residue 88 SER Chi-restraints excluded: chain AZ residue 88 SER Chi-restraints excluded: chain AZ residue 230 SER Chi-restraints excluded: chain BA residue 88 SER Chi-restraints excluded: chain BA residue 249 HIS Chi-restraints excluded: chain BB residue 88 SER Chi-restraints excluded: chain BB residue 135 MET Chi-restraints excluded: chain BC residue 78 ILE Chi-restraints excluded: chain BC residue 88 SER Chi-restraints excluded: chain BD residue 88 SER Chi-restraints excluded: chain BD residue 230 SER Chi-restraints excluded: chain BD residue 252 GLU Chi-restraints excluded: chain BE residue 88 SER Chi-restraints excluded: chain BF residue 88 SER Chi-restraints excluded: chain BG residue 78 ILE Chi-restraints excluded: chain BG residue 88 SER Chi-restraints excluded: chain BG residue 230 SER Chi-restraints excluded: chain BI residue 78 ILE Chi-restraints excluded: chain BI residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 388 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 581 optimal weight: 5.9990 chunk 476 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 700 optimal weight: 10.0000 chunk 756 optimal weight: 8.9990 chunk 623 optimal weight: 7.9990 chunk 694 optimal weight: 0.8980 chunk 238 optimal weight: 0.5980 chunk 561 optimal weight: 0.0670 overall best weight: 3.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 127 ASN AB 151 ASN AB 158 GLN AE 98 GLN ** AE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 140 GLN ** AF 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 127 ASN AJ 158 GLN AK 158 GLN ** AL 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 140 GLN ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 158 GLN AO 158 GLN AP 140 GLN ** AQ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 140 GLN AT 151 ASN AU 98 GLN AU 127 ASN ** AV 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AZ 158 GLN BA 76 GLN ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 158 GLN BE 158 GLN BF 127 ASN BH 140 GLN BI 140 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 67340 Z= 0.314 Angle : 0.645 10.688 91805 Z= 0.330 Chirality : 0.043 0.207 10360 Planarity : 0.004 0.061 11375 Dihedral : 11.322 60.079 11305 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.84 % Allowed : 14.51 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.10), residues: 7770 helix: 0.70 (0.10), residues: 3080 sheet: -0.57 (0.23), residues: 350 loop : -1.80 (0.09), residues: 4340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAR 132 HIS 0.004 0.001 HISAD 249 PHE 0.013 0.002 PHEAK 200 TYR 0.019 0.002 TYRBB 170 ARG 0.005 0.001 ARGBA 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1599 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1406 time to evaluate : 5.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8030 (mm-40) REVERT: AA 191 ARG cc_start: 0.8347 (mtt90) cc_final: 0.6578 (mpt180) REVERT: AA 231 ARG cc_start: 0.7962 (ttt90) cc_final: 0.7600 (tpm170) REVERT: AB 83 THR cc_start: 0.9339 (m) cc_final: 0.9127 (p) REVERT: AB 94 TYR cc_start: 0.8841 (t80) cc_final: 0.8199 (t80) REVERT: AB 191 ARG cc_start: 0.8302 (mtt90) cc_final: 0.6599 (mpt180) REVERT: AB 204 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: AB 231 ARG cc_start: 0.7934 (ttt90) cc_final: 0.7413 (tpm170) REVERT: AB 267 MET cc_start: 0.7572 (mmm) cc_final: 0.7263 (mmm) REVERT: AC 83 THR cc_start: 0.9317 (m) cc_final: 0.9045 (p) REVERT: AC 158 GLN cc_start: 0.9055 (mt0) cc_final: 0.8739 (mt0) REVERT: AC 191 ARG cc_start: 0.8185 (mtt90) cc_final: 0.6694 (mpt180) REVERT: AC 204 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: AC 219 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8610 (mm110) REVERT: AC 231 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7425 (tpm170) REVERT: AD 94 TYR cc_start: 0.8865 (t80) cc_final: 0.8573 (t80) REVERT: AD 136 ASP cc_start: 0.8544 (t0) cc_final: 0.8297 (t0) REVERT: AD 191 ARG cc_start: 0.8259 (mtt90) cc_final: 0.6528 (mpt180) REVERT: AE 94 TYR cc_start: 0.8959 (t80) cc_final: 0.8579 (t80) REVERT: AE 146 LYS cc_start: 0.8553 (tptm) cc_final: 0.8324 (tptm) REVERT: AE 160 MET cc_start: 0.9111 (mmm) cc_final: 0.8755 (mmm) REVERT: AE 220 MET cc_start: 0.9053 (mtm) cc_final: 0.8823 (mtp) REVERT: AE 231 ARG cc_start: 0.7936 (ttt90) cc_final: 0.7438 (tpm170) REVERT: AE 267 MET cc_start: 0.7918 (mmm) cc_final: 0.7704 (mmm) REVERT: AF 94 TYR cc_start: 0.8981 (t80) cc_final: 0.8612 (t80) REVERT: AF 191 ARG cc_start: 0.8187 (mtt90) cc_final: 0.6277 (mpt180) REVERT: AF 204 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: AF 231 ARG cc_start: 0.7737 (ttt90) cc_final: 0.7306 (tpm170) REVERT: AG 83 THR cc_start: 0.9489 (m) cc_final: 0.9234 (p) REVERT: AG 94 TYR cc_start: 0.8866 (t80) cc_final: 0.8649 (t80) REVERT: AG 116 MET cc_start: 0.9026 (ttp) cc_final: 0.8455 (ttp) REVERT: AG 136 ASP cc_start: 0.8387 (t70) cc_final: 0.8099 (t0) REVERT: AG 143 TYR cc_start: 0.8912 (m-80) cc_final: 0.8633 (m-80) REVERT: AG 170 TYR cc_start: 0.9243 (t80) cc_final: 0.8903 (t80) REVERT: AG 180 TYR cc_start: 0.8706 (t80) cc_final: 0.8016 (t80) REVERT: AG 191 ARG cc_start: 0.8360 (mtt90) cc_final: 0.6631 (mpt180) REVERT: AG 204 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: AG 231 ARG cc_start: 0.8016 (ttt90) cc_final: 0.7433 (mmp-170) REVERT: AH 54 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6459 (ppp) REVERT: AH 94 TYR cc_start: 0.8987 (t80) cc_final: 0.8673 (t80) REVERT: AH 108 MET cc_start: 0.8746 (tpt) cc_final: 0.8459 (tpt) REVERT: AH 191 ARG cc_start: 0.8238 (mtt90) cc_final: 0.6670 (mpt180) REVERT: AH 204 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: AH 215 GLU cc_start: 0.8424 (tp30) cc_final: 0.8199 (tp30) REVERT: AH 231 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7398 (tpm170) REVERT: AI 83 THR cc_start: 0.9393 (m) cc_final: 0.9179 (p) REVERT: AI 136 ASP cc_start: 0.8509 (t0) cc_final: 0.8212 (t0) REVERT: AI 204 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: AI 267 MET cc_start: 0.7627 (mmm) cc_final: 0.7342 (mmm) REVERT: AJ 94 TYR cc_start: 0.8771 (t80) cc_final: 0.8139 (t80) REVERT: AJ 98 GLN cc_start: 0.8545 (tt0) cc_final: 0.8304 (tt0) REVERT: AJ 108 MET cc_start: 0.8392 (tpt) cc_final: 0.7976 (tpt) REVERT: AJ 136 ASP cc_start: 0.8524 (t0) cc_final: 0.8279 (t0) REVERT: AJ 204 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: AK 94 TYR cc_start: 0.8916 (t80) cc_final: 0.8447 (t80) REVERT: AK 134 MET cc_start: 0.8811 (ttt) cc_final: 0.8520 (ttt) REVERT: AK 135 MET cc_start: 0.8911 (mmm) cc_final: 0.8698 (mmt) REVERT: AK 136 ASP cc_start: 0.8532 (t0) cc_final: 0.8264 (t0) REVERT: AK 181 MET cc_start: 0.8746 (tpp) cc_final: 0.8540 (ttp) REVERT: AK 204 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: AL 116 MET cc_start: 0.9165 (ttp) cc_final: 0.8844 (ttp) REVERT: AL 136 ASP cc_start: 0.8672 (t0) cc_final: 0.8376 (t0) REVERT: AM 94 TYR cc_start: 0.8988 (t80) cc_final: 0.8759 (t80) REVERT: AM 136 ASP cc_start: 0.8537 (t0) cc_final: 0.8210 (t0) REVERT: AM 184 TYR cc_start: 0.9062 (t80) cc_final: 0.8831 (t80) REVERT: AM 204 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: AM 267 MET cc_start: 0.7783 (mmm) cc_final: 0.7537 (mmm) REVERT: AN 83 THR cc_start: 0.9333 (m) cc_final: 0.9112 (p) REVERT: AN 94 TYR cc_start: 0.8924 (t80) cc_final: 0.8632 (t80) REVERT: AN 136 ASP cc_start: 0.8573 (t70) cc_final: 0.8320 (t0) REVERT: AN 181 MET cc_start: 0.8884 (tpp) cc_final: 0.8572 (tpp) REVERT: AN 204 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: AO 83 THR cc_start: 0.9320 (m) cc_final: 0.9076 (p) REVERT: AO 87 GLN cc_start: 0.9195 (tp40) cc_final: 0.8976 (tp-100) REVERT: AO 94 TYR cc_start: 0.8947 (t80) cc_final: 0.8581 (t80) REVERT: AO 204 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: AO 244 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7918 (tt0) REVERT: AP 54 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6830 (ptt) REVERT: AP 83 THR cc_start: 0.9340 (m) cc_final: 0.9107 (p) REVERT: AP 94 TYR cc_start: 0.8893 (t80) cc_final: 0.8668 (t80) REVERT: AP 136 ASP cc_start: 0.8393 (t0) cc_final: 0.8052 (t0) REVERT: AP 143 TYR cc_start: 0.8969 (m-80) cc_final: 0.8482 (m-80) REVERT: AP 267 MET cc_start: 0.7867 (mmm) cc_final: 0.7602 (mmm) REVERT: AQ 67 LEU cc_start: 0.7955 (mp) cc_final: 0.7692 (tt) REVERT: AQ 146 LYS cc_start: 0.8608 (tptm) cc_final: 0.8389 (tptm) REVERT: AQ 204 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: AR 136 ASP cc_start: 0.8446 (t0) cc_final: 0.7915 (t0) REVERT: AR 204 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: AS 116 MET cc_start: 0.9039 (ttp) cc_final: 0.8595 (ptm) REVERT: AT 94 TYR cc_start: 0.8941 (t80) cc_final: 0.8588 (t80) REVERT: AT 136 ASP cc_start: 0.8552 (t0) cc_final: 0.8277 (t0) REVERT: AT 170 TYR cc_start: 0.9249 (t80) cc_final: 0.8983 (t80) REVERT: AT 173 MET cc_start: 0.8660 (tmm) cc_final: 0.8288 (tmm) REVERT: AT 220 MET cc_start: 0.9077 (mtm) cc_final: 0.8751 (mtp) REVERT: AT 267 MET cc_start: 0.7628 (mmm) cc_final: 0.7394 (mmm) REVERT: AU 94 TYR cc_start: 0.8925 (t80) cc_final: 0.8477 (t80) REVERT: AU 116 MET cc_start: 0.8682 (ttp) cc_final: 0.8314 (ttp) REVERT: AU 204 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: AU 220 MET cc_start: 0.9073 (mtm) cc_final: 0.8750 (mtm) REVERT: AU 250 THR cc_start: 0.8790 (m) cc_final: 0.8580 (p) REVERT: AU 267 MET cc_start: 0.7562 (mmm) cc_final: 0.7319 (mmm) REVERT: AV 83 THR cc_start: 0.9300 (m) cc_final: 0.9095 (p) REVERT: AV 94 TYR cc_start: 0.8898 (t80) cc_final: 0.8595 (t80) REVERT: AV 204 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: AV 250 THR cc_start: 0.9049 (m) cc_final: 0.8715 (p) REVERT: AW 94 TYR cc_start: 0.8938 (t80) cc_final: 0.8662 (t80) REVERT: AW 204 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: AW 267 MET cc_start: 0.7771 (mmm) cc_final: 0.7220 (mmm) REVERT: AX 94 TYR cc_start: 0.8926 (t80) cc_final: 0.8657 (t80) REVERT: AX 204 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: AX 267 MET cc_start: 0.7936 (mmm) cc_final: 0.7654 (mmm) REVERT: AY 77 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8177 (tp40) REVERT: AY 94 TYR cc_start: 0.8889 (t80) cc_final: 0.8593 (t80) REVERT: AY 116 MET cc_start: 0.9084 (ttp) cc_final: 0.8831 (ttp) REVERT: AY 158 GLN cc_start: 0.9122 (mt0) cc_final: 0.8814 (mt0) REVERT: AY 204 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: AY 215 GLU cc_start: 0.8509 (tp30) cc_final: 0.8262 (tp30) REVERT: AZ 83 THR cc_start: 0.9305 (m) cc_final: 0.9104 (p) REVERT: AZ 94 TYR cc_start: 0.8825 (t80) cc_final: 0.8598 (t80) REVERT: AZ 116 MET cc_start: 0.9074 (ttp) cc_final: 0.8846 (ttp) REVERT: AZ 136 ASP cc_start: 0.8637 (t70) cc_final: 0.8043 (m-30) REVERT: AZ 267 MET cc_start: 0.7600 (mmm) cc_final: 0.7341 (mmm) REVERT: BA 94 TYR cc_start: 0.8902 (t80) cc_final: 0.8652 (t80) REVERT: BA 136 ASP cc_start: 0.8702 (t70) cc_final: 0.8151 (m-30) REVERT: BA 146 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8158 (tptm) REVERT: BA 267 MET cc_start: 0.7874 (mmm) cc_final: 0.7611 (mmm) REVERT: BB 87 GLN cc_start: 0.9036 (tp40) cc_final: 0.8262 (mm-40) REVERT: BB 94 TYR cc_start: 0.8934 (t80) cc_final: 0.8567 (t80) REVERT: BB 136 ASP cc_start: 0.8580 (t70) cc_final: 0.7840 (m-30) REVERT: BB 146 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8347 (tptm) REVERT: BB 173 MET cc_start: 0.8797 (tmm) cc_final: 0.8478 (ttp) REVERT: BB 220 MET cc_start: 0.9062 (mtm) cc_final: 0.8761 (mtp) REVERT: BB 236 ASP cc_start: 0.8166 (p0) cc_final: 0.7591 (p0) REVERT: BC 83 THR cc_start: 0.9332 (m) cc_final: 0.9089 (p) REVERT: BC 94 TYR cc_start: 0.8886 (t80) cc_final: 0.8599 (t80) REVERT: BC 146 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8241 (tptm) REVERT: BC 150 GLU cc_start: 0.7367 (tt0) cc_final: 0.7099 (tt0) REVERT: BC 204 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: BD 136 ASP cc_start: 0.8688 (t70) cc_final: 0.8405 (t0) REVERT: BD 173 MET cc_start: 0.8729 (tmm) cc_final: 0.8440 (tmm) REVERT: BD 231 ARG cc_start: 0.8194 (ttt-90) cc_final: 0.7427 (ppt170) REVERT: BD 266 ASN cc_start: 0.7909 (t0) cc_final: 0.7663 (t0) REVERT: BE 94 TYR cc_start: 0.9014 (t80) cc_final: 0.8713 (t80) REVERT: BE 116 MET cc_start: 0.9160 (ttp) cc_final: 0.8693 (ttp) REVERT: BE 136 ASP cc_start: 0.8598 (t70) cc_final: 0.7835 (m-30) REVERT: BE 204 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: BF 83 THR cc_start: 0.9288 (m) cc_final: 0.9001 (p) REVERT: BF 94 TYR cc_start: 0.8916 (t80) cc_final: 0.8558 (t80) REVERT: BF 136 ASP cc_start: 0.8300 (t70) cc_final: 0.7837 (m-30) REVERT: BF 146 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8087 (tptm) REVERT: BF 158 GLN cc_start: 0.9086 (mt0) cc_final: 0.8689 (mt0) REVERT: BF 204 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: BG 83 THR cc_start: 0.9291 (m) cc_final: 0.9066 (p) REVERT: BG 136 ASP cc_start: 0.8600 (t70) cc_final: 0.7981 (m-30) REVERT: BG 146 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8182 (tptm) REVERT: BG 204 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: BG 231 ARG cc_start: 0.8184 (ttt-90) cc_final: 0.7564 (ptt90) REVERT: BG 250 THR cc_start: 0.8988 (m) cc_final: 0.8699 (p) REVERT: BG 267 MET cc_start: 0.7753 (mmm) cc_final: 0.7465 (mmm) REVERT: BH 83 THR cc_start: 0.9336 (m) cc_final: 0.9134 (p) REVERT: BH 94 TYR cc_start: 0.8894 (t80) cc_final: 0.8670 (t80) REVERT: BH 116 MET cc_start: 0.9211 (ttp) cc_final: 0.8920 (ptm) REVERT: BI 83 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8922 (p) REVERT: BI 91 ASP cc_start: 0.8250 (m-30) cc_final: 0.8016 (m-30) REVERT: BI 94 TYR cc_start: 0.8717 (t80) cc_final: 0.8110 (t80) REVERT: BI 108 MET cc_start: 0.8445 (tpt) cc_final: 0.8235 (tpt) REVERT: BI 121 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8032 (tt0) REVERT: BI 136 ASP cc_start: 0.8302 (t70) cc_final: 0.8075 (t0) REVERT: BI 204 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: BI 258 MET cc_start: 0.8389 (ttp) cc_final: 0.8140 (ttm) outliers start: 193 outliers final: 96 residues processed: 1540 average time/residue: 0.6811 time to fit residues: 1762.1082 Evaluate side-chains 1426 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1304 time to evaluate : 5.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 56 MET Chi-restraints excluded: chain AA residue 88 SER Chi-restraints excluded: chain AA residue 206 THR Chi-restraints excluded: chain AB residue 67 LEU Chi-restraints excluded: chain AB residue 88 SER Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain AB residue 261 LEU Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 106 THR Chi-restraints excluded: chain AC residue 204 GLU Chi-restraints excluded: chain AD residue 56 MET Chi-restraints excluded: chain AD residue 88 SER Chi-restraints excluded: chain AD residue 95 GLU Chi-restraints excluded: chain AD residue 252 GLU Chi-restraints excluded: chain AE residue 88 SER Chi-restraints excluded: chain AE residue 206 THR Chi-restraints excluded: chain AE residue 252 GLU Chi-restraints excluded: chain AF residue 88 SER Chi-restraints excluded: chain AF residue 204 GLU Chi-restraints excluded: chain AF residue 206 THR Chi-restraints excluded: chain AG residue 88 SER Chi-restraints excluded: chain AG residue 204 GLU Chi-restraints excluded: chain AG residue 206 THR Chi-restraints excluded: chain AH residue 54 MET Chi-restraints excluded: chain AH residue 56 MET Chi-restraints excluded: chain AH residue 88 SER Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 204 GLU Chi-restraints excluded: chain AH residue 252 GLU Chi-restraints excluded: chain AI residue 88 SER Chi-restraints excluded: chain AI residue 204 GLU Chi-restraints excluded: chain AI residue 249 HIS Chi-restraints excluded: chain AJ residue 88 SER Chi-restraints excluded: chain AJ residue 106 THR Chi-restraints excluded: chain AJ residue 204 GLU Chi-restraints excluded: chain AJ residue 261 LEU Chi-restraints excluded: chain AK residue 56 MET Chi-restraints excluded: chain AK residue 88 SER Chi-restraints excluded: chain AK residue 204 GLU Chi-restraints excluded: chain AL residue 56 MET Chi-restraints excluded: chain AL residue 88 SER Chi-restraints excluded: chain AL residue 206 THR Chi-restraints excluded: chain AM residue 88 SER Chi-restraints excluded: chain AM residue 204 GLU Chi-restraints excluded: chain AM residue 261 LEU Chi-restraints excluded: chain AN residue 88 SER Chi-restraints excluded: chain AN residue 204 GLU Chi-restraints excluded: chain AO residue 56 MET Chi-restraints excluded: chain AO residue 88 SER Chi-restraints excluded: chain AO residue 125 SER Chi-restraints excluded: chain AO residue 204 GLU Chi-restraints excluded: chain AO residue 252 GLU Chi-restraints excluded: chain AP residue 54 MET Chi-restraints excluded: chain AP residue 56 MET Chi-restraints excluded: chain AP residue 88 SER Chi-restraints excluded: chain AP residue 206 THR Chi-restraints excluded: chain AP residue 252 GLU Chi-restraints excluded: chain AP residue 261 LEU Chi-restraints excluded: chain AQ residue 81 SER Chi-restraints excluded: chain AQ residue 88 SER Chi-restraints excluded: chain AQ residue 204 GLU Chi-restraints excluded: chain AQ residue 261 LEU Chi-restraints excluded: chain AR residue 56 MET Chi-restraints excluded: chain AR residue 88 SER Chi-restraints excluded: chain AR residue 204 GLU Chi-restraints excluded: chain AS residue 88 SER Chi-restraints excluded: chain AS residue 206 THR Chi-restraints excluded: chain AT residue 88 SER Chi-restraints excluded: chain AT residue 206 THR Chi-restraints excluded: chain AT residue 236 ASP Chi-restraints excluded: chain AU residue 88 SER Chi-restraints excluded: chain AU residue 204 GLU Chi-restraints excluded: chain AU residue 261 LEU Chi-restraints excluded: chain AV residue 54 MET Chi-restraints excluded: chain AV residue 88 SER Chi-restraints excluded: chain AV residue 135 MET Chi-restraints excluded: chain AV residue 204 GLU Chi-restraints excluded: chain AV residue 230 SER Chi-restraints excluded: chain AW residue 88 SER Chi-restraints excluded: chain AW residue 204 GLU Chi-restraints excluded: chain AW residue 244 GLU Chi-restraints excluded: chain AW residue 252 GLU Chi-restraints excluded: chain AX residue 204 GLU Chi-restraints excluded: chain AY residue 78 ILE Chi-restraints excluded: chain AY residue 88 SER Chi-restraints excluded: chain AY residue 204 GLU Chi-restraints excluded: chain AY residue 230 SER Chi-restraints excluded: chain AY residue 250 THR Chi-restraints excluded: chain AZ residue 56 MET Chi-restraints excluded: chain AZ residue 88 SER Chi-restraints excluded: chain AZ residue 252 GLU Chi-restraints excluded: chain AZ residue 261 LEU Chi-restraints excluded: chain BA residue 88 SER Chi-restraints excluded: chain BA residue 206 THR Chi-restraints excluded: chain BA residue 252 GLU Chi-restraints excluded: chain BB residue 67 LEU Chi-restraints excluded: chain BB residue 88 SER Chi-restraints excluded: chain BB residue 135 MET Chi-restraints excluded: chain BC residue 56 MET Chi-restraints excluded: chain BC residue 78 ILE Chi-restraints excluded: chain BC residue 88 SER Chi-restraints excluded: chain BC residue 204 GLU Chi-restraints excluded: chain BC residue 230 SER Chi-restraints excluded: chain BD residue 88 SER Chi-restraints excluded: chain BE residue 88 SER Chi-restraints excluded: chain BE residue 204 GLU Chi-restraints excluded: chain BE residue 206 THR Chi-restraints excluded: chain BF residue 88 SER Chi-restraints excluded: chain BF residue 204 GLU Chi-restraints excluded: chain BF residue 206 THR Chi-restraints excluded: chain BF residue 261 LEU Chi-restraints excluded: chain BG residue 56 MET Chi-restraints excluded: chain BG residue 78 ILE Chi-restraints excluded: chain BG residue 204 GLU Chi-restraints excluded: chain BH residue 56 MET Chi-restraints excluded: chain BH residue 206 THR Chi-restraints excluded: chain BH residue 252 GLU Chi-restraints excluded: chain BI residue 83 THR Chi-restraints excluded: chain BI residue 88 SER Chi-restraints excluded: chain BI residue 204 GLU Chi-restraints excluded: chain BI residue 249 HIS Chi-restraints excluded: chain BI residue 252 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 692 optimal weight: 0.8980 chunk 526 optimal weight: 9.9990 chunk 363 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 334 optimal weight: 0.5980 chunk 470 optimal weight: 7.9990 chunk 703 optimal weight: 9.9990 chunk 744 optimal weight: 0.0570 chunk 367 optimal weight: 0.9980 chunk 666 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 151 ASN AM 98 GLN ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 151 ASN AW 76 GLN ** AX 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 67340 Z= 0.166 Angle : 0.587 11.099 91805 Z= 0.296 Chirality : 0.040 0.160 10360 Planarity : 0.004 0.035 11375 Dihedral : 11.003 59.228 11305 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.03 % Allowed : 15.99 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.10), residues: 7770 helix: 0.96 (0.10), residues: 3150 sheet: -0.34 (0.25), residues: 350 loop : -1.56 (0.10), residues: 4270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAR 132 HIS 0.004 0.001 HISAP 249 PHE 0.011 0.001 PHEBD 200 TYR 0.019 0.001 TYRBF 170 ARG 0.009 0.000 ARGBF 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1573 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1435 time to evaluate : 5.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7922 (mm-40) REVERT: AA 191 ARG cc_start: 0.8159 (mtt90) cc_final: 0.6369 (mpt180) REVERT: AA 204 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: AA 231 ARG cc_start: 0.7951 (ttt90) cc_final: 0.7475 (mmp-170) REVERT: AB 82 ASN cc_start: 0.8734 (t0) cc_final: 0.8507 (t0) REVERT: AB 108 MET cc_start: 0.8353 (tpt) cc_final: 0.8075 (tpp) REVERT: AB 135 MET cc_start: 0.8885 (mmm) cc_final: 0.8595 (mmt) REVERT: AB 231 ARG cc_start: 0.7925 (ttt90) cc_final: 0.7430 (tpm170) REVERT: AB 258 MET cc_start: 0.8095 (ttm) cc_final: 0.7773 (ttm) REVERT: AB 266 ASN cc_start: 0.8439 (t0) cc_final: 0.8232 (t0) REVERT: AB 267 MET cc_start: 0.7627 (mmm) cc_final: 0.7318 (mmm) REVERT: AC 135 MET cc_start: 0.8670 (mmm) cc_final: 0.8423 (mmm) REVERT: AC 143 TYR cc_start: 0.8961 (m-80) cc_final: 0.8530 (m-80) REVERT: AC 191 ARG cc_start: 0.8082 (mtt90) cc_final: 0.6180 (pmt170) REVERT: AC 231 ARG cc_start: 0.7959 (ttt90) cc_final: 0.7331 (mmp-170) REVERT: AC 236 ASP cc_start: 0.8197 (p0) cc_final: 0.7940 (m-30) REVERT: AC 267 MET cc_start: 0.7782 (mmm) cc_final: 0.7448 (mmm) REVERT: AD 94 TYR cc_start: 0.8839 (t80) cc_final: 0.8505 (t80) REVERT: AD 136 ASP cc_start: 0.8551 (t0) cc_final: 0.8254 (t0) REVERT: AD 173 MET cc_start: 0.8640 (tmm) cc_final: 0.8347 (tmm) REVERT: AD 191 ARG cc_start: 0.8125 (mtt90) cc_final: 0.6499 (mpt180) REVERT: AD 231 ARG cc_start: 0.5325 (tpm170) cc_final: 0.4476 (tpm170) REVERT: AE 77 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8088 (tp40) REVERT: AE 94 TYR cc_start: 0.8874 (t80) cc_final: 0.8476 (t80) REVERT: AE 134 MET cc_start: 0.8882 (ttt) cc_final: 0.8586 (ttt) REVERT: AE 146 LYS cc_start: 0.8540 (tptm) cc_final: 0.8303 (tptm) REVERT: AE 160 MET cc_start: 0.9023 (mmm) cc_final: 0.8699 (mmm) REVERT: AE 231 ARG cc_start: 0.7902 (ttt90) cc_final: 0.7417 (tpm170) REVERT: AF 170 TYR cc_start: 0.9194 (t80) cc_final: 0.8948 (t80) REVERT: AF 191 ARG cc_start: 0.8105 (mtt90) cc_final: 0.6137 (pmt170) REVERT: AF 219 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8622 (mm110) REVERT: AF 231 ARG cc_start: 0.7759 (ttt90) cc_final: 0.7291 (mmp-170) REVERT: AG 116 MET cc_start: 0.8944 (ttp) cc_final: 0.8352 (ttp) REVERT: AG 136 ASP cc_start: 0.8394 (t70) cc_final: 0.8116 (t0) REVERT: AG 170 TYR cc_start: 0.9203 (t80) cc_final: 0.8861 (t80) REVERT: AG 191 ARG cc_start: 0.8198 (mtt90) cc_final: 0.6479 (mpt180) REVERT: AG 231 ARG cc_start: 0.8024 (ttt90) cc_final: 0.7464 (mmp-170) REVERT: AH 91 ASP cc_start: 0.7904 (m-30) cc_final: 0.7637 (m-30) REVERT: AH 94 TYR cc_start: 0.8868 (t80) cc_final: 0.8542 (t80) REVERT: AH 191 ARG cc_start: 0.8150 (mtt90) cc_final: 0.6649 (mpt180) REVERT: AH 231 ARG cc_start: 0.8084 (ttt90) cc_final: 0.7427 (tpm170) REVERT: AH 267 MET cc_start: 0.7745 (mmm) cc_final: 0.7490 (mmm) REVERT: AI 134 MET cc_start: 0.8888 (ttt) cc_final: 0.8656 (ttt) REVERT: AI 136 ASP cc_start: 0.8530 (t0) cc_final: 0.8202 (t0) REVERT: AI 173 MET cc_start: 0.8568 (tmm) cc_final: 0.8224 (tmm) REVERT: AI 231 ARG cc_start: 0.5445 (tpm170) cc_final: 0.4925 (tpm170) REVERT: AI 267 MET cc_start: 0.7628 (mmm) cc_final: 0.7368 (mmm) REVERT: AJ 94 TYR cc_start: 0.8700 (t80) cc_final: 0.8151 (t80) REVERT: AJ 108 MET cc_start: 0.8242 (tpt) cc_final: 0.7897 (tpt) REVERT: AJ 136 ASP cc_start: 0.8543 (t0) cc_final: 0.8276 (t0) REVERT: AJ 219 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8576 (mm110) REVERT: AJ 246 THR cc_start: 0.8937 (p) cc_final: 0.8439 (t) REVERT: AK 134 MET cc_start: 0.8774 (ttt) cc_final: 0.8478 (ttt) REVERT: AK 136 ASP cc_start: 0.8565 (t0) cc_final: 0.8263 (t0) REVERT: AK 249 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.8090 (t-90) REVERT: AL 136 ASP cc_start: 0.8668 (t0) cc_final: 0.8339 (t0) REVERT: AL 160 MET cc_start: 0.8545 (mmm) cc_final: 0.8317 (mmm) REVERT: AL 204 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: AL 219 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8541 (mm110) REVERT: AM 94 TYR cc_start: 0.8923 (t80) cc_final: 0.8686 (t80) REVERT: AM 136 ASP cc_start: 0.8533 (t0) cc_final: 0.8229 (t0) REVERT: AM 184 TYR cc_start: 0.9014 (t80) cc_final: 0.8729 (t80) REVERT: AM 267 MET cc_start: 0.7765 (mmm) cc_final: 0.7525 (mmm) REVERT: AN 83 THR cc_start: 0.9341 (m) cc_final: 0.9073 (p) REVERT: AN 94 TYR cc_start: 0.8859 (t80) cc_final: 0.8598 (t80) REVERT: AN 135 MET cc_start: 0.8944 (mmm) cc_final: 0.8683 (mmm) REVERT: AN 136 ASP cc_start: 0.8475 (t70) cc_final: 0.8211 (t0) REVERT: AN 181 MET cc_start: 0.8912 (tpp) cc_final: 0.8574 (tpp) REVERT: AN 236 ASP cc_start: 0.7874 (p0) cc_final: 0.7631 (m-30) REVERT: AN 246 THR cc_start: 0.8977 (p) cc_final: 0.8620 (t) REVERT: AO 83 THR cc_start: 0.9347 (m) cc_final: 0.9110 (p) REVERT: AO 87 GLN cc_start: 0.9036 (tp40) cc_final: 0.8626 (tp-100) REVERT: AO 94 TYR cc_start: 0.8820 (t80) cc_final: 0.8546 (t80) REVERT: AP 54 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6838 (ptt) REVERT: AP 94 TYR cc_start: 0.8838 (t80) cc_final: 0.8589 (t80) REVERT: AP 136 ASP cc_start: 0.8431 (t0) cc_final: 0.8052 (t0) REVERT: AP 143 TYR cc_start: 0.8990 (m-80) cc_final: 0.8533 (m-80) REVERT: AP 204 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: AP 267 MET cc_start: 0.7891 (mmm) cc_final: 0.7644 (mmm) REVERT: AQ 67 LEU cc_start: 0.7855 (mp) cc_final: 0.7640 (tt) REVERT: AQ 146 LYS cc_start: 0.8676 (tptm) cc_final: 0.8435 (tptm) REVERT: AQ 219 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8573 (mm110) REVERT: AR 99 LEU cc_start: 0.9306 (tp) cc_final: 0.8960 (mp) REVERT: AR 116 MET cc_start: 0.9081 (ttp) cc_final: 0.8802 (ttp) REVERT: AR 136 ASP cc_start: 0.8441 (t0) cc_final: 0.7911 (t0) REVERT: AS 116 MET cc_start: 0.8934 (ttp) cc_final: 0.8501 (ptm) REVERT: AS 136 ASP cc_start: 0.8557 (t0) cc_final: 0.8269 (t0) REVERT: AS 204 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: AS 249 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8235 (t70) REVERT: AT 94 TYR cc_start: 0.8892 (t80) cc_final: 0.8605 (t80) REVERT: AT 136 ASP cc_start: 0.8540 (t0) cc_final: 0.8293 (t0) REVERT: AT 173 MET cc_start: 0.8626 (tmm) cc_final: 0.8222 (tmm) REVERT: AT 204 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: AT 220 MET cc_start: 0.9036 (mtm) cc_final: 0.8712 (mtp) REVERT: AU 54 MET cc_start: 0.7225 (ptt) cc_final: 0.7020 (ptt) REVERT: AU 108 MET cc_start: 0.8420 (tpt) cc_final: 0.8154 (tpp) REVERT: AU 116 MET cc_start: 0.8595 (ttp) cc_final: 0.8251 (ttp) REVERT: AV 77 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7952 (tp40) REVERT: AV 136 ASP cc_start: 0.8398 (t0) cc_final: 0.8183 (t0) REVERT: AV 170 TYR cc_start: 0.9207 (t80) cc_final: 0.8947 (t80) REVERT: AV 250 THR cc_start: 0.9059 (m) cc_final: 0.8820 (p) REVERT: AV 253 ASP cc_start: 0.8673 (m-30) cc_final: 0.8434 (m-30) REVERT: AW 94 TYR cc_start: 0.8769 (t80) cc_final: 0.8549 (t80) REVERT: AW 267 MET cc_start: 0.7922 (mmm) cc_final: 0.7674 (mmm) REVERT: AY 94 TYR cc_start: 0.8794 (t80) cc_final: 0.8579 (t80) REVERT: AY 158 GLN cc_start: 0.8922 (mt0) cc_final: 0.8623 (mt0) REVERT: AY 172 GLU cc_start: 0.8267 (tp30) cc_final: 0.8005 (mm-30) REVERT: AY 236 ASP cc_start: 0.8045 (p0) cc_final: 0.7652 (m-30) REVERT: AZ 83 THR cc_start: 0.9317 (m) cc_final: 0.9065 (p) REVERT: AZ 136 ASP cc_start: 0.8606 (t70) cc_final: 0.8038 (m-30) REVERT: AZ 160 MET cc_start: 0.8718 (mmm) cc_final: 0.8155 (mmm) REVERT: BA 78 ILE cc_start: 0.9176 (tt) cc_final: 0.8927 (tp) REVERT: BA 94 TYR cc_start: 0.8892 (t80) cc_final: 0.8578 (t80) REVERT: BA 136 ASP cc_start: 0.8670 (t70) cc_final: 0.8182 (m-30) REVERT: BA 146 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7975 (tptm) REVERT: BA 180 TYR cc_start: 0.8274 (t80) cc_final: 0.8007 (t80) REVERT: BA 204 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: BA 267 MET cc_start: 0.7887 (mmm) cc_final: 0.7583 (mmm) REVERT: BB 136 ASP cc_start: 0.8564 (t70) cc_final: 0.7841 (m-30) REVERT: BB 146 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8226 (tptm) REVERT: BB 168 GLU cc_start: 0.8529 (tt0) cc_final: 0.8196 (tt0) REVERT: BB 173 MET cc_start: 0.8713 (tmm) cc_final: 0.8492 (ttp) REVERT: BB 236 ASP cc_start: 0.8043 (p0) cc_final: 0.7803 (m-30) REVERT: BC 146 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8227 (tptm) REVERT: BC 150 GLU cc_start: 0.7425 (tt0) cc_final: 0.7136 (tt0) REVERT: BD 136 ASP cc_start: 0.8647 (t70) cc_final: 0.8145 (m-30) REVERT: BD 173 MET cc_start: 0.8668 (tmm) cc_final: 0.8354 (tmm) REVERT: BD 266 ASN cc_start: 0.8017 (t0) cc_final: 0.7735 (t0) REVERT: BE 94 TYR cc_start: 0.8925 (t80) cc_final: 0.8652 (t80) REVERT: BE 116 MET cc_start: 0.9112 (ttp) cc_final: 0.8678 (ttp) REVERT: BE 136 ASP cc_start: 0.8614 (t70) cc_final: 0.7848 (m-30) REVERT: BE 180 TYR cc_start: 0.8538 (t80) cc_final: 0.8198 (t80) REVERT: BE 204 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8267 (tt0) REVERT: BF 83 THR cc_start: 0.9279 (m) cc_final: 0.9063 (p) REVERT: BF 94 TYR cc_start: 0.8846 (t80) cc_final: 0.8609 (t80) REVERT: BF 136 ASP cc_start: 0.8290 (t70) cc_final: 0.7922 (m-30) REVERT: BF 158 GLN cc_start: 0.8940 (mt0) cc_final: 0.8502 (mt0) REVERT: BF 267 MET cc_start: 0.7679 (mmm) cc_final: 0.7441 (mmm) REVERT: BG 91 ASP cc_start: 0.8286 (m-30) cc_final: 0.8081 (m-30) REVERT: BG 136 ASP cc_start: 0.8569 (t70) cc_final: 0.8085 (m-30) REVERT: BG 231 ARG cc_start: 0.8188 (ttt-90) cc_final: 0.7579 (ptt90) REVERT: BG 253 ASP cc_start: 0.8666 (m-30) cc_final: 0.8436 (m-30) REVERT: BH 116 MET cc_start: 0.9149 (ttp) cc_final: 0.8701 (ttp) REVERT: BH 160 MET cc_start: 0.8550 (mmm) cc_final: 0.8309 (mmm) REVERT: BH 215 GLU cc_start: 0.8427 (tp30) cc_final: 0.8183 (tp30) REVERT: BH 236 ASP cc_start: 0.7858 (p0) cc_final: 0.7351 (p0) REVERT: BI 83 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9041 (p) REVERT: BI 87 GLN cc_start: 0.8995 (tp40) cc_final: 0.7952 (mm-40) REVERT: BI 121 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7995 (tt0) REVERT: BI 136 ASP cc_start: 0.8380 (t70) cc_final: 0.7907 (m-30) REVERT: BI 180 TYR cc_start: 0.8654 (t80) cc_final: 0.8451 (t80) outliers start: 138 outliers final: 72 residues processed: 1514 average time/residue: 0.6708 time to fit residues: 1689.7832 Evaluate side-chains 1383 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1301 time to evaluate : 5.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 56 MET Chi-restraints excluded: chain AA residue 70 LEU Chi-restraints excluded: chain AA residue 88 SER Chi-restraints excluded: chain AA residue 204 GLU Chi-restraints excluded: chain AA residue 206 THR Chi-restraints excluded: chain AB residue 67 LEU Chi-restraints excluded: chain AB residue 88 SER Chi-restraints excluded: chain AB residue 151 ASN Chi-restraints excluded: chain AB residue 206 THR Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 206 THR Chi-restraints excluded: chain AD residue 56 MET Chi-restraints excluded: chain AD residue 88 SER Chi-restraints excluded: chain AD residue 252 GLU Chi-restraints excluded: chain AE residue 56 MET Chi-restraints excluded: chain AE residue 206 THR Chi-restraints excluded: chain AE residue 252 GLU Chi-restraints excluded: chain AF residue 206 THR Chi-restraints excluded: chain AG residue 56 MET Chi-restraints excluded: chain AG residue 88 SER Chi-restraints excluded: chain AH residue 56 MET Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 206 THR Chi-restraints excluded: chain AI residue 88 SER Chi-restraints excluded: chain AJ residue 88 SER Chi-restraints excluded: chain AJ residue 106 THR Chi-restraints excluded: chain AK residue 56 MET Chi-restraints excluded: chain AK residue 88 SER Chi-restraints excluded: chain AK residue 249 HIS Chi-restraints excluded: chain AL residue 56 MET Chi-restraints excluded: chain AL residue 88 SER Chi-restraints excluded: chain AL residue 204 GLU Chi-restraints excluded: chain AL residue 206 THR Chi-restraints excluded: chain AM residue 88 SER Chi-restraints excluded: chain AM residue 206 THR Chi-restraints excluded: chain AN residue 88 SER Chi-restraints excluded: chain AO residue 56 MET Chi-restraints excluded: chain AO residue 88 SER Chi-restraints excluded: chain AO residue 206 THR Chi-restraints excluded: chain AO residue 252 GLU Chi-restraints excluded: chain AP residue 54 MET Chi-restraints excluded: chain AP residue 88 SER Chi-restraints excluded: chain AP residue 204 GLU Chi-restraints excluded: chain AP residue 206 THR Chi-restraints excluded: chain AP residue 252 GLU Chi-restraints excluded: chain AQ residue 81 SER Chi-restraints excluded: chain AQ residue 88 SER Chi-restraints excluded: chain AQ residue 206 THR Chi-restraints excluded: chain AR residue 56 MET Chi-restraints excluded: chain AS residue 204 GLU Chi-restraints excluded: chain AS residue 249 HIS Chi-restraints excluded: chain AT residue 204 GLU Chi-restraints excluded: chain AT residue 206 THR Chi-restraints excluded: chain AV residue 56 MET Chi-restraints excluded: chain AV residue 88 SER Chi-restraints excluded: chain AW residue 88 SER Chi-restraints excluded: chain AW residue 206 THR Chi-restraints excluded: chain AW residue 252 GLU Chi-restraints excluded: chain AX residue 206 THR Chi-restraints excluded: chain AY residue 206 THR Chi-restraints excluded: chain AZ residue 56 MET Chi-restraints excluded: chain AZ residue 88 SER Chi-restraints excluded: chain BA residue 88 SER Chi-restraints excluded: chain BA residue 204 GLU Chi-restraints excluded: chain BA residue 206 THR Chi-restraints excluded: chain BA residue 252 GLU Chi-restraints excluded: chain BB residue 67 LEU Chi-restraints excluded: chain BB residue 135 MET Chi-restraints excluded: chain BB residue 249 HIS Chi-restraints excluded: chain BC residue 56 MET Chi-restraints excluded: chain BC residue 206 THR Chi-restraints excluded: chain BE residue 88 SER Chi-restraints excluded: chain BE residue 206 THR Chi-restraints excluded: chain BF residue 88 SER Chi-restraints excluded: chain BG residue 56 MET Chi-restraints excluded: chain BG residue 78 ILE Chi-restraints excluded: chain BG residue 88 SER Chi-restraints excluded: chain BH residue 56 MET Chi-restraints excluded: chain BH residue 70 LEU Chi-restraints excluded: chain BH residue 252 GLU Chi-restraints excluded: chain BI residue 83 THR Chi-restraints excluded: chain BI residue 206 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 619 optimal weight: 10.0000 chunk 422 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 554 optimal weight: 8.9990 chunk 307 optimal weight: 6.9990 chunk 635 optimal weight: 0.0970 chunk 514 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 380 optimal weight: 10.0000 chunk 668 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 overall best weight: 3.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 140 GLN ** AG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 140 GLN ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 76 GLN ** AP 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 77 GLN ** AT 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 151 ASN ** AU 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 249 HIS ** BD 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 76 GLN ** BG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 67340 Z= 0.357 Angle : 0.652 11.609 91805 Z= 0.330 Chirality : 0.044 0.204 10360 Planarity : 0.004 0.039 11375 Dihedral : 11.252 60.249 11305 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.05 % Allowed : 16.64 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.10), residues: 7770 helix: 0.78 (0.10), residues: 3255 sheet: 0.18 (0.28), residues: 350 loop : -1.35 (0.10), residues: 4165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAR 132 HIS 0.004 0.001 HISAN 249 PHE 0.013 0.002 PHEBI 200 TYR 0.021 0.002 TYRBC 198 ARG 0.010 0.001 ARGBA 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1529 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1322 time to evaluate : 5.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8002 (mm-40) REVERT: AA 204 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: AA 231 ARG cc_start: 0.8107 (ttt90) cc_final: 0.7630 (tpm170) REVERT: AB 72 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: AB 170 TYR cc_start: 0.9208 (t80) cc_final: 0.8896 (t80) REVERT: AB 204 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: AB 231 ARG cc_start: 0.8040 (ttt90) cc_final: 0.7439 (tpm170) REVERT: AB 267 MET cc_start: 0.7694 (mmm) cc_final: 0.7346 (mmm) REVERT: AC 99 LEU cc_start: 0.9377 (tp) cc_final: 0.9078 (mp) REVERT: AC 143 TYR cc_start: 0.8971 (m-80) cc_final: 0.8456 (m-80) REVERT: AC 191 ARG cc_start: 0.8245 (mtt90) cc_final: 0.6558 (mpt180) REVERT: AC 204 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: AC 231 ARG cc_start: 0.8083 (ttt90) cc_final: 0.7476 (tpm170) REVERT: AD 94 TYR cc_start: 0.8862 (t80) cc_final: 0.8609 (t80) REVERT: AD 136 ASP cc_start: 0.8590 (t0) cc_final: 0.8271 (t0) REVERT: AD 191 ARG cc_start: 0.8309 (mtt90) cc_final: 0.6530 (mpt180) REVERT: AD 197 ARG cc_start: 0.8496 (ttp-110) cc_final: 0.7838 (ttp-110) REVERT: AE 94 TYR cc_start: 0.8870 (t80) cc_final: 0.8425 (t80) REVERT: AE 146 LYS cc_start: 0.8579 (tptm) cc_final: 0.8303 (tptm) REVERT: AE 220 MET cc_start: 0.9030 (mtm) cc_final: 0.8822 (mtp) REVERT: AE 231 ARG cc_start: 0.8073 (ttt90) cc_final: 0.7458 (tpm170) REVERT: AF 170 TYR cc_start: 0.9246 (t80) cc_final: 0.8971 (t80) REVERT: AF 204 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: AF 231 ARG cc_start: 0.7925 (ttt90) cc_final: 0.7245 (tpm170) REVERT: AG 94 TYR cc_start: 0.8901 (t80) cc_final: 0.8681 (t80) REVERT: AG 99 LEU cc_start: 0.9407 (tp) cc_final: 0.9115 (mp) REVERT: AG 116 MET cc_start: 0.9005 (ttp) cc_final: 0.8404 (ttp) REVERT: AG 136 ASP cc_start: 0.8396 (t70) cc_final: 0.8138 (t0) REVERT: AG 143 TYR cc_start: 0.8870 (m-80) cc_final: 0.8618 (m-80) REVERT: AG 170 TYR cc_start: 0.9238 (t80) cc_final: 0.8905 (t80) REVERT: AG 191 ARG cc_start: 0.8412 (mtt90) cc_final: 0.6699 (mpt180) REVERT: AG 204 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: AG 231 ARG cc_start: 0.8038 (ttt90) cc_final: 0.7492 (mmp-170) REVERT: AH 204 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: AH 231 ARG cc_start: 0.8209 (ttt90) cc_final: 0.7380 (tpm170) REVERT: AH 267 MET cc_start: 0.7796 (mmm) cc_final: 0.7559 (mmm) REVERT: AI 134 MET cc_start: 0.8871 (ttt) cc_final: 0.8633 (ttt) REVERT: AI 136 ASP cc_start: 0.8568 (t0) cc_final: 0.8222 (t0) REVERT: AI 173 MET cc_start: 0.8571 (tmm) cc_final: 0.8211 (tmm) REVERT: AI 204 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: AJ 94 TYR cc_start: 0.8777 (t80) cc_final: 0.8531 (t80) REVERT: AJ 136 ASP cc_start: 0.8542 (t0) cc_final: 0.8262 (t0) REVERT: AJ 204 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: AK 134 MET cc_start: 0.8820 (ttt) cc_final: 0.8518 (ttt) REVERT: AK 136 ASP cc_start: 0.8530 (t0) cc_final: 0.8232 (t0) REVERT: AK 204 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: AK 267 MET cc_start: 0.7539 (mmm) cc_final: 0.7265 (mmm) REVERT: AL 116 MET cc_start: 0.9222 (ttp) cc_final: 0.8930 (ttp) REVERT: AL 136 ASP cc_start: 0.8694 (t0) cc_final: 0.8309 (t0) REVERT: AL 204 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: AM 94 TYR cc_start: 0.8970 (t80) cc_final: 0.8750 (t80) REVERT: AM 136 ASP cc_start: 0.8557 (t0) cc_final: 0.8168 (t0) REVERT: AM 204 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: AN 94 TYR cc_start: 0.8946 (t80) cc_final: 0.8671 (t80) REVERT: AN 136 ASP cc_start: 0.8627 (t70) cc_final: 0.8357 (t0) REVERT: AN 204 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: AN 236 ASP cc_start: 0.7919 (p0) cc_final: 0.7643 (m-30) REVERT: AO 83 THR cc_start: 0.9454 (m) cc_final: 0.9188 (p) REVERT: AO 87 GLN cc_start: 0.8969 (tp40) cc_final: 0.8561 (tp40) REVERT: AO 94 TYR cc_start: 0.8860 (t80) cc_final: 0.8557 (t80) REVERT: AO 204 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: AP 56 MET cc_start: 0.7269 (tpt) cc_final: 0.6926 (tpt) REVERT: AP 78 ILE cc_start: 0.9190 (tt) cc_final: 0.8890 (tt) REVERT: AP 94 TYR cc_start: 0.8896 (t80) cc_final: 0.8687 (t80) REVERT: AP 136 ASP cc_start: 0.8535 (t0) cc_final: 0.8154 (t0) REVERT: AP 143 TYR cc_start: 0.8945 (m-80) cc_final: 0.8401 (m-80) REVERT: AP 158 GLN cc_start: 0.9249 (mt0) cc_final: 0.9049 (mt0) REVERT: AP 173 MET cc_start: 0.8667 (tmm) cc_final: 0.8459 (tmt) REVERT: AP 204 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: AQ 67 LEU cc_start: 0.7959 (mp) cc_final: 0.7650 (tt) REVERT: AQ 108 MET cc_start: 0.8332 (tpt) cc_final: 0.7928 (tpp) REVERT: AQ 146 LYS cc_start: 0.8700 (tptm) cc_final: 0.8465 (tptm) REVERT: AQ 204 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: AR 54 MET cc_start: 0.7292 (ppp) cc_final: 0.7055 (ptm) REVERT: AR 136 ASP cc_start: 0.8431 (t0) cc_final: 0.7871 (t0) REVERT: AR 204 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: AR 220 MET cc_start: 0.9010 (mtm) cc_final: 0.8708 (mtm) REVERT: AS 116 MET cc_start: 0.9059 (ttp) cc_final: 0.8618 (ptm) REVERT: AS 136 ASP cc_start: 0.8583 (t0) cc_final: 0.8271 (t0) REVERT: AS 204 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: AT 94 TYR cc_start: 0.8929 (t80) cc_final: 0.8469 (t80) REVERT: AT 136 ASP cc_start: 0.8550 (t0) cc_final: 0.8215 (t0) REVERT: AT 204 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: AT 220 MET cc_start: 0.9114 (mtm) cc_final: 0.8792 (mtp) REVERT: AU 94 TYR cc_start: 0.8975 (t80) cc_final: 0.8693 (t80) REVERT: AU 108 MET cc_start: 0.8463 (tpt) cc_final: 0.8008 (tpp) REVERT: AU 116 MET cc_start: 0.8726 (ttp) cc_final: 0.8308 (ttp) REVERT: AU 204 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: AU 220 MET cc_start: 0.9031 (mtm) cc_final: 0.8763 (mtm) REVERT: AV 136 ASP cc_start: 0.8421 (t0) cc_final: 0.8190 (t0) REVERT: AV 204 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: AV 250 THR cc_start: 0.9041 (m) cc_final: 0.8816 (p) REVERT: AV 267 MET cc_start: 0.7601 (mmm) cc_final: 0.7339 (mmm) REVERT: AW 180 TYR cc_start: 0.8753 (t80) cc_final: 0.8552 (t80) REVERT: AW 204 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: AX 160 MET cc_start: 0.9153 (tpp) cc_final: 0.8930 (mmp) REVERT: AX 173 MET cc_start: 0.8734 (tmm) cc_final: 0.8347 (tmm) REVERT: AX 204 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: AY 77 GLN cc_start: 0.8086 (tp40) cc_final: 0.7702 (tp40) REVERT: AY 94 TYR cc_start: 0.8755 (t80) cc_final: 0.8506 (t80) REVERT: AY 158 GLN cc_start: 0.9172 (mt0) cc_final: 0.8927 (mt0) REVERT: AY 204 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: AZ 136 ASP cc_start: 0.8632 (t70) cc_final: 0.8035 (m-30) REVERT: BA 78 ILE cc_start: 0.9318 (tt) cc_final: 0.8979 (tt) REVERT: BA 94 TYR cc_start: 0.8929 (t80) cc_final: 0.8707 (t80) REVERT: BA 134 MET cc_start: 0.8863 (ttt) cc_final: 0.8573 (ttt) REVERT: BA 146 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8135 (tptm) REVERT: BA 204 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: BB 94 TYR cc_start: 0.8856 (t80) cc_final: 0.8525 (t80) REVERT: BB 108 MET cc_start: 0.7656 (tpp) cc_final: 0.7371 (tpp) REVERT: BB 146 LYS cc_start: 0.8433 (ttmt) cc_final: 0.8217 (tptm) REVERT: BB 168 GLU cc_start: 0.8644 (tt0) cc_final: 0.8251 (tt0) REVERT: BB 173 MET cc_start: 0.8717 (tmm) cc_final: 0.8446 (ttp) REVERT: BB 220 MET cc_start: 0.9024 (mtm) cc_final: 0.8692 (mtp) REVERT: BB 236 ASP cc_start: 0.8211 (p0) cc_final: 0.7649 (p0) REVERT: BC 72 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: BC 146 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8301 (tptm) REVERT: BC 150 GLU cc_start: 0.7559 (tt0) cc_final: 0.7258 (tt0) REVERT: BC 204 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: BD 136 ASP cc_start: 0.8681 (t70) cc_final: 0.8402 (t0) REVERT: BD 173 MET cc_start: 0.8623 (tmm) cc_final: 0.8300 (tmm) REVERT: BD 231 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7447 (ppt170) REVERT: BD 267 MET cc_start: 0.7648 (mmm) cc_final: 0.7437 (mmm) REVERT: BE 94 TYR cc_start: 0.8989 (t80) cc_final: 0.8702 (t80) REVERT: BE 116 MET cc_start: 0.9215 (ttp) cc_final: 0.8754 (ttp) REVERT: BE 136 ASP cc_start: 0.8566 (t70) cc_final: 0.7844 (m-30) REVERT: BE 150 GLU cc_start: 0.6774 (tt0) cc_final: 0.6404 (tt0) REVERT: BE 180 TYR cc_start: 0.8727 (t80) cc_final: 0.8294 (t80) REVERT: BE 204 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: BF 82 ASN cc_start: 0.9036 (t0) cc_final: 0.8623 (t0) REVERT: BF 83 THR cc_start: 0.9372 (m) cc_final: 0.9032 (p) REVERT: BF 94 TYR cc_start: 0.8929 (t80) cc_final: 0.8596 (t80) REVERT: BF 136 ASP cc_start: 0.8331 (t70) cc_final: 0.7969 (m-30) REVERT: BF 158 GLN cc_start: 0.9151 (mt0) cc_final: 0.8672 (mt0) REVERT: BF 204 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: BF 267 MET cc_start: 0.7368 (mmm) cc_final: 0.7135 (mmm) REVERT: BG 136 ASP cc_start: 0.8583 (t70) cc_final: 0.8119 (m-30) REVERT: BG 231 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7609 (ptt90) REVERT: BG 267 MET cc_start: 0.7562 (mmm) cc_final: 0.7264 (mmm) REVERT: BH 116 MET cc_start: 0.9217 (ttp) cc_final: 0.8762 (ttp) REVERT: BH 236 ASP cc_start: 0.7892 (p0) cc_final: 0.7562 (p0) REVERT: BI 83 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.9215 (p) REVERT: BI 87 GLN cc_start: 0.8896 (tp40) cc_final: 0.8444 (tp-100) REVERT: BI 121 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8026 (tt0) REVERT: BI 204 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8153 (tt0) outliers start: 207 outliers final: 132 residues processed: 1461 average time/residue: 0.6694 time to fit residues: 1642.3874 Evaluate side-chains 1417 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1254 time to evaluate : 5.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 70 LEU Chi-restraints excluded: chain AA residue 88 SER Chi-restraints excluded: chain AA residue 204 GLU Chi-restraints excluded: chain AA residue 206 THR Chi-restraints excluded: chain AA residue 244 GLU Chi-restraints excluded: chain AB residue 72 GLU Chi-restraints excluded: chain AB residue 88 SER Chi-restraints excluded: chain AB residue 134 MET Chi-restraints excluded: chain AB residue 145 LEU Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain AB residue 206 THR Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 106 THR Chi-restraints excluded: chain AC residue 204 GLU Chi-restraints excluded: chain AC residue 206 THR Chi-restraints excluded: chain AD residue 56 MET Chi-restraints excluded: chain AD residue 88 SER Chi-restraints excluded: chain AD residue 120 ILE Chi-restraints excluded: chain AD residue 145 LEU Chi-restraints excluded: chain AD residue 252 GLU Chi-restraints excluded: chain AE residue 56 MET Chi-restraints excluded: chain AE residue 88 SER Chi-restraints excluded: chain AE residue 145 LEU Chi-restraints excluded: chain AE residue 206 THR Chi-restraints excluded: chain AE residue 252 GLU Chi-restraints excluded: chain AF residue 88 SER Chi-restraints excluded: chain AF residue 204 GLU Chi-restraints excluded: chain AF residue 206 THR Chi-restraints excluded: chain AG residue 88 SER Chi-restraints excluded: chain AG residue 125 SER Chi-restraints excluded: chain AG residue 204 GLU Chi-restraints excluded: chain AG residue 206 THR Chi-restraints excluded: chain AG residue 260 THR Chi-restraints excluded: chain AH residue 56 MET Chi-restraints excluded: chain AH residue 88 SER Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 120 ILE Chi-restraints excluded: chain AH residue 204 GLU Chi-restraints excluded: chain AH residue 206 THR Chi-restraints excluded: chain AH residue 252 GLU Chi-restraints excluded: chain AI residue 88 SER Chi-restraints excluded: chain AI residue 145 LEU Chi-restraints excluded: chain AI residue 204 GLU Chi-restraints excluded: chain AI residue 206 THR Chi-restraints excluded: chain AJ residue 88 SER Chi-restraints excluded: chain AJ residue 106 THR Chi-restraints excluded: chain AJ residue 204 GLU Chi-restraints excluded: chain AJ residue 206 THR Chi-restraints excluded: chain AJ residue 260 THR Chi-restraints excluded: chain AK residue 56 MET Chi-restraints excluded: chain AK residue 88 SER Chi-restraints excluded: chain AK residue 125 SER Chi-restraints excluded: chain AK residue 204 GLU Chi-restraints excluded: chain AL residue 56 MET Chi-restraints excluded: chain AL residue 88 SER Chi-restraints excluded: chain AL residue 204 GLU Chi-restraints excluded: chain AL residue 206 THR Chi-restraints excluded: chain AL residue 230 SER Chi-restraints excluded: chain AL residue 244 GLU Chi-restraints excluded: chain AM residue 88 SER Chi-restraints excluded: chain AM residue 194 SER Chi-restraints excluded: chain AM residue 204 GLU Chi-restraints excluded: chain AM residue 206 THR Chi-restraints excluded: chain AM residue 252 GLU Chi-restraints excluded: chain AN residue 88 SER Chi-restraints excluded: chain AN residue 204 GLU Chi-restraints excluded: chain AN residue 206 THR Chi-restraints excluded: chain AO residue 56 MET Chi-restraints excluded: chain AO residue 88 SER Chi-restraints excluded: chain AO residue 120 ILE Chi-restraints excluded: chain AO residue 204 GLU Chi-restraints excluded: chain AO residue 252 GLU Chi-restraints excluded: chain AP residue 88 SER Chi-restraints excluded: chain AP residue 145 LEU Chi-restraints excluded: chain AP residue 204 GLU Chi-restraints excluded: chain AP residue 206 THR Chi-restraints excluded: chain AP residue 236 ASP Chi-restraints excluded: chain AP residue 252 GLU Chi-restraints excluded: chain AQ residue 81 SER Chi-restraints excluded: chain AQ residue 88 SER Chi-restraints excluded: chain AQ residue 204 GLU Chi-restraints excluded: chain AQ residue 206 THR Chi-restraints excluded: chain AR residue 56 MET Chi-restraints excluded: chain AR residue 77 GLN Chi-restraints excluded: chain AR residue 88 SER Chi-restraints excluded: chain AR residue 125 SER Chi-restraints excluded: chain AR residue 204 GLU Chi-restraints excluded: chain AR residue 206 THR Chi-restraints excluded: chain AS residue 88 SER Chi-restraints excluded: chain AS residue 204 GLU Chi-restraints excluded: chain AS residue 206 THR Chi-restraints excluded: chain AT residue 88 SER Chi-restraints excluded: chain AT residue 145 LEU Chi-restraints excluded: chain AT residue 204 GLU Chi-restraints excluded: chain AT residue 206 THR Chi-restraints excluded: chain AT residue 260 THR Chi-restraints excluded: chain AU residue 88 SER Chi-restraints excluded: chain AU residue 204 GLU Chi-restraints excluded: chain AU residue 206 THR Chi-restraints excluded: chain AU residue 235 LEU Chi-restraints excluded: chain AU residue 250 THR Chi-restraints excluded: chain AV residue 54 MET Chi-restraints excluded: chain AV residue 56 MET Chi-restraints excluded: chain AV residue 88 SER Chi-restraints excluded: chain AV residue 106 THR Chi-restraints excluded: chain AV residue 120 ILE Chi-restraints excluded: chain AV residue 204 GLU Chi-restraints excluded: chain AV residue 230 SER Chi-restraints excluded: chain AW residue 88 SER Chi-restraints excluded: chain AW residue 204 GLU Chi-restraints excluded: chain AW residue 206 THR Chi-restraints excluded: chain AW residue 244 GLU Chi-restraints excluded: chain AW residue 252 GLU Chi-restraints excluded: chain AX residue 204 GLU Chi-restraints excluded: chain AX residue 206 THR Chi-restraints excluded: chain AY residue 88 SER Chi-restraints excluded: chain AY residue 128 ILE Chi-restraints excluded: chain AY residue 176 LYS Chi-restraints excluded: chain AY residue 204 GLU Chi-restraints excluded: chain AY residue 206 THR Chi-restraints excluded: chain AY residue 250 THR Chi-restraints excluded: chain AZ residue 56 MET Chi-restraints excluded: chain AZ residue 88 SER Chi-restraints excluded: chain BA residue 88 SER Chi-restraints excluded: chain BA residue 120 ILE Chi-restraints excluded: chain BA residue 145 LEU Chi-restraints excluded: chain BA residue 204 GLU Chi-restraints excluded: chain BA residue 206 THR Chi-restraints excluded: chain BB residue 88 SER Chi-restraints excluded: chain BB residue 135 MET Chi-restraints excluded: chain BB residue 145 LEU Chi-restraints excluded: chain BB residue 241 THR Chi-restraints excluded: chain BC residue 56 MET Chi-restraints excluded: chain BC residue 72 GLU Chi-restraints excluded: chain BC residue 88 SER Chi-restraints excluded: chain BC residue 125 SER Chi-restraints excluded: chain BC residue 204 GLU Chi-restraints excluded: chain BC residue 206 THR Chi-restraints excluded: chain BC residue 250 THR Chi-restraints excluded: chain BD residue 88 SER Chi-restraints excluded: chain BE residue 88 SER Chi-restraints excluded: chain BE residue 120 ILE Chi-restraints excluded: chain BE residue 204 GLU Chi-restraints excluded: chain BE residue 206 THR Chi-restraints excluded: chain BE residue 252 GLU Chi-restraints excluded: chain BF residue 88 SER Chi-restraints excluded: chain BF residue 120 ILE Chi-restraints excluded: chain BF residue 204 GLU Chi-restraints excluded: chain BF residue 206 THR Chi-restraints excluded: chain BG residue 56 MET Chi-restraints excluded: chain BG residue 78 ILE Chi-restraints excluded: chain BG residue 88 SER Chi-restraints excluded: chain BG residue 120 ILE Chi-restraints excluded: chain BG residue 145 LEU Chi-restraints excluded: chain BH residue 56 MET Chi-restraints excluded: chain BH residue 145 LEU Chi-restraints excluded: chain BH residue 206 THR Chi-restraints excluded: chain BH residue 252 GLU Chi-restraints excluded: chain BI residue 83 THR Chi-restraints excluded: chain BI residue 88 SER Chi-restraints excluded: chain BI residue 204 GLU Chi-restraints excluded: chain BI residue 206 THR Chi-restraints excluded: chain BI residue 252 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 250 optimal weight: 5.9990 chunk 670 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 436 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 745 optimal weight: 0.0030 chunk 618 optimal weight: 0.7980 chunk 344 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 391 optimal weight: 2.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 76 GLN ** AA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 229 GLN ** AE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 229 GLN AK 76 GLN AL 76 GLN AM 98 GLN ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 77 GLN AS 140 GLN AT 76 GLN ** AT 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 151 ASN AX 76 GLN ** AX 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 76 GLN ** BB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 266 ASN BE 76 GLN ** BE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 67340 Z= 0.167 Angle : 0.587 11.329 91805 Z= 0.295 Chirality : 0.040 0.187 10360 Planarity : 0.004 0.036 11375 Dihedral : 10.869 59.413 11305 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.28 % Allowed : 17.81 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.10), residues: 7770 helix: 0.88 (0.10), residues: 3255 sheet: 0.06 (0.27), residues: 350 loop : -1.20 (0.10), residues: 4165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAK 132 HIS 0.005 0.001 HISAY 69 PHE 0.012 0.001 PHEAD 200 TYR 0.027 0.001 TYRAD 198 ARG 0.006 0.000 ARGBA 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1368 time to evaluate : 5.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 GLN cc_start: 0.8502 (tm-30) cc_final: 0.7991 (mm-40) REVERT: AA 180 TYR cc_start: 0.8482 (t80) cc_final: 0.8247 (t80) REVERT: AA 231 ARG cc_start: 0.8081 (ttt90) cc_final: 0.7616 (tpm170) REVERT: AA 258 MET cc_start: 0.7877 (ttm) cc_final: 0.7612 (ttp) REVERT: AB 72 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: AB 82 ASN cc_start: 0.8866 (t0) cc_final: 0.8626 (t0) REVERT: AB 94 TYR cc_start: 0.8795 (t80) cc_final: 0.8459 (t80) REVERT: AB 231 ARG cc_start: 0.8089 (ttt90) cc_final: 0.7474 (tpm170) REVERT: AB 258 MET cc_start: 0.8029 (ttm) cc_final: 0.7755 (ttm) REVERT: AB 267 MET cc_start: 0.7637 (mmm) cc_final: 0.7289 (mmm) REVERT: AC 54 MET cc_start: 0.7288 (ppp) cc_final: 0.6740 (ppp) REVERT: AC 72 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: AC 99 LEU cc_start: 0.9304 (tp) cc_final: 0.9065 (mp) REVERT: AC 143 TYR cc_start: 0.8933 (m-80) cc_final: 0.8485 (m-80) REVERT: AC 172 GLU cc_start: 0.8284 (tp30) cc_final: 0.7834 (mm-30) REVERT: AC 231 ARG cc_start: 0.8060 (ttt90) cc_final: 0.7355 (mmp-170) REVERT: AD 94 TYR cc_start: 0.8731 (t80) cc_final: 0.8472 (t80) REVERT: AD 136 ASP cc_start: 0.8537 (t0) cc_final: 0.8223 (t0) REVERT: AD 170 TYR cc_start: 0.9094 (t80) cc_final: 0.8729 (t80) REVERT: AD 172 GLU cc_start: 0.8452 (tp30) cc_final: 0.8097 (mm-30) REVERT: AD 191 ARG cc_start: 0.8204 (mtt90) cc_final: 0.6887 (mtm-85) REVERT: AD 231 ARG cc_start: 0.5582 (tpm170) cc_final: 0.4729 (tpm170) REVERT: AE 94 TYR cc_start: 0.8759 (t80) cc_final: 0.8373 (t80) REVERT: AE 146 LYS cc_start: 0.8541 (tptm) cc_final: 0.8303 (tptm) REVERT: AE 220 MET cc_start: 0.9007 (mtm) cc_final: 0.8796 (mtp) REVERT: AE 231 ARG cc_start: 0.7972 (ttt90) cc_final: 0.7447 (tpm170) REVERT: AF 170 TYR cc_start: 0.9207 (t80) cc_final: 0.8966 (t80) REVERT: AF 204 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: AF 219 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8569 (mm-40) REVERT: AF 231 ARG cc_start: 0.7949 (ttt90) cc_final: 0.7351 (tpm170) REVERT: AG 72 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: AG 116 MET cc_start: 0.8910 (ttp) cc_final: 0.8528 (ttp) REVERT: AG 136 ASP cc_start: 0.8411 (t70) cc_final: 0.8165 (t0) REVERT: AG 143 TYR cc_start: 0.8846 (m-80) cc_final: 0.8588 (m-80) REVERT: AG 170 TYR cc_start: 0.9199 (t80) cc_final: 0.8879 (t80) REVERT: AG 191 ARG cc_start: 0.8300 (mtt90) cc_final: 0.6989 (mtm-85) REVERT: AG 231 ARG cc_start: 0.8000 (ttt90) cc_final: 0.7514 (mmp-170) REVERT: AH 94 TYR cc_start: 0.8795 (t80) cc_final: 0.8517 (t80) REVERT: AH 231 ARG cc_start: 0.8194 (ttt90) cc_final: 0.7444 (tpm170) REVERT: AH 267 MET cc_start: 0.7805 (mmm) cc_final: 0.7544 (mmm) REVERT: AI 134 MET cc_start: 0.8847 (ttt) cc_final: 0.8615 (ttt) REVERT: AI 136 ASP cc_start: 0.8565 (t0) cc_final: 0.8219 (t0) REVERT: AI 173 MET cc_start: 0.8569 (tmm) cc_final: 0.8295 (tmm) REVERT: AJ 136 ASP cc_start: 0.8561 (t0) cc_final: 0.8274 (t0) REVERT: AJ 219 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8594 (mm110) REVERT: AK 99 LEU cc_start: 0.9296 (tp) cc_final: 0.8919 (mp) REVERT: AK 134 MET cc_start: 0.8714 (ttt) cc_final: 0.8428 (ttt) REVERT: AK 136 ASP cc_start: 0.8543 (t0) cc_final: 0.8199 (t0) REVERT: AK 267 MET cc_start: 0.7640 (mmm) cc_final: 0.7317 (mmm) REVERT: AL 116 MET cc_start: 0.9114 (ttp) cc_final: 0.8784 (ttp) REVERT: AL 136 ASP cc_start: 0.8613 (t0) cc_final: 0.8214 (t0) REVERT: AL 204 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: AL 267 MET cc_start: 0.7787 (mmm) cc_final: 0.7582 (mmm) REVERT: AM 94 TYR cc_start: 0.8880 (t80) cc_final: 0.8625 (t80) REVERT: AM 136 ASP cc_start: 0.8524 (t0) cc_final: 0.8205 (t0) REVERT: AN 94 TYR cc_start: 0.8823 (t80) cc_final: 0.8612 (t80) REVERT: AN 136 ASP cc_start: 0.8458 (t70) cc_final: 0.8192 (t0) REVERT: AN 181 MET cc_start: 0.8839 (tpp) cc_final: 0.8600 (tpp) REVERT: AO 83 THR cc_start: 0.9391 (m) cc_final: 0.9184 (p) REVERT: AO 170 TYR cc_start: 0.9271 (t80) cc_final: 0.8973 (t80) REVERT: AP 78 ILE cc_start: 0.9116 (tt) cc_final: 0.8882 (tt) REVERT: AP 94 TYR cc_start: 0.8807 (t80) cc_final: 0.8571 (t80) REVERT: AP 136 ASP cc_start: 0.8509 (t0) cc_final: 0.8151 (t0) REVERT: AP 140 GLN cc_start: 0.8709 (mt0) cc_final: 0.8368 (mt0) REVERT: AP 143 TYR cc_start: 0.8925 (m-80) cc_final: 0.8412 (m-80) REVERT: AP 204 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: AQ 108 MET cc_start: 0.8213 (tpt) cc_final: 0.7856 (tpp) REVERT: AQ 146 LYS cc_start: 0.8683 (tptm) cc_final: 0.8470 (tptm) REVERT: AQ 219 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8447 (mm110) REVERT: AR 99 LEU cc_start: 0.9279 (tp) cc_final: 0.9006 (mp) REVERT: AR 116 MET cc_start: 0.9043 (ttp) cc_final: 0.8604 (ttp) REVERT: AR 136 ASP cc_start: 0.8485 (t0) cc_final: 0.8022 (t0) REVERT: AR 140 GLN cc_start: 0.8732 (mt0) cc_final: 0.8494 (mt0) REVERT: AR 184 TYR cc_start: 0.8940 (t80) cc_final: 0.8728 (t80) REVERT: AS 99 LEU cc_start: 0.9216 (tt) cc_final: 0.8998 (mp) REVERT: AS 116 MET cc_start: 0.8949 (ttp) cc_final: 0.8434 (ptm) REVERT: AS 136 ASP cc_start: 0.8614 (t0) cc_final: 0.8299 (t0) REVERT: AS 204 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: AS 267 MET cc_start: 0.7657 (mmm) cc_final: 0.7455 (mmm) REVERT: AT 94 TYR cc_start: 0.8847 (t80) cc_final: 0.8636 (t80) REVERT: AT 136 ASP cc_start: 0.8572 (t0) cc_final: 0.8289 (t0) REVERT: AT 173 MET cc_start: 0.8489 (tmm) cc_final: 0.8033 (tmm) REVERT: AT 204 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: AT 220 MET cc_start: 0.9053 (mtm) cc_final: 0.8754 (mtp) REVERT: AU 94 TYR cc_start: 0.8968 (t80) cc_final: 0.8617 (t80) REVERT: AU 108 MET cc_start: 0.8271 (tpt) cc_final: 0.7860 (tpp) REVERT: AU 116 MET cc_start: 0.8570 (ttp) cc_final: 0.8222 (ttp) REVERT: AU 215 GLU cc_start: 0.8598 (tp30) cc_final: 0.8397 (tp30) REVERT: AV 99 LEU cc_start: 0.9408 (tp) cc_final: 0.9145 (mp) REVERT: AV 173 MET cc_start: 0.8523 (tmm) cc_final: 0.8306 (tmm) REVERT: AV 204 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: AV 267 MET cc_start: 0.7680 (mmm) cc_final: 0.7377 (mmm) REVERT: AW 180 TYR cc_start: 0.8543 (t80) cc_final: 0.8276 (t80) REVERT: AX 72 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: AX 173 MET cc_start: 0.8555 (tmm) cc_final: 0.8191 (tmm) REVERT: AY 116 MET cc_start: 0.9059 (ttp) cc_final: 0.8775 (ttp) REVERT: AY 158 GLN cc_start: 0.9007 (mt0) cc_final: 0.8743 (mt0) REVERT: AZ 135 MET cc_start: 0.9123 (mmm) cc_final: 0.8908 (mmm) REVERT: AZ 136 ASP cc_start: 0.8590 (t70) cc_final: 0.8028 (m-30) REVERT: AZ 220 MET cc_start: 0.8900 (mtm) cc_final: 0.8669 (mtt) REVERT: BA 78 ILE cc_start: 0.9202 (tt) cc_final: 0.8918 (tt) REVERT: BA 94 TYR cc_start: 0.8901 (t80) cc_final: 0.8695 (t80) REVERT: BA 134 MET cc_start: 0.8817 (ttt) cc_final: 0.8599 (ttt) REVERT: BA 136 ASP cc_start: 0.8523 (t0) cc_final: 0.8141 (m-30) REVERT: BA 146 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7998 (tptm) REVERT: BA 204 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: BB 146 LYS cc_start: 0.8331 (ttmt) cc_final: 0.8072 (tptm) REVERT: BB 168 GLU cc_start: 0.8535 (tt0) cc_final: 0.8206 (tt0) REVERT: BB 173 MET cc_start: 0.8733 (tmm) cc_final: 0.8504 (ttp) REVERT: BB 180 TYR cc_start: 0.8732 (t80) cc_final: 0.8345 (t80) REVERT: BB 236 ASP cc_start: 0.8017 (p0) cc_final: 0.7782 (m-30) REVERT: BC 72 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7682 (pm20) REVERT: BC 99 LEU cc_start: 0.9333 (tt) cc_final: 0.9038 (mp) REVERT: BC 136 ASP cc_start: 0.8510 (t0) cc_final: 0.8155 (m-30) REVERT: BC 146 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8233 (tptm) REVERT: BC 150 GLU cc_start: 0.7574 (tt0) cc_final: 0.7247 (tt0) REVERT: BD 136 ASP cc_start: 0.8695 (t70) cc_final: 0.8246 (m-30) REVERT: BD 173 MET cc_start: 0.8597 (tmm) cc_final: 0.8273 (tmm) REVERT: BD 231 ARG cc_start: 0.8124 (ttt-90) cc_final: 0.7462 (ppt170) REVERT: BE 94 TYR cc_start: 0.8921 (t80) cc_final: 0.8703 (t80) REVERT: BE 116 MET cc_start: 0.9142 (ttp) cc_final: 0.8682 (ttp) REVERT: BE 136 ASP cc_start: 0.8548 (t70) cc_final: 0.8058 (m-30) REVERT: BE 173 MET cc_start: 0.8715 (tmm) cc_final: 0.8097 (tmm) REVERT: BE 180 TYR cc_start: 0.8552 (t80) cc_final: 0.8263 (t80) REVERT: BE 204 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: BF 94 TYR cc_start: 0.8850 (t80) cc_final: 0.8602 (t80) REVERT: BF 136 ASP cc_start: 0.8293 (t70) cc_final: 0.7970 (m-30) REVERT: BF 158 GLN cc_start: 0.8982 (mt0) cc_final: 0.8492 (mt0) REVERT: BF 172 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8259 (mm-30) REVERT: BF 173 MET cc_start: 0.8291 (tmm) cc_final: 0.7773 (tmm) REVERT: BG 136 ASP cc_start: 0.8523 (t70) cc_final: 0.8159 (m-30) REVERT: BG 160 MET cc_start: 0.8625 (mmm) cc_final: 0.8174 (mmm) REVERT: BG 180 TYR cc_start: 0.8459 (t80) cc_final: 0.8018 (t80) REVERT: BG 204 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: BG 231 ARG cc_start: 0.8221 (ttt-90) cc_final: 0.7578 (ptt90) REVERT: BG 267 MET cc_start: 0.7639 (mmm) cc_final: 0.7372 (mmm) REVERT: BI 87 GLN cc_start: 0.8639 (tp40) cc_final: 0.8119 (mm-40) REVERT: BI 91 ASP cc_start: 0.8127 (m-30) cc_final: 0.7739 (m-30) REVERT: BI 121 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8042 (tt0) outliers start: 155 outliers final: 100 residues processed: 1471 average time/residue: 0.6611 time to fit residues: 1620.4435 Evaluate side-chains 1384 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1270 time to evaluate : 5.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 70 LEU Chi-restraints excluded: chain AA residue 88 SER Chi-restraints excluded: chain AA residue 145 LEU Chi-restraints excluded: chain AA residue 206 THR Chi-restraints excluded: chain AB residue 72 GLU Chi-restraints excluded: chain AB residue 88 SER Chi-restraints excluded: chain AB residue 206 THR Chi-restraints excluded: chain AB residue 252 GLU Chi-restraints excluded: chain AC residue 72 GLU Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 106 THR Chi-restraints excluded: chain AC residue 120 ILE Chi-restraints excluded: chain AC residue 206 THR Chi-restraints excluded: chain AD residue 56 MET Chi-restraints excluded: chain AD residue 88 SER Chi-restraints excluded: chain AD residue 252 GLU Chi-restraints excluded: chain AE residue 56 MET Chi-restraints excluded: chain AE residue 88 SER Chi-restraints excluded: chain AE residue 206 THR Chi-restraints excluded: chain AF residue 88 SER Chi-restraints excluded: chain AF residue 204 GLU Chi-restraints excluded: chain AF residue 206 THR Chi-restraints excluded: chain AG residue 72 GLU Chi-restraints excluded: chain AG residue 206 THR Chi-restraints excluded: chain AH residue 56 MET Chi-restraints excluded: chain AH residue 88 SER Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 120 ILE Chi-restraints excluded: chain AH residue 145 LEU Chi-restraints excluded: chain AH residue 206 THR Chi-restraints excluded: chain AI residue 88 SER Chi-restraints excluded: chain AI residue 145 LEU Chi-restraints excluded: chain AI residue 206 THR Chi-restraints excluded: chain AJ residue 88 SER Chi-restraints excluded: chain AJ residue 106 THR Chi-restraints excluded: chain AJ residue 206 THR Chi-restraints excluded: chain AJ residue 260 THR Chi-restraints excluded: chain AK residue 56 MET Chi-restraints excluded: chain AK residue 88 SER Chi-restraints excluded: chain AL residue 56 MET Chi-restraints excluded: chain AL residue 88 SER Chi-restraints excluded: chain AL residue 204 GLU Chi-restraints excluded: chain AL residue 206 THR Chi-restraints excluded: chain AL residue 244 GLU Chi-restraints excluded: chain AM residue 88 SER Chi-restraints excluded: chain AM residue 194 SER Chi-restraints excluded: chain AM residue 206 THR Chi-restraints excluded: chain AM residue 252 GLU Chi-restraints excluded: chain AN residue 88 SER Chi-restraints excluded: chain AN residue 206 THR Chi-restraints excluded: chain AO residue 56 MET Chi-restraints excluded: chain AO residue 81 SER Chi-restraints excluded: chain AO residue 88 SER Chi-restraints excluded: chain AO residue 120 ILE Chi-restraints excluded: chain AO residue 159 ILE Chi-restraints excluded: chain AO residue 252 GLU Chi-restraints excluded: chain AP residue 204 GLU Chi-restraints excluded: chain AP residue 206 THR Chi-restraints excluded: chain AQ residue 88 SER Chi-restraints excluded: chain AQ residue 206 THR Chi-restraints excluded: chain AR residue 56 MET Chi-restraints excluded: chain AR residue 77 GLN Chi-restraints excluded: chain AR residue 88 SER Chi-restraints excluded: chain AR residue 98 GLN Chi-restraints excluded: chain AR residue 206 THR Chi-restraints excluded: chain AS residue 88 SER Chi-restraints excluded: chain AS residue 204 GLU Chi-restraints excluded: chain AS residue 206 THR Chi-restraints excluded: chain AT residue 204 GLU Chi-restraints excluded: chain AT residue 206 THR Chi-restraints excluded: chain AT residue 260 THR Chi-restraints excluded: chain AU residue 88 SER Chi-restraints excluded: chain AU residue 206 THR Chi-restraints excluded: chain AU residue 260 THR Chi-restraints excluded: chain AV residue 56 MET Chi-restraints excluded: chain AV residue 88 SER Chi-restraints excluded: chain AV residue 101 TYR Chi-restraints excluded: chain AV residue 120 ILE Chi-restraints excluded: chain AV residue 204 GLU Chi-restraints excluded: chain AW residue 88 SER Chi-restraints excluded: chain AW residue 206 THR Chi-restraints excluded: chain AX residue 72 GLU Chi-restraints excluded: chain AX residue 206 THR Chi-restraints excluded: chain AY residue 206 THR Chi-restraints excluded: chain AZ residue 56 MET Chi-restraints excluded: chain BA residue 88 SER Chi-restraints excluded: chain BA residue 204 GLU Chi-restraints excluded: chain BA residue 206 THR Chi-restraints excluded: chain BA residue 252 GLU Chi-restraints excluded: chain BB residue 67 LEU Chi-restraints excluded: chain BB residue 135 MET Chi-restraints excluded: chain BC residue 56 MET Chi-restraints excluded: chain BC residue 72 GLU Chi-restraints excluded: chain BC residue 206 THR Chi-restraints excluded: chain BD residue 88 SER Chi-restraints excluded: chain BD residue 106 THR Chi-restraints excluded: chain BD residue 252 GLU Chi-restraints excluded: chain BD residue 260 THR Chi-restraints excluded: chain BE residue 88 SER Chi-restraints excluded: chain BE residue 204 GLU Chi-restraints excluded: chain BE residue 206 THR Chi-restraints excluded: chain BE residue 252 GLU Chi-restraints excluded: chain BE residue 260 THR Chi-restraints excluded: chain BF residue 88 SER Chi-restraints excluded: chain BF residue 206 THR Chi-restraints excluded: chain BG residue 56 MET Chi-restraints excluded: chain BG residue 88 SER Chi-restraints excluded: chain BG residue 120 ILE Chi-restraints excluded: chain BG residue 204 GLU Chi-restraints excluded: chain BH residue 56 MET Chi-restraints excluded: chain BH residue 206 THR Chi-restraints excluded: chain BI residue 72 GLU Chi-restraints excluded: chain BI residue 88 SER Chi-restraints excluded: chain BI residue 206 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 718 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 424 optimal weight: 1.9990 chunk 544 optimal weight: 0.0980 chunk 421 optimal weight: 0.5980 chunk 627 optimal weight: 0.6980 chunk 416 optimal weight: 0.9980 chunk 742 optimal weight: 8.9990 chunk 464 optimal weight: 20.0000 chunk 452 optimal weight: 0.8980 chunk 342 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 76 GLN ** AD 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 98 GLN ** AE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 229 GLN AF 76 GLN AH 76 GLN AK 76 GLN AM 76 GLN ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 76 GLN AR 76 GLN AS 76 GLN AS 140 GLN ** AT 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 151 ASN AU 76 GLN AV 76 GLN ** AW 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 76 GLN ** BB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 76 GLN BD 76 GLN BF 76 GLN ** BG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 76 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 67340 Z= 0.163 Angle : 0.590 11.558 91805 Z= 0.293 Chirality : 0.040 0.195 10360 Planarity : 0.004 0.037 11375 Dihedral : 10.738 59.543 11305 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.02 % Allowed : 19.28 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.10), residues: 7770 helix: 1.05 (0.10), residues: 3220 sheet: 0.11 (0.27), residues: 350 loop : -1.22 (0.10), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAR 132 HIS 0.006 0.001 HISAL 249 PHE 0.011 0.001 PHEAL 200 TYR 0.031 0.001 TYRAJ 198 ARG 0.007 0.000 ARGBF 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1500 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1363 time to evaluate : 5.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7952 (mm-40) REVERT: AA 231 ARG cc_start: 0.8058 (ttt90) cc_final: 0.7580 (tpm170) REVERT: AA 258 MET cc_start: 0.7850 (ttm) cc_final: 0.7599 (ttp) REVERT: AB 72 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: AB 82 ASN cc_start: 0.8847 (t0) cc_final: 0.8617 (t0) REVERT: AB 231 ARG cc_start: 0.8068 (ttt90) cc_final: 0.7478 (tpm170) REVERT: AB 258 MET cc_start: 0.8050 (ttm) cc_final: 0.7754 (ttm) REVERT: AB 267 MET cc_start: 0.7633 (mmm) cc_final: 0.7325 (mmm) REVERT: AC 54 MET cc_start: 0.7234 (ppp) cc_final: 0.6564 (ppp) REVERT: AC 72 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: AC 99 LEU cc_start: 0.9242 (tp) cc_final: 0.9023 (mp) REVERT: AC 143 TYR cc_start: 0.8897 (m-80) cc_final: 0.8274 (m-80) REVERT: AC 204 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: AC 231 ARG cc_start: 0.8084 (ttt90) cc_final: 0.7361 (mmp-170) REVERT: AD 136 ASP cc_start: 0.8518 (t0) cc_final: 0.8241 (t0) REVERT: AD 170 TYR cc_start: 0.9110 (t80) cc_final: 0.8750 (t80) REVERT: AD 191 ARG cc_start: 0.8149 (mtt90) cc_final: 0.6962 (mtm-85) REVERT: AD 220 MET cc_start: 0.8858 (mtm) cc_final: 0.8600 (mtm) REVERT: AD 231 ARG cc_start: 0.5574 (tpm170) cc_final: 0.4836 (tpm170) REVERT: AE 94 TYR cc_start: 0.8598 (t80) cc_final: 0.8343 (t80) REVERT: AE 146 LYS cc_start: 0.8548 (tptm) cc_final: 0.8323 (tptm) REVERT: AE 220 MET cc_start: 0.8968 (mtm) cc_final: 0.8765 (mtp) REVERT: AE 231 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7513 (tpm170) REVERT: AE 267 MET cc_start: 0.7722 (mmm) cc_final: 0.7497 (mmm) REVERT: AF 172 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7564 (mm-30) REVERT: AF 197 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7542 (ttp-110) REVERT: AF 204 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: AF 219 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8544 (mm-40) REVERT: AF 231 ARG cc_start: 0.7978 (ttt90) cc_final: 0.7356 (tpm170) REVERT: AF 236 ASP cc_start: 0.8121 (p0) cc_final: 0.7787 (m-30) REVERT: AG 72 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: AG 94 TYR cc_start: 0.8613 (t80) cc_final: 0.8290 (t80) REVERT: AG 116 MET cc_start: 0.8893 (ttp) cc_final: 0.8478 (ttp) REVERT: AG 136 ASP cc_start: 0.8371 (t70) cc_final: 0.8122 (t0) REVERT: AG 143 TYR cc_start: 0.8843 (m-80) cc_final: 0.8566 (m-80) REVERT: AG 204 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: AG 231 ARG cc_start: 0.8031 (ttt90) cc_final: 0.7627 (tpm170) REVERT: AH 204 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: AH 231 ARG cc_start: 0.8223 (ttt90) cc_final: 0.7457 (tpm170) REVERT: AH 267 MET cc_start: 0.7819 (mmm) cc_final: 0.7534 (mmm) REVERT: AI 134 MET cc_start: 0.8810 (ttt) cc_final: 0.8603 (ttt) REVERT: AI 136 ASP cc_start: 0.8554 (t0) cc_final: 0.8181 (t0) REVERT: AI 173 MET cc_start: 0.8601 (tmm) cc_final: 0.8365 (tmm) REVERT: AI 184 TYR cc_start: 0.8983 (t80) cc_final: 0.8781 (t80) REVERT: AI 231 ARG cc_start: 0.5596 (tpm170) cc_final: 0.4939 (tpm170) REVERT: AJ 94 TYR cc_start: 0.8803 (t80) cc_final: 0.8571 (t80) REVERT: AJ 108 MET cc_start: 0.8154 (tpt) cc_final: 0.7760 (tpp) REVERT: AJ 136 ASP cc_start: 0.8560 (t0) cc_final: 0.8257 (t0) REVERT: AJ 219 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8663 (mm110) REVERT: AK 99 LEU cc_start: 0.9357 (tp) cc_final: 0.8956 (mp) REVERT: AK 134 MET cc_start: 0.8629 (ttt) cc_final: 0.8354 (ttt) REVERT: AK 136 ASP cc_start: 0.8482 (t0) cc_final: 0.8162 (t0) REVERT: AK 267 MET cc_start: 0.7727 (mmm) cc_final: 0.7452 (mmm) REVERT: AL 99 LEU cc_start: 0.9294 (tp) cc_final: 0.9015 (mp) REVERT: AL 116 MET cc_start: 0.9085 (ttp) cc_final: 0.8749 (ttp) REVERT: AL 136 ASP cc_start: 0.8563 (t0) cc_final: 0.8115 (t0) REVERT: AL 204 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: AM 136 ASP cc_start: 0.8485 (t0) cc_final: 0.8153 (t0) REVERT: AM 219 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8811 (mm110) REVERT: AN 94 TYR cc_start: 0.8740 (t80) cc_final: 0.8255 (t80) REVERT: AN 108 MET cc_start: 0.8421 (tpt) cc_final: 0.8074 (tpt) REVERT: AN 136 ASP cc_start: 0.8502 (t70) cc_final: 0.8200 (t0) REVERT: AN 219 GLN cc_start: 0.9112 (mm110) cc_final: 0.8850 (mm110) REVERT: AO 83 THR cc_start: 0.9412 (m) cc_final: 0.9201 (p) REVERT: AO 87 GLN cc_start: 0.8960 (tp40) cc_final: 0.8449 (tp-100) REVERT: AO 170 TYR cc_start: 0.9274 (t80) cc_final: 0.8954 (t80) REVERT: AP 136 ASP cc_start: 0.8497 (t0) cc_final: 0.8112 (t0) REVERT: AP 143 TYR cc_start: 0.8918 (m-80) cc_final: 0.8424 (m-80) REVERT: AP 204 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: AP 246 THR cc_start: 0.8836 (p) cc_final: 0.8431 (t) REVERT: AP 267 MET cc_start: 0.7721 (mmm) cc_final: 0.7425 (mmm) REVERT: AQ 146 LYS cc_start: 0.8724 (tptm) cc_final: 0.8455 (tptm) REVERT: AQ 173 MET cc_start: 0.8441 (tmm) cc_final: 0.7917 (tmm) REVERT: AQ 219 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8445 (mm110) REVERT: AR 99 LEU cc_start: 0.9291 (tp) cc_final: 0.9014 (mp) REVERT: AR 136 ASP cc_start: 0.8504 (t0) cc_final: 0.8069 (t0) REVERT: AR 267 MET cc_start: 0.7758 (mmm) cc_final: 0.7532 (mmm) REVERT: AS 99 LEU cc_start: 0.9288 (tt) cc_final: 0.9088 (mp) REVERT: AS 116 MET cc_start: 0.8875 (ttp) cc_final: 0.8395 (ptm) REVERT: AS 136 ASP cc_start: 0.8594 (t0) cc_final: 0.8218 (t0) REVERT: AS 204 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: AS 267 MET cc_start: 0.7718 (mmm) cc_final: 0.7451 (mmm) REVERT: AT 136 ASP cc_start: 0.8549 (t0) cc_final: 0.8259 (t0) REVERT: AT 173 MET cc_start: 0.8374 (tmm) cc_final: 0.7993 (tmm) REVERT: AT 204 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: AT 220 MET cc_start: 0.9051 (mtm) cc_final: 0.8748 (mtp) REVERT: AU 77 GLN cc_start: 0.7640 (tp40) cc_final: 0.7396 (tp40) REVERT: AU 94 TYR cc_start: 0.8909 (t80) cc_final: 0.8540 (t80) REVERT: AU 116 MET cc_start: 0.8527 (ttp) cc_final: 0.8310 (ttp) REVERT: AV 173 MET cc_start: 0.8554 (tmm) cc_final: 0.8328 (tmm) REVERT: AV 204 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: AV 267 MET cc_start: 0.7677 (mmm) cc_final: 0.7444 (mmm) REVERT: AW 99 LEU cc_start: 0.9332 (tp) cc_final: 0.8910 (mp) REVERT: AW 267 MET cc_start: 0.7776 (mmm) cc_final: 0.7506 (mmm) REVERT: AX 72 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: AX 99 LEU cc_start: 0.9367 (tp) cc_final: 0.8969 (mp) REVERT: AX 134 MET cc_start: 0.8648 (tpp) cc_final: 0.8126 (ttt) REVERT: AX 173 MET cc_start: 0.8446 (tmm) cc_final: 0.8058 (tmm) REVERT: AY 116 MET cc_start: 0.9078 (ttp) cc_final: 0.8825 (ttp) REVERT: AY 158 GLN cc_start: 0.8947 (mt0) cc_final: 0.8676 (mt0) REVERT: AY 172 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8013 (mm-30) REVERT: AZ 94 TYR cc_start: 0.8803 (t80) cc_final: 0.8555 (t80) REVERT: AZ 99 LEU cc_start: 0.9288 (tt) cc_final: 0.8916 (mp) REVERT: AZ 135 MET cc_start: 0.9118 (mmm) cc_final: 0.8877 (mmm) REVERT: AZ 136 ASP cc_start: 0.8623 (t70) cc_final: 0.8062 (m-30) REVERT: AZ 220 MET cc_start: 0.8875 (mtm) cc_final: 0.8625 (mtt) REVERT: BA 78 ILE cc_start: 0.9144 (tt) cc_final: 0.8859 (tt) REVERT: BA 134 MET cc_start: 0.8784 (ttt) cc_final: 0.8574 (ttt) REVERT: BA 136 ASP cc_start: 0.8557 (t0) cc_final: 0.8158 (m-30) REVERT: BA 146 LYS cc_start: 0.8268 (ttmt) cc_final: 0.8004 (tptm) REVERT: BA 204 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: BB 136 ASP cc_start: 0.8573 (t0) cc_final: 0.7883 (m-30) REVERT: BB 146 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7959 (tptm) REVERT: BB 168 GLU cc_start: 0.8509 (tt0) cc_final: 0.8224 (tt0) REVERT: BB 173 MET cc_start: 0.8728 (tmm) cc_final: 0.8516 (ttp) REVERT: BB 180 TYR cc_start: 0.8670 (t80) cc_final: 0.8358 (t80) REVERT: BB 220 MET cc_start: 0.8961 (mtm) cc_final: 0.8642 (mtp) REVERT: BC 72 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: BC 99 LEU cc_start: 0.9318 (tt) cc_final: 0.9073 (mp) REVERT: BC 146 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8236 (tptm) REVERT: BC 150 GLU cc_start: 0.7364 (tt0) cc_final: 0.7122 (tt0) REVERT: BD 136 ASP cc_start: 0.8667 (t70) cc_final: 0.8203 (m-30) REVERT: BD 173 MET cc_start: 0.8700 (tmm) cc_final: 0.8410 (tmm) REVERT: BD 231 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7475 (ppt170) REVERT: BE 72 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: BE 116 MET cc_start: 0.9134 (ttp) cc_final: 0.8565 (ttp) REVERT: BE 136 ASP cc_start: 0.8573 (t70) cc_final: 0.8026 (m-30) REVERT: BE 173 MET cc_start: 0.8690 (tmm) cc_final: 0.8056 (tmm) REVERT: BE 180 TYR cc_start: 0.8590 (t80) cc_final: 0.8257 (t80) REVERT: BE 204 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: BF 94 TYR cc_start: 0.8846 (t80) cc_final: 0.8612 (t80) REVERT: BF 136 ASP cc_start: 0.8297 (t70) cc_final: 0.7999 (m-30) REVERT: BF 173 MET cc_start: 0.8272 (tmm) cc_final: 0.7784 (tmm) REVERT: BF 267 MET cc_start: 0.7505 (mmm) cc_final: 0.7270 (mmm) REVERT: BG 99 LEU cc_start: 0.9243 (tt) cc_final: 0.8985 (mp) REVERT: BG 136 ASP cc_start: 0.8521 (t70) cc_final: 0.8190 (m-30) REVERT: BG 160 MET cc_start: 0.8664 (mmm) cc_final: 0.8217 (mmm) REVERT: BG 204 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: BG 231 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7558 (ptt90) REVERT: BG 267 MET cc_start: 0.7655 (mmm) cc_final: 0.7397 (mmm) REVERT: BI 121 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8042 (tt0) outliers start: 137 outliers final: 80 residues processed: 1462 average time/residue: 0.6553 time to fit residues: 1599.4427 Evaluate side-chains 1367 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1269 time to evaluate : 5.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 56 MET Chi-restraints excluded: chain AA residue 206 THR Chi-restraints excluded: chain AB residue 72 GLU Chi-restraints excluded: chain AB residue 88 SER Chi-restraints excluded: chain AB residue 206 THR Chi-restraints excluded: chain AC residue 72 GLU Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 106 THR Chi-restraints excluded: chain AC residue 204 GLU Chi-restraints excluded: chain AC residue 206 THR Chi-restraints excluded: chain AD residue 56 MET Chi-restraints excluded: chain AD residue 67 LEU Chi-restraints excluded: chain AD residue 252 GLU Chi-restraints excluded: chain AE residue 56 MET Chi-restraints excluded: chain AE residue 206 THR Chi-restraints excluded: chain AF residue 88 SER Chi-restraints excluded: chain AF residue 204 GLU Chi-restraints excluded: chain AF residue 206 THR Chi-restraints excluded: chain AF residue 220 MET Chi-restraints excluded: chain AG residue 72 GLU Chi-restraints excluded: chain AG residue 88 SER Chi-restraints excluded: chain AG residue 204 GLU Chi-restraints excluded: chain AH residue 56 MET Chi-restraints excluded: chain AH residue 88 SER Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 120 ILE Chi-restraints excluded: chain AH residue 204 GLU Chi-restraints excluded: chain AH residue 206 THR Chi-restraints excluded: chain AI residue 206 THR Chi-restraints excluded: chain AJ residue 72 GLU Chi-restraints excluded: chain AJ residue 106 THR Chi-restraints excluded: chain AJ residue 206 THR Chi-restraints excluded: chain AJ residue 260 THR Chi-restraints excluded: chain AK residue 56 MET Chi-restraints excluded: chain AK residue 88 SER Chi-restraints excluded: chain AL residue 56 MET Chi-restraints excluded: chain AL residue 204 GLU Chi-restraints excluded: chain AL residue 206 THR Chi-restraints excluded: chain AL residue 244 GLU Chi-restraints excluded: chain AM residue 88 SER Chi-restraints excluded: chain AM residue 206 THR Chi-restraints excluded: chain AN residue 88 SER Chi-restraints excluded: chain AN residue 206 THR Chi-restraints excluded: chain AO residue 56 MET Chi-restraints excluded: chain AO residue 81 SER Chi-restraints excluded: chain AO residue 88 SER Chi-restraints excluded: chain AO residue 120 ILE Chi-restraints excluded: chain AO residue 159 ILE Chi-restraints excluded: chain AO residue 252 GLU Chi-restraints excluded: chain AP residue 204 GLU Chi-restraints excluded: chain AP residue 206 THR Chi-restraints excluded: chain AQ residue 206 THR Chi-restraints excluded: chain AR residue 56 MET Chi-restraints excluded: chain AR residue 88 SER Chi-restraints excluded: chain AR residue 206 THR Chi-restraints excluded: chain AS residue 88 SER Chi-restraints excluded: chain AS residue 204 GLU Chi-restraints excluded: chain AS residue 206 THR Chi-restraints excluded: chain AT residue 204 GLU Chi-restraints excluded: chain AT residue 206 THR Chi-restraints excluded: chain AT residue 260 THR Chi-restraints excluded: chain AU residue 88 SER Chi-restraints excluded: chain AU residue 206 THR Chi-restraints excluded: chain AV residue 56 MET Chi-restraints excluded: chain AV residue 101 TYR Chi-restraints excluded: chain AV residue 106 THR Chi-restraints excluded: chain AV residue 120 ILE Chi-restraints excluded: chain AV residue 204 GLU Chi-restraints excluded: chain AW residue 88 SER Chi-restraints excluded: chain AW residue 206 THR Chi-restraints excluded: chain AX residue 72 GLU Chi-restraints excluded: chain AX residue 206 THR Chi-restraints excluded: chain AY residue 206 THR Chi-restraints excluded: chain AZ residue 145 LEU Chi-restraints excluded: chain BA residue 88 SER Chi-restraints excluded: chain BA residue 204 GLU Chi-restraints excluded: chain BA residue 206 THR Chi-restraints excluded: chain BB residue 67 LEU Chi-restraints excluded: chain BB residue 135 MET Chi-restraints excluded: chain BC residue 72 GLU Chi-restraints excluded: chain BD residue 88 SER Chi-restraints excluded: chain BD residue 106 THR Chi-restraints excluded: chain BD residue 260 THR Chi-restraints excluded: chain BE residue 72 GLU Chi-restraints excluded: chain BE residue 204 GLU Chi-restraints excluded: chain BE residue 206 THR Chi-restraints excluded: chain BE residue 260 THR Chi-restraints excluded: chain BF residue 88 SER Chi-restraints excluded: chain BF residue 120 ILE Chi-restraints excluded: chain BF residue 206 THR Chi-restraints excluded: chain BG residue 56 MET Chi-restraints excluded: chain BG residue 88 SER Chi-restraints excluded: chain BG residue 204 GLU Chi-restraints excluded: chain BH residue 56 MET Chi-restraints excluded: chain BH residue 145 LEU Chi-restraints excluded: chain BH residue 206 THR Chi-restraints excluded: chain BI residue 88 SER Chi-restraints excluded: chain BI residue 206 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 459 optimal weight: 8.9990 chunk 296 optimal weight: 0.9990 chunk 443 optimal weight: 0.7980 chunk 223 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 471 optimal weight: 3.9990 chunk 505 optimal weight: 7.9990 chunk 366 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 583 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 229 GLN AB 77 GLN ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 140 GLN ** AD 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 98 GLN ** AE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 229 GLN AH 76 GLN AJ 76 GLN AK 76 GLN ** AL 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 76 GLN ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 76 GLN ** AT 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 151 ASN ** AU 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 140 GLN ** AX 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 76 GLN ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 76 GLN ** BB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 76 GLN ** BG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 76 GLN ** BH 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 67340 Z= 0.229 Angle : 0.619 12.965 91805 Z= 0.309 Chirality : 0.041 0.198 10360 Planarity : 0.004 0.039 11375 Dihedral : 10.842 59.795 11305 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.37 % Allowed : 19.69 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.10), residues: 7770 helix: 1.10 (0.10), residues: 3185 sheet: 0.32 (0.27), residues: 350 loop : -1.18 (0.10), residues: 4235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAR 132 HIS 0.004 0.001 HISAI 69 PHE 0.012 0.001 PHEAD 200 TYR 0.026 0.002 TYRAA 180 ARG 0.009 0.000 ARGAD 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1483 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1322 time to evaluate : 5.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7951 (mm-40) REVERT: AA 231 ARG cc_start: 0.8135 (ttt90) cc_final: 0.7630 (tpm170) REVERT: AB 72 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: AB 94 TYR cc_start: 0.8745 (t80) cc_final: 0.8353 (t80) REVERT: AB 231 ARG cc_start: 0.8031 (ttt90) cc_final: 0.7450 (tpm170) REVERT: AB 258 MET cc_start: 0.8125 (ttm) cc_final: 0.7789 (ttm) REVERT: AB 267 MET cc_start: 0.7657 (mmm) cc_final: 0.7387 (mmm) REVERT: AC 54 MET cc_start: 0.7313 (ppp) cc_final: 0.6654 (ppp) REVERT: AC 72 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: AC 99 LEU cc_start: 0.9246 (tp) cc_final: 0.9024 (mp) REVERT: AC 143 TYR cc_start: 0.8938 (m-80) cc_final: 0.8416 (m-80) REVERT: AC 204 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: AC 231 ARG cc_start: 0.8091 (ttt90) cc_final: 0.7351 (mmp-170) REVERT: AD 94 TYR cc_start: 0.8905 (t80) cc_final: 0.8665 (t80) REVERT: AD 136 ASP cc_start: 0.8525 (t0) cc_final: 0.8265 (t0) REVERT: AD 172 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8073 (mm-30) REVERT: AD 191 ARG cc_start: 0.8209 (mtt90) cc_final: 0.6996 (mtm-85) REVERT: AD 220 MET cc_start: 0.8932 (mtm) cc_final: 0.8667 (mtm) REVERT: AD 231 ARG cc_start: 0.5599 (tpm170) cc_final: 0.4945 (tpm170) REVERT: AE 134 MET cc_start: 0.8740 (ttt) cc_final: 0.8539 (ttt) REVERT: AE 146 LYS cc_start: 0.8576 (tptm) cc_final: 0.8349 (tptm) REVERT: AE 172 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8233 (mt-10) REVERT: AE 220 MET cc_start: 0.8969 (mtm) cc_final: 0.8768 (mtp) REVERT: AE 231 ARG cc_start: 0.8098 (ttt90) cc_final: 0.7520 (tpm170) REVERT: AF 204 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: AF 219 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8631 (mm110) REVERT: AF 231 ARG cc_start: 0.7984 (ttt90) cc_final: 0.7336 (tpm170) REVERT: AG 116 MET cc_start: 0.8928 (ttp) cc_final: 0.8320 (ttp) REVERT: AG 136 ASP cc_start: 0.8386 (t70) cc_final: 0.8126 (t0) REVERT: AG 143 TYR cc_start: 0.8829 (m-80) cc_final: 0.8607 (m-80) REVERT: AG 204 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: AG 231 ARG cc_start: 0.8039 (ttt90) cc_final: 0.7663 (tpm170) REVERT: AH 99 LEU cc_start: 0.9334 (tp) cc_final: 0.8980 (mp) REVERT: AH 204 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: AH 231 ARG cc_start: 0.8172 (ttt90) cc_final: 0.7462 (tpm170) REVERT: AH 267 MET cc_start: 0.7830 (mmm) cc_final: 0.7544 (mmm) REVERT: AI 134 MET cc_start: 0.8792 (ttt) cc_final: 0.8571 (ttt) REVERT: AI 136 ASP cc_start: 0.8410 (t0) cc_final: 0.8065 (t0) REVERT: AI 146 LYS cc_start: 0.8596 (tptm) cc_final: 0.8237 (tptm) REVERT: AI 173 MET cc_start: 0.8603 (tmm) cc_final: 0.8370 (tmm) REVERT: AI 204 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: AI 231 ARG cc_start: 0.5870 (tpm170) cc_final: 0.5561 (tpm170) REVERT: AJ 94 TYR cc_start: 0.8819 (t80) cc_final: 0.8566 (t80) REVERT: AJ 108 MET cc_start: 0.8220 (tpt) cc_final: 0.7815 (tpp) REVERT: AJ 136 ASP cc_start: 0.8562 (t0) cc_final: 0.8260 (t0) REVERT: AJ 172 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8007 (mm-30) REVERT: AJ 204 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: AJ 219 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8576 (mm110) REVERT: AK 99 LEU cc_start: 0.9342 (tp) cc_final: 0.9018 (mp) REVERT: AK 134 MET cc_start: 0.8667 (ttt) cc_final: 0.8363 (ttt) REVERT: AK 136 ASP cc_start: 0.8500 (t0) cc_final: 0.8183 (t0) REVERT: AK 204 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: AL 98 GLN cc_start: 0.8215 (tt0) cc_final: 0.7944 (mt0) REVERT: AL 99 LEU cc_start: 0.9298 (tp) cc_final: 0.9012 (mp) REVERT: AL 116 MET cc_start: 0.9086 (ttp) cc_final: 0.8770 (ttp) REVERT: AL 136 ASP cc_start: 0.8609 (t0) cc_final: 0.8186 (t0) REVERT: AL 204 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: AM 136 ASP cc_start: 0.8548 (t0) cc_final: 0.8205 (t0) REVERT: AM 204 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: AN 94 TYR cc_start: 0.8772 (t80) cc_final: 0.8520 (t80) REVERT: AN 136 ASP cc_start: 0.8486 (t70) cc_final: 0.8177 (t0) REVERT: AN 172 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7907 (mt-10) REVERT: AN 204 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: AO 83 THR cc_start: 0.9444 (m) cc_final: 0.9240 (p) REVERT: AO 267 MET cc_start: 0.7412 (mmm) cc_final: 0.7123 (mmm) REVERT: AP 136 ASP cc_start: 0.8496 (t0) cc_final: 0.8113 (t0) REVERT: AP 143 TYR cc_start: 0.8959 (m-80) cc_final: 0.8483 (m-80) REVERT: AP 204 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: AP 267 MET cc_start: 0.7677 (mmm) cc_final: 0.7372 (mmm) REVERT: AQ 99 LEU cc_start: 0.9341 (tp) cc_final: 0.8946 (mp) REVERT: AQ 146 LYS cc_start: 0.8800 (tptm) cc_final: 0.8577 (tptm) REVERT: AQ 172 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8117 (mm-30) REVERT: AQ 219 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8446 (mm110) REVERT: AR 99 LEU cc_start: 0.9284 (tp) cc_final: 0.9026 (mp) REVERT: AR 116 MET cc_start: 0.9054 (ttp) cc_final: 0.8780 (ttp) REVERT: AR 136 ASP cc_start: 0.8486 (t0) cc_final: 0.8050 (t0) REVERT: AR 172 GLU cc_start: 0.8258 (tp30) cc_final: 0.7876 (mm-30) REVERT: AS 99 LEU cc_start: 0.9284 (tt) cc_final: 0.9034 (mp) REVERT: AS 116 MET cc_start: 0.8939 (ttp) cc_final: 0.8459 (ptm) REVERT: AS 136 ASP cc_start: 0.8647 (t0) cc_final: 0.8285 (t0) REVERT: AS 204 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: AS 253 ASP cc_start: 0.8734 (m-30) cc_final: 0.8531 (m-30) REVERT: AT 136 ASP cc_start: 0.8539 (t0) cc_final: 0.8176 (t0) REVERT: AT 140 GLN cc_start: 0.8262 (mt0) cc_final: 0.7969 (mt0) REVERT: AT 173 MET cc_start: 0.8358 (tmm) cc_final: 0.8072 (tmm) REVERT: AT 204 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: AT 220 MET cc_start: 0.9079 (mtm) cc_final: 0.8747 (mtp) REVERT: AU 77 GLN cc_start: 0.7929 (tp40) cc_final: 0.7636 (tp40) REVERT: AU 94 TYR cc_start: 0.8950 (t80) cc_final: 0.8737 (t80) REVERT: AU 116 MET cc_start: 0.8629 (ttp) cc_final: 0.8322 (ttp) REVERT: AU 204 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: AV 173 MET cc_start: 0.8512 (tmm) cc_final: 0.8275 (tmm) REVERT: AV 204 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: AV 267 MET cc_start: 0.7758 (mmm) cc_final: 0.7513 (mmm) REVERT: AW 67 LEU cc_start: 0.7917 (mp) cc_final: 0.7630 (tt) REVERT: AW 99 LEU cc_start: 0.9297 (tp) cc_final: 0.9043 (mp) REVERT: AW 204 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: AW 267 MET cc_start: 0.7726 (mmm) cc_final: 0.7420 (mmm) REVERT: AX 72 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: AY 116 MET cc_start: 0.9118 (ttp) cc_final: 0.8890 (ttp) REVERT: AY 158 GLN cc_start: 0.9075 (mt0) cc_final: 0.8761 (mt0) REVERT: AY 204 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: AY 215 GLU cc_start: 0.8503 (tp30) cc_final: 0.8291 (tp30) REVERT: AZ 99 LEU cc_start: 0.9289 (tt) cc_final: 0.8909 (mp) REVERT: AZ 136 ASP cc_start: 0.8643 (t70) cc_final: 0.8055 (m-30) REVERT: BA 78 ILE cc_start: 0.9234 (tt) cc_final: 0.8929 (tt) REVERT: BA 136 ASP cc_start: 0.8573 (t0) cc_final: 0.8158 (m-30) REVERT: BA 146 LYS cc_start: 0.8318 (ttmt) cc_final: 0.8059 (tptm) REVERT: BA 204 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: BB 136 ASP cc_start: 0.8610 (t0) cc_final: 0.7908 (m-30) REVERT: BB 146 LYS cc_start: 0.8303 (ttmt) cc_final: 0.8059 (tptm) REVERT: BB 168 GLU cc_start: 0.8549 (tt0) cc_final: 0.8263 (tt0) REVERT: BB 173 MET cc_start: 0.8722 (tmm) cc_final: 0.8488 (ttp) REVERT: BB 180 TYR cc_start: 0.8711 (t80) cc_final: 0.8430 (t80) REVERT: BB 220 MET cc_start: 0.8958 (mtm) cc_final: 0.8642 (mtp) REVERT: BC 136 ASP cc_start: 0.8495 (t0) cc_final: 0.8142 (m-30) REVERT: BC 146 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8288 (tptm) REVERT: BC 150 GLU cc_start: 0.7340 (tt0) cc_final: 0.7112 (tt0) REVERT: BD 136 ASP cc_start: 0.8679 (t70) cc_final: 0.8224 (m-30) REVERT: BD 173 MET cc_start: 0.8701 (tmm) cc_final: 0.8433 (tmm) REVERT: BD 231 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.7371 (ppt170) REVERT: BD 244 GLU cc_start: 0.8036 (tt0) cc_final: 0.7826 (tt0) REVERT: BE 72 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: BE 116 MET cc_start: 0.9181 (ttp) cc_final: 0.8578 (ttp) REVERT: BE 136 ASP cc_start: 0.8517 (t70) cc_final: 0.8169 (m-30) REVERT: BE 180 TYR cc_start: 0.8578 (t80) cc_final: 0.8139 (t80) REVERT: BE 204 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: BF 94 TYR cc_start: 0.8892 (t80) cc_final: 0.8610 (t80) REVERT: BF 136 ASP cc_start: 0.8310 (t70) cc_final: 0.8008 (m-30) REVERT: BF 267 MET cc_start: 0.7544 (mmm) cc_final: 0.7282 (mmm) REVERT: BG 99 LEU cc_start: 0.9260 (tt) cc_final: 0.8999 (mp) REVERT: BG 134 MET cc_start: 0.8361 (tpp) cc_final: 0.8106 (ttt) REVERT: BG 136 ASP cc_start: 0.8382 (t70) cc_final: 0.8175 (m-30) REVERT: BG 160 MET cc_start: 0.8741 (mmm) cc_final: 0.8153 (mmm) REVERT: BG 204 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: BG 231 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7573 (ptt90) REVERT: BG 267 MET cc_start: 0.7688 (mmm) cc_final: 0.7488 (mmm) REVERT: BI 121 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8118 (tt0) REVERT: BI 143 TYR cc_start: 0.9049 (m-80) cc_final: 0.8703 (m-80) outliers start: 161 outliers final: 101 residues processed: 1441 average time/residue: 0.6575 time to fit residues: 1611.0920 Evaluate side-chains 1402 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1277 time to evaluate : 5.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 56 MET Chi-restraints excluded: chain AA residue 206 THR Chi-restraints excluded: chain AB residue 72 GLU Chi-restraints excluded: chain AB residue 88 SER Chi-restraints excluded: chain AB residue 206 THR Chi-restraints excluded: chain AB residue 252 GLU Chi-restraints excluded: chain AC residue 72 GLU Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 106 THR Chi-restraints excluded: chain AC residue 204 GLU Chi-restraints excluded: chain AC residue 206 THR Chi-restraints excluded: chain AD residue 56 MET Chi-restraints excluded: chain AD residue 67 LEU Chi-restraints excluded: chain AD residue 252 GLU Chi-restraints excluded: chain AE residue 88 SER Chi-restraints excluded: chain AE residue 206 THR Chi-restraints excluded: chain AF residue 88 SER Chi-restraints excluded: chain AF residue 204 GLU Chi-restraints excluded: chain AF residue 206 THR Chi-restraints excluded: chain AF residue 252 GLU Chi-restraints excluded: chain AG residue 88 SER Chi-restraints excluded: chain AG residue 204 GLU Chi-restraints excluded: chain AG residue 230 SER Chi-restraints excluded: chain AH residue 56 MET Chi-restraints excluded: chain AH residue 76 GLN Chi-restraints excluded: chain AH residue 88 SER Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 120 ILE Chi-restraints excluded: chain AH residue 145 LEU Chi-restraints excluded: chain AH residue 204 GLU Chi-restraints excluded: chain AH residue 206 THR Chi-restraints excluded: chain AI residue 145 LEU Chi-restraints excluded: chain AI residue 204 GLU Chi-restraints excluded: chain AI residue 206 THR Chi-restraints excluded: chain AJ residue 72 GLU Chi-restraints excluded: chain AJ residue 88 SER Chi-restraints excluded: chain AJ residue 106 THR Chi-restraints excluded: chain AJ residue 204 GLU Chi-restraints excluded: chain AJ residue 206 THR Chi-restraints excluded: chain AJ residue 260 THR Chi-restraints excluded: chain AK residue 56 MET Chi-restraints excluded: chain AK residue 88 SER Chi-restraints excluded: chain AK residue 204 GLU Chi-restraints excluded: chain AL residue 56 MET Chi-restraints excluded: chain AL residue 88 SER Chi-restraints excluded: chain AL residue 145 LEU Chi-restraints excluded: chain AL residue 204 GLU Chi-restraints excluded: chain AL residue 206 THR Chi-restraints excluded: chain AL residue 244 GLU Chi-restraints excluded: chain AM residue 88 SER Chi-restraints excluded: chain AM residue 135 MET Chi-restraints excluded: chain AM residue 194 SER Chi-restraints excluded: chain AM residue 204 GLU Chi-restraints excluded: chain AM residue 206 THR Chi-restraints excluded: chain AM residue 252 GLU Chi-restraints excluded: chain AN residue 88 SER Chi-restraints excluded: chain AN residue 204 GLU Chi-restraints excluded: chain AN residue 206 THR Chi-restraints excluded: chain AO residue 56 MET Chi-restraints excluded: chain AO residue 81 SER Chi-restraints excluded: chain AO residue 88 SER Chi-restraints excluded: chain AO residue 120 ILE Chi-restraints excluded: chain AO residue 252 GLU Chi-restraints excluded: chain AP residue 204 GLU Chi-restraints excluded: chain AP residue 206 THR Chi-restraints excluded: chain AQ residue 206 THR Chi-restraints excluded: chain AR residue 56 MET Chi-restraints excluded: chain AR residue 76 GLN Chi-restraints excluded: chain AR residue 88 SER Chi-restraints excluded: chain AR residue 206 THR Chi-restraints excluded: chain AS residue 88 SER Chi-restraints excluded: chain AS residue 204 GLU Chi-restraints excluded: chain AS residue 206 THR Chi-restraints excluded: chain AT residue 151 ASN Chi-restraints excluded: chain AT residue 204 GLU Chi-restraints excluded: chain AT residue 206 THR Chi-restraints excluded: chain AT residue 250 THR Chi-restraints excluded: chain AT residue 260 THR Chi-restraints excluded: chain AU residue 88 SER Chi-restraints excluded: chain AU residue 204 GLU Chi-restraints excluded: chain AU residue 206 THR Chi-restraints excluded: chain AU residue 260 THR Chi-restraints excluded: chain AV residue 56 MET Chi-restraints excluded: chain AV residue 101 TYR Chi-restraints excluded: chain AV residue 106 THR Chi-restraints excluded: chain AV residue 120 ILE Chi-restraints excluded: chain AV residue 204 GLU Chi-restraints excluded: chain AW residue 88 SER Chi-restraints excluded: chain AW residue 204 GLU Chi-restraints excluded: chain AW residue 206 THR Chi-restraints excluded: chain AX residue 72 GLU Chi-restraints excluded: chain AX residue 206 THR Chi-restraints excluded: chain AY residue 128 ILE Chi-restraints excluded: chain AY residue 204 GLU Chi-restraints excluded: chain AY residue 206 THR Chi-restraints excluded: chain AZ residue 88 SER Chi-restraints excluded: chain AZ residue 145 LEU Chi-restraints excluded: chain BA residue 88 SER Chi-restraints excluded: chain BA residue 204 GLU Chi-restraints excluded: chain BA residue 206 THR Chi-restraints excluded: chain BB residue 135 MET Chi-restraints excluded: chain BB residue 250 THR Chi-restraints excluded: chain BC residue 56 MET Chi-restraints excluded: chain BC residue 88 SER Chi-restraints excluded: chain BC residue 206 THR Chi-restraints excluded: chain BD residue 88 SER Chi-restraints excluded: chain BD residue 106 THR Chi-restraints excluded: chain BD residue 206 THR Chi-restraints excluded: chain BD residue 260 THR Chi-restraints excluded: chain BE residue 72 GLU Chi-restraints excluded: chain BE residue 88 SER Chi-restraints excluded: chain BE residue 204 GLU Chi-restraints excluded: chain BE residue 206 THR Chi-restraints excluded: chain BE residue 260 THR Chi-restraints excluded: chain BF residue 88 SER Chi-restraints excluded: chain BF residue 120 ILE Chi-restraints excluded: chain BF residue 206 THR Chi-restraints excluded: chain BG residue 56 MET Chi-restraints excluded: chain BG residue 88 SER Chi-restraints excluded: chain BG residue 204 GLU Chi-restraints excluded: chain BH residue 56 MET Chi-restraints excluded: chain BH residue 145 LEU Chi-restraints excluded: chain BH residue 206 THR Chi-restraints excluded: chain BI residue 88 SER Chi-restraints excluded: chain BI residue 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 675 optimal weight: 0.9990 chunk 711 optimal weight: 1.9990 chunk 648 optimal weight: 0.6980 chunk 691 optimal weight: 9.9990 chunk 710 optimal weight: 5.9990 chunk 416 optimal weight: 7.9990 chunk 301 optimal weight: 8.9990 chunk 543 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 624 optimal weight: 0.9980 chunk 654 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 76 GLN ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 229 GLN AH 76 GLN AI 98 GLN AJ 76 GLN AK 76 GLN ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 151 ASN AU 76 GLN AY 76 GLN BA 76 GLN ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 77 GLN BF 76 GLN BG 76 GLN ** BG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 67340 Z= 0.186 Angle : 0.611 12.023 91805 Z= 0.306 Chirality : 0.040 0.215 10360 Planarity : 0.004 0.048 11375 Dihedral : 10.739 59.502 11305 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.43 % Allowed : 19.93 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.10), residues: 7770 helix: 1.06 (0.10), residues: 3185 sheet: 0.29 (0.27), residues: 350 loop : -1.14 (0.10), residues: 4235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAW 132 HIS 0.006 0.001 HISAM 69 PHE 0.011 0.001 PHEAL 200 TYR 0.030 0.001 TYRAG 94 ARG 0.011 0.000 ARGAJ 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1494 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1329 time to evaluate : 5.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7867 (mm-40) REVERT: AA 231 ARG cc_start: 0.8119 (ttt90) cc_final: 0.7641 (tpm170) REVERT: AB 72 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: AB 82 ASN cc_start: 0.8897 (t0) cc_final: 0.8663 (t0) REVERT: AB 94 TYR cc_start: 0.8699 (t80) cc_final: 0.8315 (t80) REVERT: AB 231 ARG cc_start: 0.8036 (ttt90) cc_final: 0.7458 (tpm170) REVERT: AB 258 MET cc_start: 0.8030 (ttm) cc_final: 0.7698 (ttm) REVERT: AB 267 MET cc_start: 0.7635 (mmm) cc_final: 0.7407 (mmm) REVERT: AC 54 MET cc_start: 0.7275 (ppp) cc_final: 0.6676 (ppp) REVERT: AC 72 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: AC 99 LEU cc_start: 0.9233 (tp) cc_final: 0.9025 (mp) REVERT: AC 160 MET cc_start: 0.8594 (mtp) cc_final: 0.8268 (mtp) REVERT: AC 204 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: AC 231 ARG cc_start: 0.8088 (ttt90) cc_final: 0.7350 (mmp-170) REVERT: AD 136 ASP cc_start: 0.8423 (t0) cc_final: 0.8156 (t0) REVERT: AD 172 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7888 (mm-30) REVERT: AD 191 ARG cc_start: 0.8184 (mtt90) cc_final: 0.6539 (mpt180) REVERT: AD 220 MET cc_start: 0.8901 (mtm) cc_final: 0.8657 (mtm) REVERT: AD 231 ARG cc_start: 0.5577 (tpm170) cc_final: 0.4930 (tpm170) REVERT: AE 172 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8147 (mt-10) REVERT: AE 231 ARG cc_start: 0.8113 (ttt90) cc_final: 0.7524 (tpm170) REVERT: AE 267 MET cc_start: 0.7727 (mmm) cc_final: 0.7507 (mmm) REVERT: AF 135 MET cc_start: 0.9007 (mmm) cc_final: 0.8764 (mmm) REVERT: AF 170 TYR cc_start: 0.9060 (t80) cc_final: 0.8826 (t80) REVERT: AF 172 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8010 (mt-10) REVERT: AF 204 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: AF 219 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8550 (mm-40) REVERT: AF 231 ARG cc_start: 0.7976 (ttt90) cc_final: 0.7333 (tpm170) REVERT: AF 236 ASP cc_start: 0.8212 (p0) cc_final: 0.7762 (m-30) REVERT: AG 72 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: AG 94 TYR cc_start: 0.8628 (t80) cc_final: 0.8297 (t80) REVERT: AG 101 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8651 (m-10) REVERT: AG 116 MET cc_start: 0.8911 (ttp) cc_final: 0.8538 (ttp) REVERT: AG 121 GLU cc_start: 0.8309 (mm-30) cc_final: 0.6509 (mm-30) REVERT: AG 136 ASP cc_start: 0.8372 (t70) cc_final: 0.8098 (t0) REVERT: AG 143 TYR cc_start: 0.8822 (m-80) cc_final: 0.8565 (m-80) REVERT: AG 172 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8073 (mm-30) REVERT: AG 180 TYR cc_start: 0.8740 (t80) cc_final: 0.8182 (t80) REVERT: AG 204 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: AG 231 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7691 (tpm170) REVERT: AG 236 ASP cc_start: 0.8030 (p0) cc_final: 0.7550 (m-30) REVERT: AH 99 LEU cc_start: 0.9322 (tp) cc_final: 0.9035 (mp) REVERT: AH 204 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: AH 231 ARG cc_start: 0.8184 (ttt90) cc_final: 0.7463 (tpm170) REVERT: AH 267 MET cc_start: 0.7795 (mmm) cc_final: 0.7483 (mmm) REVERT: AI 134 MET cc_start: 0.8742 (ttt) cc_final: 0.8528 (ttt) REVERT: AI 136 ASP cc_start: 0.8369 (t0) cc_final: 0.7986 (t0) REVERT: AI 173 MET cc_start: 0.8583 (tmm) cc_final: 0.8360 (tmm) REVERT: AJ 136 ASP cc_start: 0.8545 (t0) cc_final: 0.8237 (t0) REVERT: AJ 204 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: AJ 219 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8434 (mm110) REVERT: AK 99 LEU cc_start: 0.9326 (tp) cc_final: 0.9016 (mp) REVERT: AK 134 MET cc_start: 0.8715 (ttt) cc_final: 0.8393 (ttt) REVERT: AK 136 ASP cc_start: 0.8496 (t0) cc_final: 0.8177 (t0) REVERT: AL 98 GLN cc_start: 0.8105 (tt0) cc_final: 0.7816 (tt0) REVERT: AL 99 LEU cc_start: 0.9246 (tp) cc_final: 0.8955 (mp) REVERT: AL 116 MET cc_start: 0.9036 (ttp) cc_final: 0.8785 (ttp) REVERT: AL 136 ASP cc_start: 0.8525 (t0) cc_final: 0.8071 (t0) REVERT: AL 204 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: AM 136 ASP cc_start: 0.8542 (t0) cc_final: 0.8220 (t0) REVERT: AM 204 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: AN 136 ASP cc_start: 0.8448 (t70) cc_final: 0.8146 (t0) REVERT: AO 83 THR cc_start: 0.9439 (m) cc_final: 0.9237 (p) REVERT: AO 170 TYR cc_start: 0.9292 (t80) cc_final: 0.8986 (t80) REVERT: AO 267 MET cc_start: 0.7419 (mmm) cc_final: 0.7085 (mmm) REVERT: AP 134 MET cc_start: 0.8730 (ttt) cc_final: 0.8440 (ttt) REVERT: AP 136 ASP cc_start: 0.8546 (t0) cc_final: 0.8131 (t0) REVERT: AP 143 TYR cc_start: 0.8953 (m-80) cc_final: 0.8515 (m-80) REVERT: AP 173 MET cc_start: 0.8668 (tmm) cc_final: 0.8407 (tmt) REVERT: AP 204 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: AP 267 MET cc_start: 0.7714 (mmm) cc_final: 0.7422 (mmm) REVERT: AQ 99 LEU cc_start: 0.9263 (tp) cc_final: 0.8991 (mp) REVERT: AQ 146 LYS cc_start: 0.8791 (tptm) cc_final: 0.8482 (tptm) REVERT: AQ 173 MET cc_start: 0.8427 (tmm) cc_final: 0.7912 (tmm) REVERT: AQ 219 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8437 (mm110) REVERT: AR 99 LEU cc_start: 0.9278 (tp) cc_final: 0.9024 (mp) REVERT: AR 116 MET cc_start: 0.9052 (ttp) cc_final: 0.8780 (ttp) REVERT: AR 136 ASP cc_start: 0.8490 (t0) cc_final: 0.8035 (t0) REVERT: AR 172 GLU cc_start: 0.8258 (tp30) cc_final: 0.7877 (mm-30) REVERT: AR 204 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: AS 99 LEU cc_start: 0.9261 (tt) cc_final: 0.8940 (mt) REVERT: AS 116 MET cc_start: 0.8925 (ttp) cc_final: 0.8460 (ptm) REVERT: AS 136 ASP cc_start: 0.8604 (t0) cc_final: 0.8241 (t0) REVERT: AS 204 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: AS 267 MET cc_start: 0.7761 (mmm) cc_final: 0.7525 (mmm) REVERT: AT 136 ASP cc_start: 0.8512 (t0) cc_final: 0.8148 (t0) REVERT: AT 204 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: AT 220 MET cc_start: 0.9056 (mtm) cc_final: 0.8734 (mtp) REVERT: AU 94 TYR cc_start: 0.8912 (t80) cc_final: 0.8696 (t80) REVERT: AU 116 MET cc_start: 0.8609 (ttp) cc_final: 0.8305 (ttp) REVERT: AU 204 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: AV 146 LYS cc_start: 0.8362 (tptm) cc_final: 0.8140 (tptm) REVERT: AV 173 MET cc_start: 0.8550 (tmm) cc_final: 0.8322 (tmm) REVERT: AV 204 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: AV 267 MET cc_start: 0.7789 (mmm) cc_final: 0.7553 (mmm) REVERT: AW 67 LEU cc_start: 0.7946 (mp) cc_final: 0.7697 (tt) REVERT: AW 204 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: AW 267 MET cc_start: 0.7764 (mmm) cc_final: 0.7525 (mmm) REVERT: AX 54 MET cc_start: 0.6675 (ptm) cc_final: 0.6429 (ppp) REVERT: AX 72 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: AX 99 LEU cc_start: 0.9366 (tp) cc_final: 0.8879 (mp) REVERT: AX 173 MET cc_start: 0.8373 (tmm) cc_final: 0.7981 (tmm) REVERT: AY 116 MET cc_start: 0.9096 (ttp) cc_final: 0.8884 (ttp) REVERT: AY 186 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8856 (mp) REVERT: AY 204 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: AZ 99 LEU cc_start: 0.9271 (tt) cc_final: 0.8891 (mt) REVERT: AZ 135 MET cc_start: 0.9083 (mmm) cc_final: 0.8773 (mmm) REVERT: AZ 136 ASP cc_start: 0.8648 (t70) cc_final: 0.8082 (m-30) REVERT: BA 78 ILE cc_start: 0.9205 (tt) cc_final: 0.8936 (tt) REVERT: BA 134 MET cc_start: 0.8636 (ttt) cc_final: 0.8338 (ttt) REVERT: BA 136 ASP cc_start: 0.8689 (t0) cc_final: 0.8215 (m-30) REVERT: BA 143 TYR cc_start: 0.9086 (m-80) cc_final: 0.8884 (m-80) REVERT: BA 146 LYS cc_start: 0.8269 (ttmt) cc_final: 0.8017 (tptm) REVERT: BA 204 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: BA 267 MET cc_start: 0.7702 (mmm) cc_final: 0.7441 (mmm) REVERT: BB 136 ASP cc_start: 0.8667 (t0) cc_final: 0.8018 (m-30) REVERT: BB 146 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7960 (tptm) REVERT: BB 168 GLU cc_start: 0.8477 (tt0) cc_final: 0.8191 (tt0) REVERT: BB 173 MET cc_start: 0.8711 (tmm) cc_final: 0.8490 (ttp) REVERT: BB 180 TYR cc_start: 0.8624 (t80) cc_final: 0.8317 (t80) REVERT: BC 136 ASP cc_start: 0.8526 (t0) cc_final: 0.8175 (m-30) REVERT: BC 146 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8277 (tptm) REVERT: BC 150 GLU cc_start: 0.7288 (tt0) cc_final: 0.7061 (tt0) REVERT: BC 170 TYR cc_start: 0.9116 (t80) cc_final: 0.8846 (t80) REVERT: BC 197 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7682 (ttp80) REVERT: BD 136 ASP cc_start: 0.8704 (t70) cc_final: 0.8307 (m-30) REVERT: BD 173 MET cc_start: 0.8756 (tmm) cc_final: 0.8516 (tmm) REVERT: BD 231 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7401 (ppt170) REVERT: BD 244 GLU cc_start: 0.8098 (tt0) cc_final: 0.7893 (tt0) REVERT: BE 72 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: BE 116 MET cc_start: 0.9126 (ttp) cc_final: 0.8542 (ttp) REVERT: BE 136 ASP cc_start: 0.8501 (t70) cc_final: 0.8172 (m-30) REVERT: BE 180 TYR cc_start: 0.8502 (t80) cc_final: 0.8153 (t80) REVERT: BE 204 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: BF 94 TYR cc_start: 0.8837 (t80) cc_final: 0.8589 (t80) REVERT: BF 136 ASP cc_start: 0.8290 (t70) cc_final: 0.8020 (m-30) REVERT: BF 267 MET cc_start: 0.7625 (mmm) cc_final: 0.7348 (mmm) REVERT: BG 94 TYR cc_start: 0.8632 (t80) cc_final: 0.8352 (t80) REVERT: BG 99 LEU cc_start: 0.9232 (tt) cc_final: 0.9003 (mp) REVERT: BG 134 MET cc_start: 0.8395 (tpp) cc_final: 0.7998 (ttt) REVERT: BG 160 MET cc_start: 0.8678 (mmm) cc_final: 0.8219 (mmm) REVERT: BG 204 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: BG 231 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7486 (ptt90) REVERT: BI 99 LEU cc_start: 0.9285 (tt) cc_final: 0.8898 (mp) REVERT: BI 121 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8119 (tt0) REVERT: BI 143 TYR cc_start: 0.9043 (m-80) cc_final: 0.8726 (m-80) outliers start: 165 outliers final: 108 residues processed: 1448 average time/residue: 0.6502 time to fit residues: 1566.2287 Evaluate side-chains 1413 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1280 time to evaluate : 5.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 56 MET Chi-restraints excluded: chain AA residue 145 LEU Chi-restraints excluded: chain AA residue 206 THR Chi-restraints excluded: chain AB residue 72 GLU Chi-restraints excluded: chain AB residue 88 SER Chi-restraints excluded: chain AB residue 206 THR Chi-restraints excluded: chain AB residue 252 GLU Chi-restraints excluded: chain AC residue 72 GLU Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 106 THR Chi-restraints excluded: chain AC residue 145 LEU Chi-restraints excluded: chain AC residue 204 GLU Chi-restraints excluded: chain AC residue 206 THR Chi-restraints excluded: chain AD residue 56 MET Chi-restraints excluded: chain AD residue 67 LEU Chi-restraints excluded: chain AD residue 145 LEU Chi-restraints excluded: chain AD residue 252 GLU Chi-restraints excluded: chain AE residue 206 THR Chi-restraints excluded: chain AF residue 88 SER Chi-restraints excluded: chain AF residue 204 GLU Chi-restraints excluded: chain AF residue 206 THR Chi-restraints excluded: chain AF residue 252 GLU Chi-restraints excluded: chain AG residue 72 GLU Chi-restraints excluded: chain AG residue 88 SER Chi-restraints excluded: chain AG residue 101 TYR Chi-restraints excluded: chain AG residue 204 GLU Chi-restraints excluded: chain AG residue 206 THR Chi-restraints excluded: chain AG residue 230 SER Chi-restraints excluded: chain AG residue 260 THR Chi-restraints excluded: chain AH residue 56 MET Chi-restraints excluded: chain AH residue 76 GLN Chi-restraints excluded: chain AH residue 88 SER Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 120 ILE Chi-restraints excluded: chain AH residue 145 LEU Chi-restraints excluded: chain AH residue 204 GLU Chi-restraints excluded: chain AH residue 206 THR Chi-restraints excluded: chain AH residue 252 GLU Chi-restraints excluded: chain AI residue 145 LEU Chi-restraints excluded: chain AI residue 206 THR Chi-restraints excluded: chain AJ residue 72 GLU Chi-restraints excluded: chain AJ residue 88 SER Chi-restraints excluded: chain AJ residue 106 THR Chi-restraints excluded: chain AJ residue 204 GLU Chi-restraints excluded: chain AJ residue 206 THR Chi-restraints excluded: chain AJ residue 260 THR Chi-restraints excluded: chain AK residue 56 MET Chi-restraints excluded: chain AK residue 88 SER Chi-restraints excluded: chain AL residue 56 MET Chi-restraints excluded: chain AL residue 88 SER Chi-restraints excluded: chain AL residue 204 GLU Chi-restraints excluded: chain AL residue 206 THR Chi-restraints excluded: chain AL residue 244 GLU Chi-restraints excluded: chain AM residue 88 SER Chi-restraints excluded: chain AM residue 135 MET Chi-restraints excluded: chain AM residue 194 SER Chi-restraints excluded: chain AM residue 204 GLU Chi-restraints excluded: chain AM residue 206 THR Chi-restraints excluded: chain AM residue 252 GLU Chi-restraints excluded: chain AN residue 88 SER Chi-restraints excluded: chain AN residue 206 THR Chi-restraints excluded: chain AO residue 81 SER Chi-restraints excluded: chain AO residue 88 SER Chi-restraints excluded: chain AO residue 120 ILE Chi-restraints excluded: chain AO residue 159 ILE Chi-restraints excluded: chain AO residue 206 THR Chi-restraints excluded: chain AO residue 252 GLU Chi-restraints excluded: chain AP residue 204 GLU Chi-restraints excluded: chain AP residue 206 THR Chi-restraints excluded: chain AQ residue 206 THR Chi-restraints excluded: chain AR residue 56 MET Chi-restraints excluded: chain AR residue 88 SER Chi-restraints excluded: chain AR residue 204 GLU Chi-restraints excluded: chain AR residue 206 THR Chi-restraints excluded: chain AS residue 88 SER Chi-restraints excluded: chain AS residue 204 GLU Chi-restraints excluded: chain AS residue 206 THR Chi-restraints excluded: chain AT residue 88 SER Chi-restraints excluded: chain AT residue 145 LEU Chi-restraints excluded: chain AT residue 204 GLU Chi-restraints excluded: chain AT residue 206 THR Chi-restraints excluded: chain AT residue 250 THR Chi-restraints excluded: chain AT residue 252 GLU Chi-restraints excluded: chain AT residue 260 THR Chi-restraints excluded: chain AU residue 88 SER Chi-restraints excluded: chain AU residue 204 GLU Chi-restraints excluded: chain AU residue 206 THR Chi-restraints excluded: chain AU residue 260 THR Chi-restraints excluded: chain AV residue 54 MET Chi-restraints excluded: chain AV residue 101 TYR Chi-restraints excluded: chain AV residue 106 THR Chi-restraints excluded: chain AV residue 120 ILE Chi-restraints excluded: chain AV residue 204 GLU Chi-restraints excluded: chain AW residue 88 SER Chi-restraints excluded: chain AW residue 204 GLU Chi-restraints excluded: chain AW residue 206 THR Chi-restraints excluded: chain AX residue 72 GLU Chi-restraints excluded: chain AX residue 206 THR Chi-restraints excluded: chain AY residue 186 LEU Chi-restraints excluded: chain AY residue 204 GLU Chi-restraints excluded: chain AY residue 206 THR Chi-restraints excluded: chain BA residue 88 SER Chi-restraints excluded: chain BA residue 145 LEU Chi-restraints excluded: chain BA residue 204 GLU Chi-restraints excluded: chain BA residue 206 THR Chi-restraints excluded: chain BB residue 135 MET Chi-restraints excluded: chain BB residue 250 THR Chi-restraints excluded: chain BC residue 56 MET Chi-restraints excluded: chain BC residue 88 SER Chi-restraints excluded: chain BC residue 206 THR Chi-restraints excluded: chain BD residue 88 SER Chi-restraints excluded: chain BD residue 106 THR Chi-restraints excluded: chain BD residue 206 THR Chi-restraints excluded: chain BD residue 260 THR Chi-restraints excluded: chain BE residue 72 GLU Chi-restraints excluded: chain BE residue 88 SER Chi-restraints excluded: chain BE residue 204 GLU Chi-restraints excluded: chain BE residue 206 THR Chi-restraints excluded: chain BE residue 250 THR Chi-restraints excluded: chain BE residue 260 THR Chi-restraints excluded: chain BF residue 88 SER Chi-restraints excluded: chain BF residue 120 ILE Chi-restraints excluded: chain BF residue 206 THR Chi-restraints excluded: chain BG residue 56 MET Chi-restraints excluded: chain BG residue 88 SER Chi-restraints excluded: chain BG residue 204 GLU Chi-restraints excluded: chain BG residue 260 THR Chi-restraints excluded: chain BH residue 56 MET Chi-restraints excluded: chain BH residue 145 LEU Chi-restraints excluded: chain BH residue 206 THR Chi-restraints excluded: chain BI residue 71 LEU Chi-restraints excluded: chain BI residue 88 SER Chi-restraints excluded: chain BI residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 689 optimal weight: 4.9990 chunk 454 optimal weight: 6.9990 chunk 731 optimal weight: 0.8980 chunk 446 optimal weight: 0.9980 chunk 346 optimal weight: 0.0980 chunk 508 optimal weight: 9.9990 chunk 767 optimal weight: 8.9990 chunk 706 optimal weight: 20.0000 chunk 610 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 471 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 76 GLN ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 229 GLN AH 76 GLN AH 229 GLN AI 98 GLN AK 76 GLN ** AL 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 76 GLN ** AT 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 76 GLN AY 76 GLN AY 158 GLN ** BB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 77 GLN BF 76 GLN ** BG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 76 GLN ** BH 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 67340 Z= 0.180 Angle : 0.617 13.709 91805 Z= 0.309 Chirality : 0.040 0.211 10360 Planarity : 0.004 0.063 11375 Dihedral : 10.712 59.369 11305 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.00 % Allowed : 20.80 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.10), residues: 7770 helix: 0.93 (0.09), residues: 3220 sheet: 0.28 (0.26), residues: 350 loop : -1.12 (0.10), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAK 132 HIS 0.005 0.001 HISAD 162 PHE 0.012 0.001 PHEAJ 200 TYR 0.032 0.001 TYRAG 94 ARG 0.010 0.000 ARGBE 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1337 time to evaluate : 5.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7811 (mm-40) REVERT: AA 108 MET cc_start: 0.7487 (ttm) cc_final: 0.7221 (ppp) REVERT: AA 231 ARG cc_start: 0.8118 (ttt90) cc_final: 0.7670 (tpm170) REVERT: AB 82 ASN cc_start: 0.8836 (t0) cc_final: 0.8591 (t0) REVERT: AB 94 TYR cc_start: 0.8672 (t80) cc_final: 0.8293 (t80) REVERT: AB 204 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: AB 231 ARG cc_start: 0.8040 (ttt90) cc_final: 0.7564 (tpm170) REVERT: AB 258 MET cc_start: 0.8065 (ttm) cc_final: 0.7736 (ttm) REVERT: AC 54 MET cc_start: 0.7223 (ppp) cc_final: 0.6603 (ppp) REVERT: AC 72 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: AC 94 TYR cc_start: 0.8607 (t80) cc_final: 0.8383 (t80) REVERT: AC 204 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: AC 231 ARG cc_start: 0.8091 (ttt90) cc_final: 0.7345 (mmp-170) REVERT: AD 94 TYR cc_start: 0.8817 (t80) cc_final: 0.8464 (t80) REVERT: AD 136 ASP cc_start: 0.8425 (t0) cc_final: 0.8162 (t0) REVERT: AD 191 ARG cc_start: 0.8160 (mtt90) cc_final: 0.6528 (mpt180) REVERT: AD 220 MET cc_start: 0.8887 (mtm) cc_final: 0.8661 (mtm) REVERT: AD 231 ARG cc_start: 0.5565 (tpm170) cc_final: 0.4935 (tpm170) REVERT: AE 172 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8128 (mt-10) REVERT: AE 231 ARG cc_start: 0.8085 (ttt90) cc_final: 0.7509 (tpm170) REVERT: AE 267 MET cc_start: 0.7694 (mmm) cc_final: 0.7476 (mmm) REVERT: AF 135 MET cc_start: 0.8996 (mmm) cc_final: 0.8738 (mmm) REVERT: AF 204 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: AF 219 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8560 (mm-40) REVERT: AF 231 ARG cc_start: 0.7987 (ttt90) cc_final: 0.7343 (tpm170) REVERT: AF 236 ASP cc_start: 0.8190 (p0) cc_final: 0.7789 (m-30) REVERT: AG 72 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: AG 94 TYR cc_start: 0.8565 (t80) cc_final: 0.7068 (t80) REVERT: AG 101 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8693 (m-10) REVERT: AG 108 MET cc_start: 0.7812 (ttp) cc_final: 0.7609 (tmm) REVERT: AG 116 MET cc_start: 0.8852 (ttp) cc_final: 0.8424 (ttp) REVERT: AG 136 ASP cc_start: 0.8353 (t70) cc_final: 0.8059 (t0) REVERT: AG 204 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: AG 231 ARG cc_start: 0.8062 (ttt90) cc_final: 0.7662 (tpm170) REVERT: AG 236 ASP cc_start: 0.7968 (p0) cc_final: 0.7600 (m-30) REVERT: AH 99 LEU cc_start: 0.9305 (tp) cc_final: 0.9051 (mp) REVERT: AH 204 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: AH 229 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8113 (tp40) REVERT: AH 231 ARG cc_start: 0.8191 (ttt90) cc_final: 0.7466 (tpm170) REVERT: AH 267 MET cc_start: 0.7809 (mmm) cc_final: 0.7400 (mmt) REVERT: AI 108 MET cc_start: 0.8025 (ttm) cc_final: 0.7740 (tpp) REVERT: AI 134 MET cc_start: 0.8702 (ttt) cc_final: 0.8496 (ttt) REVERT: AI 136 ASP cc_start: 0.8390 (t0) cc_final: 0.8029 (t0) REVERT: AI 146 LYS cc_start: 0.8506 (tptm) cc_final: 0.8096 (tptm) REVERT: AI 173 MET cc_start: 0.8577 (tmm) cc_final: 0.8323 (tmm) REVERT: AJ 136 ASP cc_start: 0.8540 (t0) cc_final: 0.8245 (t0) REVERT: AJ 176 LYS cc_start: 0.8668 (tppt) cc_final: 0.8334 (mptt) REVERT: AJ 204 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: AJ 219 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8498 (mm110) REVERT: AK 99 LEU cc_start: 0.9314 (tp) cc_final: 0.9102 (mp) REVERT: AK 134 MET cc_start: 0.8695 (ttt) cc_final: 0.8364 (ttt) REVERT: AK 136 ASP cc_start: 0.8479 (t0) cc_final: 0.8183 (t0) REVERT: AK 172 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7696 (mt-10) REVERT: AL 99 LEU cc_start: 0.9287 (tp) cc_final: 0.8968 (mp) REVERT: AL 116 MET cc_start: 0.9037 (ttp) cc_final: 0.8768 (ttp) REVERT: AL 136 ASP cc_start: 0.8511 (t0) cc_final: 0.8060 (t0) REVERT: AL 204 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: AM 136 ASP cc_start: 0.8536 (t0) cc_final: 0.8227 (t0) REVERT: AM 172 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8198 (mm-30) REVERT: AM 204 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: AN 136 ASP cc_start: 0.8410 (t70) cc_final: 0.8122 (t0) REVERT: AO 170 TYR cc_start: 0.9290 (t80) cc_final: 0.8987 (t80) REVERT: AO 267 MET cc_start: 0.7414 (mmm) cc_final: 0.7072 (mmm) REVERT: AP 134 MET cc_start: 0.8755 (ttt) cc_final: 0.8509 (ttt) REVERT: AP 136 ASP cc_start: 0.8481 (t0) cc_final: 0.7975 (t0) REVERT: AP 143 TYR cc_start: 0.8962 (m-80) cc_final: 0.8535 (m-80) REVERT: AP 146 LYS cc_start: 0.8575 (tptm) cc_final: 0.8332 (tptm) REVERT: AP 173 MET cc_start: 0.8689 (tmm) cc_final: 0.8438 (tmt) REVERT: AP 204 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: AP 267 MET cc_start: 0.7708 (mmm) cc_final: 0.7402 (mmm) REVERT: AQ 146 LYS cc_start: 0.8804 (tptm) cc_final: 0.8501 (tptm) REVERT: AQ 173 MET cc_start: 0.8383 (tmm) cc_final: 0.7864 (tmm) REVERT: AQ 219 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8414 (mm110) REVERT: AR 99 LEU cc_start: 0.9291 (tp) cc_final: 0.9036 (mp) REVERT: AR 116 MET cc_start: 0.9049 (ttp) cc_final: 0.8789 (ttp) REVERT: AR 136 ASP cc_start: 0.8536 (t0) cc_final: 0.8079 (t0) REVERT: AR 158 GLN cc_start: 0.8919 (mt0) cc_final: 0.8385 (mt0) REVERT: AR 204 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: AS 99 LEU cc_start: 0.9231 (tt) cc_final: 0.8944 (mt) REVERT: AS 108 MET cc_start: 0.7761 (ppp) cc_final: 0.7390 (ppp) REVERT: AS 116 MET cc_start: 0.8913 (ttp) cc_final: 0.8475 (ptm) REVERT: AS 136 ASP cc_start: 0.8586 (t0) cc_final: 0.8217 (t0) REVERT: AS 204 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: AS 267 MET cc_start: 0.7774 (mmm) cc_final: 0.7509 (mmm) REVERT: AT 136 ASP cc_start: 0.8520 (t0) cc_final: 0.8117 (t0) REVERT: AT 204 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: AU 94 TYR cc_start: 0.8851 (t80) cc_final: 0.8602 (t80) REVERT: AU 116 MET cc_start: 0.8598 (ttp) cc_final: 0.8359 (ttp) REVERT: AU 136 ASP cc_start: 0.8488 (t0) cc_final: 0.8205 (t0) REVERT: AU 173 MET cc_start: 0.8395 (ttp) cc_final: 0.7778 (tmm) REVERT: AU 204 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: AV 173 MET cc_start: 0.8554 (tmm) cc_final: 0.8326 (tmm) REVERT: AV 180 TYR cc_start: 0.8736 (t80) cc_final: 0.8399 (t80) REVERT: AV 215 GLU cc_start: 0.8290 (tp30) cc_final: 0.8088 (tp30) REVERT: AV 267 MET cc_start: 0.7784 (mmm) cc_final: 0.7561 (mmm) REVERT: AW 204 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: AW 267 MET cc_start: 0.7759 (mmm) cc_final: 0.7551 (mmm) REVERT: AX 72 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: AX 173 MET cc_start: 0.8413 (tmm) cc_final: 0.8057 (tmm) REVERT: AY 94 TYR cc_start: 0.8420 (t80) cc_final: 0.8008 (t80) REVERT: AY 186 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8798 (mp) REVERT: AZ 99 LEU cc_start: 0.9307 (tt) cc_final: 0.9010 (mt) REVERT: AZ 136 ASP cc_start: 0.8654 (t70) cc_final: 0.8074 (m-30) REVERT: BA 78 ILE cc_start: 0.9158 (tt) cc_final: 0.8871 (tt) REVERT: BA 136 ASP cc_start: 0.8696 (t0) cc_final: 0.8241 (m-30) REVERT: BA 146 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7987 (tptm) REVERT: BA 172 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8143 (mm-30) REVERT: BA 204 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: BA 267 MET cc_start: 0.7697 (mmm) cc_final: 0.7429 (mmm) REVERT: BB 94 TYR cc_start: 0.8578 (t80) cc_final: 0.8299 (t80) REVERT: BB 136 ASP cc_start: 0.8683 (t0) cc_final: 0.8034 (m-30) REVERT: BB 146 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7936 (tptm) REVERT: BB 168 GLU cc_start: 0.8405 (tt0) cc_final: 0.8076 (tt0) REVERT: BB 173 MET cc_start: 0.8707 (tmm) cc_final: 0.8472 (ttp) REVERT: BB 180 TYR cc_start: 0.8616 (t80) cc_final: 0.8342 (t80) REVERT: BB 220 MET cc_start: 0.8954 (mtm) cc_final: 0.8717 (mtt) REVERT: BC 136 ASP cc_start: 0.8548 (t0) cc_final: 0.8219 (m-30) REVERT: BC 146 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8243 (tptm) REVERT: BC 170 TYR cc_start: 0.9124 (t80) cc_final: 0.8865 (t80) REVERT: BC 204 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: BD 136 ASP cc_start: 0.8673 (t70) cc_final: 0.8314 (m-30) REVERT: BD 173 MET cc_start: 0.8757 (tmm) cc_final: 0.8516 (tmm) REVERT: BD 231 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7397 (ppt170) REVERT: BE 99 LEU cc_start: 0.9215 (tp) cc_final: 0.8889 (mp) REVERT: BE 116 MET cc_start: 0.9098 (ttp) cc_final: 0.8567 (ttp) REVERT: BE 136 ASP cc_start: 0.8513 (t70) cc_final: 0.8199 (m-30) REVERT: BE 180 TYR cc_start: 0.8511 (t80) cc_final: 0.8177 (t80) REVERT: BE 204 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: BF 82 ASN cc_start: 0.8737 (t0) cc_final: 0.8439 (t0) REVERT: BF 99 LEU cc_start: 0.9353 (tp) cc_final: 0.8993 (mp) REVERT: BF 136 ASP cc_start: 0.8277 (t70) cc_final: 0.8016 (m-30) REVERT: BF 173 MET cc_start: 0.8224 (tmm) cc_final: 0.7745 (tmm) REVERT: BF 267 MET cc_start: 0.7550 (mmm) cc_final: 0.7277 (mmm) REVERT: BG 112 MET cc_start: 0.8724 (mmp) cc_final: 0.8471 (mpp) REVERT: BG 134 MET cc_start: 0.8418 (tpp) cc_final: 0.7944 (ttt) REVERT: BG 160 MET cc_start: 0.8661 (mmm) cc_final: 0.8214 (mmm) REVERT: BG 204 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: BG 231 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7479 (ptt90) REVERT: BH 116 MET cc_start: 0.9150 (ttp) cc_final: 0.8436 (ttp) REVERT: BI 87 GLN cc_start: 0.8855 (tp40) cc_final: 0.8508 (mm-40) REVERT: BI 99 LEU cc_start: 0.9315 (tt) cc_final: 0.8940 (mp) REVERT: BI 121 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8127 (tt0) REVERT: BI 143 TYR cc_start: 0.9067 (m-80) cc_final: 0.8718 (m-80) outliers start: 136 outliers final: 92 residues processed: 1432 average time/residue: 0.6531 time to fit residues: 1558.1794 Evaluate side-chains 1407 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1292 time to evaluate : 5.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 56 MET Chi-restraints excluded: chain AA residue 145 LEU Chi-restraints excluded: chain AA residue 206 THR Chi-restraints excluded: chain AB residue 76 GLN Chi-restraints excluded: chain AB residue 88 SER Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain AB residue 206 THR Chi-restraints excluded: chain AB residue 252 GLU Chi-restraints excluded: chain AC residue 72 GLU Chi-restraints excluded: chain AC residue 88 SER Chi-restraints excluded: chain AC residue 106 THR Chi-restraints excluded: chain AC residue 204 GLU Chi-restraints excluded: chain AC residue 206 THR Chi-restraints excluded: chain AD residue 56 MET Chi-restraints excluded: chain AD residue 67 LEU Chi-restraints excluded: chain AD residue 145 LEU Chi-restraints excluded: chain AD residue 252 GLU Chi-restraints excluded: chain AE residue 88 SER Chi-restraints excluded: chain AE residue 206 THR Chi-restraints excluded: chain AF residue 204 GLU Chi-restraints excluded: chain AF residue 206 THR Chi-restraints excluded: chain AF residue 252 GLU Chi-restraints excluded: chain AG residue 72 GLU Chi-restraints excluded: chain AG residue 88 SER Chi-restraints excluded: chain AG residue 101 TYR Chi-restraints excluded: chain AG residue 204 GLU Chi-restraints excluded: chain AG residue 206 THR Chi-restraints excluded: chain AG residue 260 THR Chi-restraints excluded: chain AH residue 56 MET Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 204 GLU Chi-restraints excluded: chain AH residue 206 THR Chi-restraints excluded: chain AI residue 206 THR Chi-restraints excluded: chain AI residue 260 THR Chi-restraints excluded: chain AJ residue 72 GLU Chi-restraints excluded: chain AJ residue 106 THR Chi-restraints excluded: chain AJ residue 204 GLU Chi-restraints excluded: chain AJ residue 206 THR Chi-restraints excluded: chain AJ residue 260 THR Chi-restraints excluded: chain AL residue 88 SER Chi-restraints excluded: chain AL residue 145 LEU Chi-restraints excluded: chain AL residue 204 GLU Chi-restraints excluded: chain AL residue 206 THR Chi-restraints excluded: chain AM residue 88 SER Chi-restraints excluded: chain AM residue 135 MET Chi-restraints excluded: chain AM residue 194 SER Chi-restraints excluded: chain AM residue 204 GLU Chi-restraints excluded: chain AM residue 206 THR Chi-restraints excluded: chain AM residue 252 GLU Chi-restraints excluded: chain AN residue 206 THR Chi-restraints excluded: chain AO residue 120 ILE Chi-restraints excluded: chain AO residue 206 THR Chi-restraints excluded: chain AO residue 252 GLU Chi-restraints excluded: chain AP residue 204 GLU Chi-restraints excluded: chain AP residue 206 THR Chi-restraints excluded: chain AQ residue 206 THR Chi-restraints excluded: chain AR residue 56 MET Chi-restraints excluded: chain AR residue 76 GLN Chi-restraints excluded: chain AR residue 88 SER Chi-restraints excluded: chain AR residue 204 GLU Chi-restraints excluded: chain AR residue 206 THR Chi-restraints excluded: chain AS residue 88 SER Chi-restraints excluded: chain AS residue 204 GLU Chi-restraints excluded: chain AS residue 206 THR Chi-restraints excluded: chain AT residue 204 GLU Chi-restraints excluded: chain AT residue 206 THR Chi-restraints excluded: chain AT residue 252 GLU Chi-restraints excluded: chain AT residue 260 THR Chi-restraints excluded: chain AU residue 88 SER Chi-restraints excluded: chain AU residue 204 GLU Chi-restraints excluded: chain AU residue 206 THR Chi-restraints excluded: chain AU residue 260 THR Chi-restraints excluded: chain AV residue 54 MET Chi-restraints excluded: chain AV residue 101 TYR Chi-restraints excluded: chain AV residue 120 ILE Chi-restraints excluded: chain AW residue 88 SER Chi-restraints excluded: chain AW residue 204 GLU Chi-restraints excluded: chain AW residue 206 THR Chi-restraints excluded: chain AX residue 67 LEU Chi-restraints excluded: chain AX residue 72 GLU Chi-restraints excluded: chain AX residue 206 THR Chi-restraints excluded: chain AY residue 186 LEU Chi-restraints excluded: chain AY residue 206 THR Chi-restraints excluded: chain AZ residue 108 MET Chi-restraints excluded: chain AZ residue 145 LEU Chi-restraints excluded: chain BA residue 88 SER Chi-restraints excluded: chain BA residue 204 GLU Chi-restraints excluded: chain BA residue 206 THR Chi-restraints excluded: chain BB residue 135 MET Chi-restraints excluded: chain BB residue 250 THR Chi-restraints excluded: chain BC residue 56 MET Chi-restraints excluded: chain BC residue 88 SER Chi-restraints excluded: chain BC residue 159 ILE Chi-restraints excluded: chain BC residue 204 GLU Chi-restraints excluded: chain BC residue 206 THR Chi-restraints excluded: chain BD residue 88 SER Chi-restraints excluded: chain BD residue 206 THR Chi-restraints excluded: chain BD residue 260 THR Chi-restraints excluded: chain BE residue 88 SER Chi-restraints excluded: chain BE residue 204 GLU Chi-restraints excluded: chain BE residue 206 THR Chi-restraints excluded: chain BE residue 250 THR Chi-restraints excluded: chain BE residue 260 THR Chi-restraints excluded: chain BF residue 88 SER Chi-restraints excluded: chain BF residue 120 ILE Chi-restraints excluded: chain BF residue 206 THR Chi-restraints excluded: chain BG residue 56 MET Chi-restraints excluded: chain BG residue 88 SER Chi-restraints excluded: chain BG residue 108 MET Chi-restraints excluded: chain BG residue 204 GLU Chi-restraints excluded: chain BG residue 260 THR Chi-restraints excluded: chain BH residue 56 MET Chi-restraints excluded: chain BH residue 145 LEU Chi-restraints excluded: chain BH residue 206 THR Chi-restraints excluded: chain BI residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 374 optimal weight: 1.9990 chunk 485 optimal weight: 20.0000 chunk 650 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 563 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 611 optimal weight: 0.9980 chunk 256 optimal weight: 7.9990 chunk 628 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 229 GLN ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 229 GLN AH 76 GLN AK 76 GLN ** AL 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 76 GLN ** AR 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 76 GLN ** AW 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 76 GLN AZ 76 GLN ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 76 GLN ** BG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098320 restraints weight = 111350.461| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.55 r_work: 0.3254 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 67340 Z= 0.192 Angle : 0.624 14.451 91805 Z= 0.314 Chirality : 0.041 0.231 10360 Planarity : 0.004 0.057 11375 Dihedral : 10.719 59.470 11305 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.27 % Allowed : 21.06 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.10), residues: 7770 helix: 0.86 (0.09), residues: 3220 sheet: 0.36 (0.26), residues: 350 loop : -1.11 (0.10), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAY 132 HIS 0.005 0.001 HISAP 69 PHE 0.011 0.001 PHEAQ 200 TYR 0.034 0.001 TYRBC 198 ARG 0.008 0.000 ARGBE 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23314.76 seconds wall clock time: 398 minutes 59.58 seconds (23939.58 seconds total)