Starting phenix.real_space_refine on Wed Nov 20 01:30:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgh_43200/11_2024/8vgh_43200.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgh_43200/11_2024/8vgh_43200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgh_43200/11_2024/8vgh_43200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgh_43200/11_2024/8vgh_43200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgh_43200/11_2024/8vgh_43200.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgh_43200/11_2024/8vgh_43200.cif" } resolution = 2.9 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= -0.011 sd= 0.279 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 12988 2.51 5 N 3488 2.21 5 O 3912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20472 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "B" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "C" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "D" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "G" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1573 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Chain: "F" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1573 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Chain: "J" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1573 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1573 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "I" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Time building chain proxies: 11.36, per 1000 atoms: 0.55 Number of scatterers: 20472 At special positions: 0 Unit cell: (97, 111, 181, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3912 8.00 N 3488 7.00 C 12988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.02 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 58 " distance=2.02 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 182 " distance=2.02 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 58 " distance=2.02 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 182 " distance=2.02 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 58 " distance=2.02 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 182 " distance=2.02 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 200 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 144 " - pdb=" SG CYS K 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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: 5.32 Conformation dependent library (CDL) restraints added in 2.8 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 56 sheets defined 9.9% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 60E through 62 No H-bonds generated for 'chain 'A' and resid 60E through 62' Processing helix chain 'A' and resid 164 through 173A Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 60E through 62 No H-bonds generated for 'chain 'B' and resid 60E through 62' Processing helix chain 'B' and resid 164 through 173A Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 60E through 62 No H-bonds generated for 'chain 'C' and resid 60E through 62' Processing helix chain 'C' and resid 164 through 173A Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 60E through 62 No H-bonds generated for 'chain 'D' and resid 60E through 62' Processing helix chain 'D' and resid 164 through 173A Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.927A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 183 through 187 Processing helix chain 'H' and resid 62 through 65 removed outlier: 4.079A pdb=" N SER H 65 " --> pdb=" O TRP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 189 through 195 removed outlier: 3.546A pdb=" N GLY H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 208 Processing helix chain 'F' and resid 62 through 65 removed outlier: 4.077A pdb=" N SER F 65 " --> pdb=" O TRP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 189 through 195 removed outlier: 3.545A pdb=" N GLY F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 208 Processing helix chain 'J' and resid 62 through 65 removed outlier: 4.078A pdb=" N SER J 65 " --> pdb=" O TRP J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 189 through 195 removed outlier: 3.545A pdb=" N GLY J 194 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 208 Processing helix chain 'K' and resid 62 through 65 removed outlier: 4.080A pdb=" N SER K 65 " --> pdb=" O TRP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 189 through 195 removed outlier: 3.543A pdb=" N GLY K 194 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 208 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.926A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.926A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.926A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 35 removed outlier: 3.755A pdb=" N CYS A 42 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL A 35 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N HIS A 40 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL A 85 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 64 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160 removed outlier: 4.123A pdb=" N CYS A 136 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 199 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 213 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR A 230 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS A 182 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 30 through 35 removed outlier: 3.751A pdb=" N CYS B 42 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL B 35 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N HIS B 40 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL B 85 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU B 64 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 160 removed outlier: 4.121A pdb=" N CYS B 136 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 139 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 199 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 213 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR B 229 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS B 182 " --> pdb=" O MET B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 35 removed outlier: 3.760A pdb=" N CYS C 42 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL C 35 " --> pdb=" O HIS C 40 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N HIS C 40 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL C 85 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU C 64 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 156 through 160 removed outlier: 4.126A pdb=" N CYS C 136 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR C 139 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU C 199 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL C 213 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N THR C 229 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS C 182 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 35 removed outlier: 3.754A pdb=" N CYS D 42 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL D 35 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N HIS D 40 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP D 51 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL D 85 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU D 64 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 156 through 160 removed outlier: 4.122A pdb=" N CYS D 136 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR D 139 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU D 199 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL D 213 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N THR D 229 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS D 182 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.687A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS G 107 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA G 13 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.687A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS G 107 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA G 13 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 114 through 118 removed outlier: 5.077A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AB5, first strand: chain 'G' and resid 153 through 155 removed outlier: 4.678A pdb=" N TRP G 148 " --> pdb=" O GLN G 155 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 196 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL G 205 " --> pdb=" O VAL G 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.839A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.910A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.722A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.722A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER H 181 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 173 " --> pdb=" O SER H 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.839A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.910A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 124 through 128 removed outlier: 5.722A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 124 through 128 removed outlier: 5.722A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER F 181 " --> pdb=" O VAL F 173 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL F 173 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 155 through 158 Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.838A pdb=" N ALA J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.911A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 124 through 128 removed outlier: 5.725A pdb=" N TYR J 180 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 124 through 128 removed outlier: 5.725A pdb=" N TYR J 180 " --> pdb=" O ASP J 148 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER J 181 " --> pdb=" O VAL J 173 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL J 173 " --> pdb=" O SER J 181 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 155 through 158 Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.839A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.912A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 124 through 128 removed outlier: 5.724A pdb=" N TYR K 180 " --> pdb=" O ASP K 148 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 124 through 128 removed outlier: 5.724A pdb=" N TYR K 180 " --> pdb=" O ASP K 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 181 " --> pdb=" O VAL K 173 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL K 173 " --> pdb=" O SER K 181 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 155 through 158 Processing sheet with id=AE3, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.688A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS E 107 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.688A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS E 107 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.078A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AE8, first strand: chain 'E' and resid 153 through 155 removed outlier: 4.678A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 196 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL E 205 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.687A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS I 107 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA I 13 " --> pdb=" O LYS I 107 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.687A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS I 107 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA I 13 " --> pdb=" O LYS I 107 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 114 through 118 removed outlier: 5.076A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AF5, first strand: chain 'I' and resid 153 through 155 removed outlier: 4.677A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL I 196 " --> pdb=" O VAL I 205 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL I 205 " --> pdb=" O VAL I 196 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.686A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.686A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.078A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 129 through 130 Processing sheet with id=AG2, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.678A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.13 Time building geometry restraints manager: 6.17 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: 6575 1.34 - 1.46: 5142 1.46 - 1.58: 9195 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 21016 Sorted by residual: bond pdb=" CB TRP D 29 " pdb=" CG TRP D 29 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.51e+00 bond pdb=" CB TRP B 29 " pdb=" CG TRP B 29 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.46e+00 bond pdb=" CB TRP A 29 " pdb=" CG TRP A 29 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.43e+00 bond pdb=" CB TRP C 29 " pdb=" CG TRP C 29 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.40e+00 bond pdb=" CA TRP A 51 " pdb=" CB TRP A 51 " ideal model delta sigma weight residual 1.534 1.485 0.049 2.47e-02 1.64e+03 3.99e+00 ... (remaining 21011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 26342 1.60 - 3.21: 2002 3.21 - 4.81: 253 4.81 - 6.41: 75 6.41 - 8.01: 16 Bond angle restraints: 28688 Sorted by residual: angle pdb=" N PRO B 152A" pdb=" CA PRO B 152A" pdb=" C PRO B 152A" ideal model delta sigma weight residual 110.70 116.33 -5.63 1.22e+00 6.72e-01 2.13e+01 angle pdb=" N PRO C 152A" pdb=" CA PRO C 152A" pdb=" C PRO C 152A" ideal model delta sigma weight residual 110.70 116.32 -5.62 1.22e+00 6.72e-01 2.12e+01 angle pdb=" N PRO D 152A" pdb=" CA PRO D 152A" pdb=" C PRO D 152A" ideal model delta sigma weight residual 110.70 116.28 -5.58 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N PRO A 152A" pdb=" CA PRO A 152A" pdb=" C PRO A 152A" ideal model delta sigma weight residual 110.70 116.07 -5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" CA PRO C 152A" pdb=" C PRO C 152A" pdb=" N PRO C 152B" ideal model delta sigma weight residual 117.93 122.03 -4.10 1.20e+00 6.94e-01 1.17e+01 ... (remaining 28683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 11499 17.14 - 34.27: 855 34.27 - 51.41: 106 51.41 - 68.54: 26 68.54 - 85.68: 30 Dihedral angle restraints: 12516 sinusoidal: 4852 harmonic: 7664 Sorted by residual: dihedral pdb=" CA SER A 25 " pdb=" C SER A 25 " pdb=" N LYS A 26 " pdb=" CA LYS A 26 " ideal model delta harmonic sigma weight residual -180.00 -149.70 -30.30 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA SER B 25 " pdb=" C SER B 25 " pdb=" N LYS B 26 " pdb=" CA LYS B 26 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA SER D 25 " pdb=" C SER D 25 " pdb=" N LYS D 26 " pdb=" CA LYS D 26 " ideal model delta harmonic sigma weight residual -180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 12513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1866 0.042 - 0.083: 901 0.083 - 0.125: 401 0.125 - 0.166: 42 0.166 - 0.208: 14 Chirality restraints: 3224 Sorted by residual: chirality pdb=" CA LYS B 26 " pdb=" N LYS B 26 " pdb=" C LYS B 26 " pdb=" CB LYS B 26 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LYS C 26 " pdb=" N LYS C 26 " pdb=" C LYS C 26 " pdb=" CB LYS C 26 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA LYS D 26 " pdb=" N LYS D 26 " pdb=" C LYS D 26 " pdb=" CB LYS D 26 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 3221 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 97 " -0.161 9.50e-02 1.11e+02 7.30e-02 4.45e+00 pdb=" NE ARG F 97 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG F 97 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG F 97 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG F 97 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 97 " 0.162 9.50e-02 1.11e+02 7.34e-02 4.45e+00 pdb=" NE ARG J 97 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG J 97 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG J 97 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG J 97 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 97 " -0.162 9.50e-02 1.11e+02 7.32e-02 4.43e+00 pdb=" NE ARG K 97 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG K 97 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG K 97 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG K 97 " 0.000 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4660 2.77 - 3.30: 20426 3.30 - 3.84: 33979 3.84 - 4.37: 40483 4.37 - 4.90: 68767 Nonbonded interactions: 168315 Sorted by model distance: nonbonded pdb=" OD1 ASN K 208 " pdb=" NZ LYS K 210 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASN H 208 " pdb=" NZ LYS H 210 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASN F 208 " pdb=" NZ LYS F 210 " model vdw 2.240 3.120 nonbonded pdb=" OD1 ASN J 208 " pdb=" NZ LYS J 210 " model vdw 2.241 3.120 nonbonded pdb=" O SER I 77 " pdb=" NE2 GLN I 79 " model vdw 2.273 3.120 ... (remaining 168310 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' } 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: 17.950 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 47.580 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.011 0.066 21016 Z= 0.741 Angle : 0.941 8.013 28688 Z= 0.498 Chirality : 0.055 0.208 3224 Planarity : 0.007 0.073 3668 Dihedral : 12.792 85.677 7516 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.13 % Favored : 92.41 % Rotamer: Outliers : 0.13 % Allowed : 2.09 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.33 (0.15), residues: 2636 helix: -3.23 (0.28), residues: 164 sheet: -0.23 (0.16), residues: 931 loop : -1.01 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 27 HIS 0.008 0.003 HIS A 91 PHE 0.024 0.003 PHE C 153 TYR 0.029 0.004 TYR B 75 ARG 0.019 0.003 ARG F 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 618 time to evaluate : 2.625 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: A 128 GLU cc_start: 0.9403 (tp30) cc_final: 0.9157 (tp30) REVERT: A 146 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8638 (m-40) REVERT: A 149 GLU cc_start: 0.9135 (mp0) cc_final: 0.8877 (mp0) REVERT: A 180 MET cc_start: 0.9535 (mtt) cc_final: 0.9289 (mtp) REVERT: A 209 GLN cc_start: 0.9440 (tt0) cc_final: 0.9199 (tt0) REVERT: B 128 GLU cc_start: 0.9399 (tp30) cc_final: 0.9147 (tp30) REVERT: B 146 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8630 (m-40) REVERT: B 149 GLU cc_start: 0.9208 (mp0) cc_final: 0.8741 (mp0) REVERT: B 209 GLN cc_start: 0.9426 (tt0) cc_final: 0.9193 (tt0) REVERT: C 128 GLU cc_start: 0.9399 (tp30) cc_final: 0.9149 (tp30) REVERT: C 146 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8634 (m-40) REVERT: C 149 GLU cc_start: 0.9144 (mp0) cc_final: 0.8885 (mp0) REVERT: C 180 MET cc_start: 0.9538 (mtt) cc_final: 0.9293 (mtp) REVERT: C 209 GLN cc_start: 0.9430 (tt0) cc_final: 0.9193 (tt0) REVERT: D 21 GLU cc_start: 0.8990 (tt0) cc_final: 0.8790 (pp20) REVERT: D 128 GLU cc_start: 0.9392 (tp30) cc_final: 0.9140 (tp30) REVERT: D 149 GLU cc_start: 0.9082 (mp0) cc_final: 0.8663 (mp0) REVERT: D 180 MET cc_start: 0.9529 (mtt) cc_final: 0.9288 (mtp) REVERT: D 209 GLN cc_start: 0.9426 (tt0) cc_final: 0.9197 (tt0) REVERT: G 31 ASN cc_start: 0.9197 (m110) cc_final: 0.8997 (m-40) REVERT: G 36 TYR cc_start: 0.8830 (m-80) cc_final: 0.8124 (m-80) REVERT: G 50 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8822 (tp30) REVERT: G 67 SER cc_start: 0.9158 (m) cc_final: 0.8889 (p) REVERT: G 93 ASP cc_start: 0.9332 (t0) cc_final: 0.8897 (t0) REVERT: G 103 LYS cc_start: 0.9145 (mttt) cc_final: 0.8627 (mtpp) REVERT: G 106 ILE cc_start: 0.8702 (mt) cc_final: 0.8055 (pp) REVERT: G 117 ILE cc_start: 0.7180 (tt) cc_final: 0.6897 (tt) REVERT: G 148 TRP cc_start: 0.6944 (m100) cc_final: 0.6448 (m100) REVERT: H 3 GLN cc_start: 0.8852 (pm20) cc_final: 0.8451 (pm20) REVERT: H 46 GLU cc_start: 0.8916 (tt0) cc_final: 0.8157 (pt0) REVERT: H 72 ASP cc_start: 0.8737 (t0) cc_final: 0.8522 (t0) REVERT: H 100 LEU cc_start: 0.9656 (mt) cc_final: 0.9195 (mp) REVERT: H 105 GLN cc_start: 0.9406 (mt0) cc_final: 0.9099 (mm110) REVERT: F 3 GLN cc_start: 0.8855 (pm20) cc_final: 0.8453 (pm20) REVERT: F 46 GLU cc_start: 0.8919 (tt0) cc_final: 0.8203 (pt0) REVERT: F 72 ASP cc_start: 0.8746 (t0) cc_final: 0.8525 (t0) REVERT: F 100 LEU cc_start: 0.9654 (mt) cc_final: 0.9190 (mp) REVERT: F 105 GLN cc_start: 0.9395 (mt0) cc_final: 0.9088 (mm110) REVERT: J 3 GLN cc_start: 0.8847 (pm20) cc_final: 0.8452 (pm20) REVERT: J 46 GLU cc_start: 0.8904 (tt0) cc_final: 0.8176 (pt0) REVERT: J 72 ASP cc_start: 0.8722 (t0) cc_final: 0.8497 (t0) REVERT: J 100 LEU cc_start: 0.9654 (mt) cc_final: 0.9192 (mp) REVERT: J 105 GLN cc_start: 0.9395 (mt0) cc_final: 0.9087 (mm110) REVERT: K 3 GLN cc_start: 0.8856 (pm20) cc_final: 0.8460 (pm20) REVERT: K 46 GLU cc_start: 0.8906 (tt0) cc_final: 0.8176 (pt0) REVERT: K 72 ASP cc_start: 0.8724 (t0) cc_final: 0.8500 (t0) REVERT: K 100 LEU cc_start: 0.9655 (mt) cc_final: 0.9195 (mp) REVERT: K 105 GLN cc_start: 0.9399 (mt0) cc_final: 0.9092 (mm110) REVERT: E 36 TYR cc_start: 0.8823 (m-80) cc_final: 0.8138 (m-80) REVERT: E 50 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8822 (tp30) REVERT: E 67 SER cc_start: 0.9150 (m) cc_final: 0.8876 (p) REVERT: E 93 ASP cc_start: 0.9338 (t0) cc_final: 0.8905 (t0) REVERT: E 103 LYS cc_start: 0.9149 (mttt) cc_final: 0.8636 (mtpp) REVERT: E 106 ILE cc_start: 0.8689 (mt) cc_final: 0.8025 (pp) REVERT: E 117 ILE cc_start: 0.7209 (tt) cc_final: 0.6925 (tt) REVERT: E 148 TRP cc_start: 0.6939 (m100) cc_final: 0.6436 (m100) REVERT: I 31 ASN cc_start: 0.9182 (m110) cc_final: 0.8980 (m-40) REVERT: I 36 TYR cc_start: 0.8825 (m-80) cc_final: 0.8119 (m-80) REVERT: I 50 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8813 (tp30) REVERT: I 67 SER cc_start: 0.9158 (m) cc_final: 0.8906 (p) REVERT: I 93 ASP cc_start: 0.9342 (t0) cc_final: 0.8909 (t0) REVERT: I 103 LYS cc_start: 0.9149 (mttt) cc_final: 0.8637 (mtpp) REVERT: I 106 ILE cc_start: 0.8721 (mt) cc_final: 0.8070 (pp) REVERT: I 117 ILE cc_start: 0.7202 (tt) cc_final: 0.6917 (tt) REVERT: I 148 TRP cc_start: 0.6956 (m100) cc_final: 0.6452 (m100) REVERT: L 36 TYR cc_start: 0.8837 (m-80) cc_final: 0.8154 (m-80) REVERT: L 50 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8819 (tp30) REVERT: L 67 SER cc_start: 0.9148 (m) cc_final: 0.8893 (p) REVERT: L 93 ASP cc_start: 0.9341 (t0) cc_final: 0.8908 (t0) REVERT: L 103 LYS cc_start: 0.9152 (mttt) cc_final: 0.8642 (mtpp) REVERT: L 106 ILE cc_start: 0.8704 (mt) cc_final: 0.8054 (pp) REVERT: L 117 ILE cc_start: 0.7179 (tt) cc_final: 0.6898 (tt) REVERT: L 148 TRP cc_start: 0.6932 (m100) cc_final: 0.6422 (m100) outliers start: 3 outliers final: 0 residues processed: 621 average time/residue: 1.3135 time to fit residues: 926.3677 Evaluate side-chains 376 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 373 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain C residue 146 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 240 HIS B 165 ASN B 239 HIS C 165 ASN C 239 HIS D 146 ASN D 165 ASN D 239 HIS H 76 ASN H 208 ASN F 76 ASN F 208 ASN J 76 ASN J 208 ASN K 76 ASN K 208 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21016 Z= 0.267 Angle : 0.761 7.235 28688 Z= 0.403 Chirality : 0.048 0.163 3224 Planarity : 0.006 0.056 3668 Dihedral : 6.472 45.955 2866 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.79 % Allowed : 13.35 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.46 (0.16), residues: 2636 helix: -2.45 (0.33), residues: 144 sheet: 0.29 (0.17), residues: 880 loop : -0.39 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 51 HIS 0.005 0.001 HIS D 173 PHE 0.029 0.003 PHE L 209 TYR 0.018 0.002 TYR F 180 ARG 0.012 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 479 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.9470 (tp30) cc_final: 0.9153 (tp30) REVERT: A 230 THR cc_start: 0.9650 (m) cc_final: 0.9293 (p) REVERT: B 109 GLU cc_start: 0.8732 (tp30) cc_final: 0.8429 (tp30) REVERT: B 128 GLU cc_start: 0.9470 (tp30) cc_final: 0.9147 (tp30) REVERT: B 229 THR cc_start: 0.9649 (m) cc_final: 0.9270 (p) REVERT: C 109 GLU cc_start: 0.8732 (tp30) cc_final: 0.8433 (tp30) REVERT: C 128 GLU cc_start: 0.9467 (tp30) cc_final: 0.9146 (tp30) REVERT: C 229 THR cc_start: 0.9634 (m) cc_final: 0.9271 (p) REVERT: D 109 GLU cc_start: 0.8761 (tp30) cc_final: 0.8464 (tp30) REVERT: D 128 GLU cc_start: 0.9459 (tp30) cc_final: 0.9134 (tp30) REVERT: D 149 GLU cc_start: 0.9178 (mp0) cc_final: 0.8929 (mp0) REVERT: D 229 THR cc_start: 0.9655 (m) cc_final: 0.9289 (p) REVERT: G 67 SER cc_start: 0.9106 (m) cc_final: 0.8888 (p) REVERT: G 93 ASP cc_start: 0.9295 (t0) cc_final: 0.8921 (t70) REVERT: G 103 LYS cc_start: 0.9289 (mttt) cc_final: 0.8753 (mtpp) REVERT: G 106 ILE cc_start: 0.8858 (mt) cc_final: 0.8024 (pp) REVERT: H 3 GLN cc_start: 0.8888 (pm20) cc_final: 0.8503 (pm20) REVERT: H 46 GLU cc_start: 0.8934 (tt0) cc_final: 0.8480 (tt0) REVERT: H 72 ASP cc_start: 0.9055 (t0) cc_final: 0.8620 (OUTLIER) REVERT: H 77 GLN cc_start: 0.9114 (mt0) cc_final: 0.8429 (mm110) REVERT: H 86 ASP cc_start: 0.9116 (m-30) cc_final: 0.8709 (m-30) REVERT: H 94 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8371 (tmm-80) REVERT: H 95 ASP cc_start: 0.9525 (t0) cc_final: 0.9037 (t0) REVERT: H 100 LEU cc_start: 0.9717 (mt) cc_final: 0.9481 (mm) REVERT: H 105 GLN cc_start: 0.9373 (mt0) cc_final: 0.9148 (mm110) REVERT: H 199 ILE cc_start: 0.8503 (mm) cc_final: 0.8211 (tp) REVERT: F 3 GLN cc_start: 0.8891 (pm20) cc_final: 0.8503 (pm20) REVERT: F 46 GLU cc_start: 0.8936 (tt0) cc_final: 0.8483 (tt0) REVERT: F 72 ASP cc_start: 0.9061 (t0) cc_final: 0.8627 (OUTLIER) REVERT: F 77 GLN cc_start: 0.9125 (mt0) cc_final: 0.8448 (mm110) REVERT: F 86 ASP cc_start: 0.9122 (m-30) cc_final: 0.8714 (m-30) REVERT: F 94 ARG cc_start: 0.8660 (tmm-80) cc_final: 0.8365 (tmm-80) REVERT: F 95 ASP cc_start: 0.9519 (t0) cc_final: 0.9032 (t0) REVERT: F 100 LEU cc_start: 0.9717 (mt) cc_final: 0.9482 (mm) REVERT: F 105 GLN cc_start: 0.9361 (mt0) cc_final: 0.9138 (mm110) REVERT: J 3 GLN cc_start: 0.8883 (pm20) cc_final: 0.8500 (pm20) REVERT: J 46 GLU cc_start: 0.8918 (tt0) cc_final: 0.8468 (tt0) REVERT: J 72 ASP cc_start: 0.9044 (t0) cc_final: 0.8607 (OUTLIER) REVERT: J 77 GLN cc_start: 0.9102 (mt0) cc_final: 0.8454 (mm110) REVERT: J 86 ASP cc_start: 0.9107 (m-30) cc_final: 0.8693 (m-30) REVERT: J 95 ASP cc_start: 0.9518 (t0) cc_final: 0.9021 (t0) REVERT: J 100 LEU cc_start: 0.9719 (mt) cc_final: 0.9485 (mm) REVERT: J 105 GLN cc_start: 0.9363 (mt0) cc_final: 0.9138 (mm110) REVERT: J 199 ILE cc_start: 0.8567 (mm) cc_final: 0.8281 (tp) REVERT: K 3 GLN cc_start: 0.8891 (pm20) cc_final: 0.8508 (pm20) REVERT: K 46 GLU cc_start: 0.8925 (tt0) cc_final: 0.8475 (tt0) REVERT: K 72 ASP cc_start: 0.9047 (t0) cc_final: 0.8613 (OUTLIER) REVERT: K 77 GLN cc_start: 0.9107 (mt0) cc_final: 0.8456 (mm110) REVERT: K 86 ASP cc_start: 0.9115 (m-30) cc_final: 0.8698 (m-30) REVERT: K 94 ARG cc_start: 0.8658 (tmm-80) cc_final: 0.8327 (tmm-80) REVERT: K 95 ASP cc_start: 0.9521 (t0) cc_final: 0.9041 (t0) REVERT: K 100 LEU cc_start: 0.9717 (mt) cc_final: 0.9487 (mm) REVERT: K 105 GLN cc_start: 0.9366 (mt0) cc_final: 0.9142 (mm110) REVERT: E 67 SER cc_start: 0.9097 (m) cc_final: 0.8875 (p) REVERT: E 93 ASP cc_start: 0.9298 (t0) cc_final: 0.8923 (t70) REVERT: E 103 LYS cc_start: 0.9296 (mttt) cc_final: 0.8764 (mtpp) REVERT: E 106 ILE cc_start: 0.8846 (mt) cc_final: 0.7998 (pp) REVERT: I 67 SER cc_start: 0.9110 (m) cc_final: 0.8894 (p) REVERT: I 93 ASP cc_start: 0.9304 (t0) cc_final: 0.8931 (t70) REVERT: I 103 LYS cc_start: 0.9295 (mttt) cc_final: 0.8765 (mtpp) REVERT: I 106 ILE cc_start: 0.8853 (mt) cc_final: 0.7996 (pp) REVERT: L 67 SER cc_start: 0.9095 (m) cc_final: 0.8876 (p) REVERT: L 93 ASP cc_start: 0.9302 (t0) cc_final: 0.8926 (t70) REVERT: L 103 LYS cc_start: 0.9297 (mttt) cc_final: 0.8769 (mtpp) REVERT: L 106 ILE cc_start: 0.8868 (mt) cc_final: 0.8028 (pp) outliers start: 64 outliers final: 22 residues processed: 500 average time/residue: 1.1052 time to fit residues: 649.1232 Evaluate side-chains 426 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 408 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain E residue 209 PHE Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 0.0670 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 209 GLN B 146 ASN B 209 GLN C 146 ASN C 209 GLN D 146 ASN D 209 GLN H 76 ASN H 208 ASN F 76 ASN F 208 ASN J 76 ASN J 208 ASN K 76 ASN K 208 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21016 Z= 0.394 Angle : 0.723 9.000 28688 Z= 0.376 Chirality : 0.048 0.237 3224 Planarity : 0.005 0.057 3668 Dihedral : 5.854 21.899 2860 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.06 % Allowed : 16.58 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.38 (0.16), residues: 2636 helix: -2.17 (0.35), residues: 144 sheet: 0.34 (0.17), residues: 876 loop : -0.35 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 51 HIS 0.004 0.001 HIS D 173 PHE 0.029 0.002 PHE L 209 TYR 0.020 0.002 TYR K 180 ARG 0.008 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 414 time to evaluate : 2.394 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: A 109 GLU cc_start: 0.8875 (tp30) cc_final: 0.8597 (tp30) REVERT: A 110 GLU cc_start: 0.9156 (mp0) cc_final: 0.8830 (mp0) REVERT: A 128 GLU cc_start: 0.9489 (tp30) cc_final: 0.9170 (tp30) REVERT: A 164 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: A 194 ASP cc_start: 0.8596 (m-30) cc_final: 0.7983 (m-30) REVERT: B 109 GLU cc_start: 0.8803 (tp30) cc_final: 0.8353 (tp30) REVERT: B 128 GLU cc_start: 0.9488 (tp30) cc_final: 0.9161 (tp30) REVERT: B 164 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: C 109 GLU cc_start: 0.8798 (tp30) cc_final: 0.8442 (tp30) REVERT: C 128 GLU cc_start: 0.9485 (tp30) cc_final: 0.9163 (tp30) REVERT: C 164 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: C 194 ASP cc_start: 0.8685 (m-30) cc_final: 0.8068 (m-30) REVERT: D 109 GLU cc_start: 0.8804 (tp30) cc_final: 0.8394 (tp30) REVERT: D 128 GLU cc_start: 0.9477 (tp30) cc_final: 0.9150 (tp30) REVERT: D 164 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: G 67 SER cc_start: 0.9153 (m) cc_final: 0.8908 (p) REVERT: G 93 ASP cc_start: 0.9295 (t0) cc_final: 0.8922 (t70) REVERT: G 103 LYS cc_start: 0.9305 (mttt) cc_final: 0.8777 (mtpp) REVERT: G 105 GLU cc_start: 0.7942 (tp30) cc_final: 0.7325 (tp30) REVERT: G 106 ILE cc_start: 0.8616 (mt) cc_final: 0.8056 (pp) REVERT: H 3 GLN cc_start: 0.9048 (pm20) cc_final: 0.8618 (pm20) REVERT: H 6 GLU cc_start: 0.8125 (mp0) cc_final: 0.7244 (mp0) REVERT: H 46 GLU cc_start: 0.8875 (tt0) cc_final: 0.8390 (tt0) REVERT: H 72 ASP cc_start: 0.9017 (t0) cc_final: 0.8588 (t0) REVERT: H 95 ASP cc_start: 0.9552 (t0) cc_final: 0.9199 (t0) REVERT: H 100 LEU cc_start: 0.9749 (mt) cc_final: 0.9543 (mp) REVERT: H 105 GLN cc_start: 0.9442 (mt0) cc_final: 0.9121 (pm20) REVERT: H 157 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.8015 (p) REVERT: H 199 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8477 (tp) REVERT: F 3 GLN cc_start: 0.9034 (pm20) cc_final: 0.8639 (pm20) REVERT: F 6 GLU cc_start: 0.8128 (mp0) cc_final: 0.7243 (mp0) REVERT: F 46 GLU cc_start: 0.8879 (tt0) cc_final: 0.8378 (pt0) REVERT: F 72 ASP cc_start: 0.9022 (t0) cc_final: 0.8608 (t0) REVERT: F 95 ASP cc_start: 0.9551 (t0) cc_final: 0.9198 (t0) REVERT: F 100 LEU cc_start: 0.9750 (mt) cc_final: 0.9544 (mp) REVERT: F 105 GLN cc_start: 0.9409 (mt0) cc_final: 0.9093 (pm20) REVERT: F 157 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8157 (t) REVERT: F 213 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6755 (ttpp) REVERT: J 3 GLN cc_start: 0.9031 (pm20) cc_final: 0.8641 (pm20) REVERT: J 6 GLU cc_start: 0.8134 (mp0) cc_final: 0.7267 (mp0) REVERT: J 46 GLU cc_start: 0.8861 (tt0) cc_final: 0.8367 (pt0) REVERT: J 72 ASP cc_start: 0.9004 (t0) cc_final: 0.8568 (t0) REVERT: J 95 ASP cc_start: 0.9553 (t0) cc_final: 0.9159 (t0) REVERT: J 105 GLN cc_start: 0.9434 (mt0) cc_final: 0.9114 (pm20) REVERT: J 157 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.8006 (p) REVERT: J 199 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8453 (tp) REVERT: K 3 GLN cc_start: 0.9019 (pm20) cc_final: 0.8629 (pm20) REVERT: K 6 GLU cc_start: 0.8133 (mp0) cc_final: 0.7269 (mp0) REVERT: K 46 GLU cc_start: 0.8865 (tt0) cc_final: 0.8350 (pt0) REVERT: K 72 ASP cc_start: 0.9009 (t0) cc_final: 0.8593 (t0) REVERT: K 95 ASP cc_start: 0.9552 (t0) cc_final: 0.9202 (t0) REVERT: K 105 GLN cc_start: 0.9414 (mt0) cc_final: 0.9090 (pm20) REVERT: K 157 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.8145 (t) REVERT: K 213 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6729 (ttpp) REVERT: E 67 SER cc_start: 0.9145 (m) cc_final: 0.8897 (p) REVERT: E 93 ASP cc_start: 0.9313 (t0) cc_final: 0.8940 (t70) REVERT: E 103 LYS cc_start: 0.9319 (mttt) cc_final: 0.8793 (mtpp) REVERT: E 105 GLU cc_start: 0.7943 (tp30) cc_final: 0.7322 (tp30) REVERT: E 106 ILE cc_start: 0.8625 (mt) cc_final: 0.8061 (pp) REVERT: I 67 SER cc_start: 0.9163 (m) cc_final: 0.8929 (p) REVERT: I 93 ASP cc_start: 0.9317 (t0) cc_final: 0.8947 (t70) REVERT: I 103 LYS cc_start: 0.9319 (mttt) cc_final: 0.8793 (mtpp) REVERT: I 105 GLU cc_start: 0.7919 (tp30) cc_final: 0.7367 (tp30) REVERT: I 106 ILE cc_start: 0.8620 (mt) cc_final: 0.8061 (pp) REVERT: L 67 SER cc_start: 0.9149 (m) cc_final: 0.8911 (p) REVERT: L 93 ASP cc_start: 0.9312 (t0) cc_final: 0.8941 (t70) REVERT: L 103 LYS cc_start: 0.9312 (mttt) cc_final: 0.8792 (mtpp) REVERT: L 105 GLU cc_start: 0.7938 (tp30) cc_final: 0.7322 (tp30) REVERT: L 106 ILE cc_start: 0.8625 (mt) cc_final: 0.8061 (pp) outliers start: 93 outliers final: 25 residues processed: 462 average time/residue: 1.0651 time to fit residues: 575.7275 Evaluate side-chains 425 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 388 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 157 SER Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 209 PHE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 209 GLN B 146 ASN B 209 GLN C 146 ASN C 209 GLN D 146 ASN D 209 GLN F 76 ASN J 76 ASN K 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21016 Z= 0.292 Angle : 0.698 7.790 28688 Z= 0.361 Chirality : 0.047 0.161 3224 Planarity : 0.005 0.059 3668 Dihedral : 5.538 21.007 2860 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.19 % Allowed : 18.85 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.16), residues: 2636 helix: -2.11 (0.37), residues: 144 sheet: 0.64 (0.17), residues: 807 loop : -0.39 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 158 HIS 0.004 0.001 HIS D 173 PHE 0.037 0.002 PHE G 209 TYR 0.019 0.002 TYR F 149 ARG 0.007 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 430 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.9043 (pm20) REVERT: A 109 GLU cc_start: 0.8904 (tp30) cc_final: 0.8037 (tt0) REVERT: A 110 GLU cc_start: 0.9148 (mp0) cc_final: 0.8905 (mp0) REVERT: A 128 GLU cc_start: 0.9485 (tp30) cc_final: 0.9192 (tp30) REVERT: A 164 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: B 20 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8870 (pm20) REVERT: B 109 GLU cc_start: 0.8818 (tp30) cc_final: 0.8333 (tp30) REVERT: B 128 GLU cc_start: 0.9484 (tp30) cc_final: 0.9182 (tp30) REVERT: B 149 GLU cc_start: 0.9204 (mp0) cc_final: 0.8953 (mp0) REVERT: B 164 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: B 194 ASP cc_start: 0.8554 (m-30) cc_final: 0.7892 (m-30) REVERT: C 109 GLU cc_start: 0.8818 (tp30) cc_final: 0.8333 (tp30) REVERT: C 128 GLU cc_start: 0.9480 (tp30) cc_final: 0.9184 (tp30) REVERT: C 164 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: D 109 GLU cc_start: 0.8834 (tp30) cc_final: 0.8529 (mm-30) REVERT: D 128 GLU cc_start: 0.9471 (tp30) cc_final: 0.9170 (tp30) REVERT: D 149 GLU cc_start: 0.9261 (mp0) cc_final: 0.9040 (mp0) REVERT: D 164 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: D 194 ASP cc_start: 0.8548 (m-30) cc_final: 0.7871 (m-30) REVERT: G 49 TYR cc_start: 0.9220 (p90) cc_final: 0.8891 (p90) REVERT: G 50 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8939 (mp0) REVERT: G 67 SER cc_start: 0.9188 (m) cc_final: 0.8947 (p) REVERT: G 93 ASP cc_start: 0.9303 (t0) cc_final: 0.8937 (t70) REVERT: G 103 LYS cc_start: 0.9307 (mttt) cc_final: 0.8765 (mtpp) REVERT: G 105 GLU cc_start: 0.7862 (tp30) cc_final: 0.7310 (tp30) REVERT: G 106 ILE cc_start: 0.8630 (mt) cc_final: 0.7927 (pp) REVERT: H 3 GLN cc_start: 0.9065 (pm20) cc_final: 0.8621 (pm20) REVERT: H 6 GLU cc_start: 0.8101 (mp0) cc_final: 0.7204 (mp0) REVERT: H 46 GLU cc_start: 0.8870 (tt0) cc_final: 0.8448 (pt0) REVERT: H 72 ASP cc_start: 0.8971 (t0) cc_final: 0.8528 (t0) REVERT: H 77 GLN cc_start: 0.8989 (mt0) cc_final: 0.8523 (mm110) REVERT: H 95 ASP cc_start: 0.9544 (t0) cc_final: 0.9161 (t0) REVERT: H 105 GLN cc_start: 0.9440 (mt0) cc_final: 0.9111 (pm20) REVERT: H 163 LEU cc_start: 0.9516 (mp) cc_final: 0.9269 (tm) REVERT: H 199 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8502 (tp) REVERT: F 3 GLN cc_start: 0.9077 (pm20) cc_final: 0.8689 (pm20) REVERT: F 6 GLU cc_start: 0.8100 (mp0) cc_final: 0.7203 (mp0) REVERT: F 46 GLU cc_start: 0.8874 (tt0) cc_final: 0.8452 (pt0) REVERT: F 72 ASP cc_start: 0.8979 (t0) cc_final: 0.8536 (t0) REVERT: F 77 GLN cc_start: 0.9006 (mt0) cc_final: 0.8502 (mm110) REVERT: F 95 ASP cc_start: 0.9547 (t0) cc_final: 0.9148 (t0) REVERT: F 105 GLN cc_start: 0.9416 (mt0) cc_final: 0.9074 (pm20) REVERT: J 3 GLN cc_start: 0.9071 (pm20) cc_final: 0.8688 (pm20) REVERT: J 6 GLU cc_start: 0.8104 (mp0) cc_final: 0.7223 (mp0) REVERT: J 46 GLU cc_start: 0.8856 (tt0) cc_final: 0.8445 (pt0) REVERT: J 72 ASP cc_start: 0.8962 (t0) cc_final: 0.8498 (t0) REVERT: J 77 GLN cc_start: 0.8998 (mt0) cc_final: 0.8498 (mm110) REVERT: J 95 ASP cc_start: 0.9523 (t0) cc_final: 0.9133 (t0) REVERT: J 105 GLN cc_start: 0.9433 (mt0) cc_final: 0.9104 (pm20) REVERT: J 163 LEU cc_start: 0.9512 (mp) cc_final: 0.9275 (tm) REVERT: J 199 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8483 (tp) REVERT: K 3 GLN cc_start: 0.9079 (pm20) cc_final: 0.8696 (pm20) REVERT: K 6 GLU cc_start: 0.8104 (mp0) cc_final: 0.7230 (mp0) REVERT: K 46 GLU cc_start: 0.8862 (tt0) cc_final: 0.8449 (pt0) REVERT: K 72 ASP cc_start: 0.8968 (t0) cc_final: 0.8525 (t0) REVERT: K 77 GLN cc_start: 0.9001 (mt0) cc_final: 0.8502 (mm110) REVERT: K 95 ASP cc_start: 0.9518 (t0) cc_final: 0.9174 (t0) REVERT: K 99 TYR cc_start: 0.9096 (m-10) cc_final: 0.8697 (m-10) REVERT: K 105 GLN cc_start: 0.9421 (mt0) cc_final: 0.9070 (pm20) REVERT: E 49 TYR cc_start: 0.9224 (p90) cc_final: 0.8892 (p90) REVERT: E 50 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8941 (mp0) REVERT: E 67 SER cc_start: 0.9180 (m) cc_final: 0.8934 (p) REVERT: E 93 ASP cc_start: 0.9304 (t0) cc_final: 0.8954 (t70) REVERT: E 103 LYS cc_start: 0.9313 (mttt) cc_final: 0.8776 (mtpp) REVERT: E 105 GLU cc_start: 0.7857 (tp30) cc_final: 0.7304 (tp30) REVERT: E 106 ILE cc_start: 0.8614 (mt) cc_final: 0.7901 (pp) REVERT: I 67 SER cc_start: 0.9192 (m) cc_final: 0.8947 (p) REVERT: I 93 ASP cc_start: 0.9307 (t0) cc_final: 0.8958 (t70) REVERT: I 103 LYS cc_start: 0.9313 (mttt) cc_final: 0.8776 (mtpp) REVERT: I 105 GLU cc_start: 0.7876 (tp30) cc_final: 0.7337 (tp30) REVERT: I 106 ILE cc_start: 0.8610 (mt) cc_final: 0.7896 (pp) REVERT: L 49 TYR cc_start: 0.9226 (p90) cc_final: 0.8894 (p90) REVERT: L 50 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8942 (mp0) REVERT: L 67 SER cc_start: 0.9184 (m) cc_final: 0.8939 (p) REVERT: L 93 ASP cc_start: 0.9299 (t0) cc_final: 0.8946 (t70) REVERT: L 103 LYS cc_start: 0.9315 (mttt) cc_final: 0.8781 (mtpp) REVERT: L 105 GLU cc_start: 0.7864 (tp30) cc_final: 0.7321 (tp30) REVERT: L 106 ILE cc_start: 0.8615 (mt) cc_final: 0.7900 (pp) outliers start: 96 outliers final: 33 residues processed: 487 average time/residue: 1.1271 time to fit residues: 639.3484 Evaluate side-chains 436 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 395 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN C 146 ASN D 146 ASN G 124 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN H 208 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN F 208 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN J 208 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN K 208 ASN I 124 GLN L 124 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 21016 Z= 0.470 Angle : 0.737 7.971 28688 Z= 0.383 Chirality : 0.048 0.150 3224 Planarity : 0.005 0.060 3668 Dihedral : 5.520 22.683 2860 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.54 % Allowed : 19.85 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.39 (0.16), residues: 2636 helix: -2.07 (0.35), residues: 144 sheet: 0.39 (0.17), residues: 884 loop : -0.41 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 158 HIS 0.004 0.001 HIS C 173 PHE 0.038 0.002 PHE L 209 TYR 0.014 0.002 TYR L 36 ARG 0.011 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 394 time to evaluate : 2.762 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: A 20 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.9072 (pm20) REVERT: A 109 GLU cc_start: 0.8929 (tp30) cc_final: 0.8034 (tt0) REVERT: A 110 GLU cc_start: 0.9188 (mp0) cc_final: 0.8915 (mp0) REVERT: A 128 GLU cc_start: 0.9512 (tp30) cc_final: 0.9221 (tp30) REVERT: A 164 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: A 194 ASP cc_start: 0.8600 (m-30) cc_final: 0.7945 (m-30) REVERT: B 20 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: B 109 GLU cc_start: 0.8846 (tp30) cc_final: 0.8421 (tp30) REVERT: B 128 GLU cc_start: 0.9513 (tp30) cc_final: 0.9216 (tp30) REVERT: B 164 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: B 194 ASP cc_start: 0.8565 (m-30) cc_final: 0.7842 (m-30) REVERT: C 20 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8946 (pm20) REVERT: C 109 GLU cc_start: 0.8841 (tp30) cc_final: 0.8416 (tp30) REVERT: C 128 GLU cc_start: 0.9507 (tp30) cc_final: 0.9214 (tp30) REVERT: C 164 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: C 194 ASP cc_start: 0.8640 (m-30) cc_final: 0.7956 (m-30) REVERT: D 20 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8947 (pm20) REVERT: D 109 GLU cc_start: 0.8829 (tp30) cc_final: 0.8398 (tp30) REVERT: D 128 GLU cc_start: 0.9497 (tp30) cc_final: 0.9199 (tp30) REVERT: D 149 GLU cc_start: 0.9279 (mp0) cc_final: 0.9004 (mp0) REVERT: D 164 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: D 194 ASP cc_start: 0.8559 (m-30) cc_final: 0.7847 (m-30) REVERT: G 50 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9022 (mp0) REVERT: G 67 SER cc_start: 0.9211 (m) cc_final: 0.8962 (p) REVERT: G 93 ASP cc_start: 0.9337 (t0) cc_final: 0.8956 (t70) REVERT: G 103 LYS cc_start: 0.9369 (mttt) cc_final: 0.8837 (mtpp) REVERT: G 105 GLU cc_start: 0.7896 (tp30) cc_final: 0.7412 (tp30) REVERT: G 106 ILE cc_start: 0.8678 (mt) cc_final: 0.8120 (pp) REVERT: G 185 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7523 (p0) REVERT: H 3 GLN cc_start: 0.9118 (pm20) cc_final: 0.8698 (pm20) REVERT: H 6 GLU cc_start: 0.8080 (mp0) cc_final: 0.7159 (mp0) REVERT: H 27 PHE cc_start: 0.8311 (t80) cc_final: 0.8093 (t80) REVERT: H 46 GLU cc_start: 0.8858 (tt0) cc_final: 0.8426 (tt0) REVERT: H 72 ASP cc_start: 0.8921 (t0) cc_final: 0.8492 (t0) REVERT: H 95 ASP cc_start: 0.9560 (t0) cc_final: 0.9247 (t0) REVERT: H 105 GLN cc_start: 0.9436 (mt0) cc_final: 0.9028 (pm20) REVERT: H 163 LEU cc_start: 0.9521 (mp) cc_final: 0.9296 (tm) REVERT: H 213 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7153 (ttpp) REVERT: F 3 GLN cc_start: 0.9114 (pm20) cc_final: 0.8765 (pm20) REVERT: F 6 GLU cc_start: 0.8087 (mp0) cc_final: 0.7168 (mp0) REVERT: F 46 GLU cc_start: 0.8860 (tt0) cc_final: 0.8431 (tt0) REVERT: F 72 ASP cc_start: 0.8924 (t0) cc_final: 0.8490 (t0) REVERT: F 94 ARG cc_start: 0.8797 (tmm-80) cc_final: 0.8591 (tmm-80) REVERT: F 95 ASP cc_start: 0.9553 (t0) cc_final: 0.9223 (t0) REVERT: F 105 GLN cc_start: 0.9431 (mt0) cc_final: 0.9046 (pm20) REVERT: F 213 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7025 (ttpp) REVERT: J 3 GLN cc_start: 0.9093 (pm20) cc_final: 0.8753 (pm20) REVERT: J 6 GLU cc_start: 0.8092 (mp0) cc_final: 0.7190 (mp0) REVERT: J 16 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8230 (pm20) REVERT: J 26 ARG cc_start: 0.8816 (tmm-80) cc_final: 0.8307 (tmm-80) REVERT: J 27 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: J 46 GLU cc_start: 0.8843 (tt0) cc_final: 0.8411 (tt0) REVERT: J 72 ASP cc_start: 0.8904 (t0) cc_final: 0.8470 (t0) REVERT: J 95 ASP cc_start: 0.9580 (t0) cc_final: 0.9217 (t0) REVERT: J 105 GLN cc_start: 0.9427 (mt0) cc_final: 0.9020 (pm20) REVERT: J 163 LEU cc_start: 0.9522 (mp) cc_final: 0.9302 (tm) REVERT: J 199 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8577 (tp) REVERT: K 3 GLN cc_start: 0.9102 (pm20) cc_final: 0.8762 (pm20) REVERT: K 6 GLU cc_start: 0.8096 (mp0) cc_final: 0.7204 (mp0) REVERT: K 16 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8246 (pm20) REVERT: K 26 ARG cc_start: 0.8824 (tmm-80) cc_final: 0.8320 (tmm-80) REVERT: K 27 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: K 46 GLU cc_start: 0.8851 (tt0) cc_final: 0.8387 (tt0) REVERT: K 72 ASP cc_start: 0.8911 (t0) cc_final: 0.8454 (t0) REVERT: K 95 ASP cc_start: 0.9591 (t0) cc_final: 0.9240 (t0) REVERT: K 105 GLN cc_start: 0.9433 (mt0) cc_final: 0.9042 (pm20) REVERT: K 213 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7014 (ttpp) REVERT: E 50 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9024 (mp0) REVERT: E 67 SER cc_start: 0.9201 (m) cc_final: 0.8950 (p) REVERT: E 93 ASP cc_start: 0.9363 (t0) cc_final: 0.8981 (t70) REVERT: E 103 LYS cc_start: 0.9376 (mttt) cc_final: 0.8848 (mtpp) REVERT: E 105 GLU cc_start: 0.7928 (tp30) cc_final: 0.7467 (tp30) REVERT: E 106 ILE cc_start: 0.8690 (mt) cc_final: 0.8143 (pp) REVERT: E 185 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7391 (p0) REVERT: E 195 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.5237 (tm-30) REVERT: E 196 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8756 (m) REVERT: I 50 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8972 (mp0) REVERT: I 67 SER cc_start: 0.9207 (m) cc_final: 0.8966 (p) REVERT: I 93 ASP cc_start: 0.9342 (t0) cc_final: 0.8975 (t70) REVERT: I 103 LYS cc_start: 0.9375 (mttt) cc_final: 0.8848 (mtpp) REVERT: I 105 GLU cc_start: 0.7863 (tp30) cc_final: 0.7394 (tp30) REVERT: I 106 ILE cc_start: 0.8650 (mt) cc_final: 0.8073 (pp) REVERT: L 50 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9035 (mp0) REVERT: L 67 SER cc_start: 0.9201 (m) cc_final: 0.8955 (p) REVERT: L 93 ASP cc_start: 0.9358 (t0) cc_final: 0.8975 (t70) REVERT: L 103 LYS cc_start: 0.9377 (mttt) cc_final: 0.8852 (mtpp) REVERT: L 105 GLU cc_start: 0.7914 (tp30) cc_final: 0.7451 (tp30) REVERT: L 106 ILE cc_start: 0.8693 (mt) cc_final: 0.8154 (pp) REVERT: L 185 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7530 (p0) REVERT: L 195 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.5221 (tm-30) REVERT: L 196 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8754 (m) outliers start: 104 outliers final: 44 residues processed: 467 average time/residue: 1.0855 time to fit residues: 592.7334 Evaluate side-chains 441 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 376 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 134 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN C 146 ASN D 146 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21016 Z= 0.258 Angle : 0.674 8.234 28688 Z= 0.346 Chirality : 0.046 0.192 3224 Planarity : 0.005 0.060 3668 Dihedral : 5.258 20.663 2860 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.10 % Allowed : 20.46 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.22 (0.16), residues: 2636 helix: -1.22 (0.41), residues: 144 sheet: 0.64 (0.18), residues: 798 loop : -0.42 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 158 HIS 0.004 0.001 HIS C 173 PHE 0.043 0.002 PHE E 209 TYR 0.014 0.001 TYR G 36 ARG 0.008 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 444 time to evaluate : 2.391 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: A 20 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.9077 (pm20) REVERT: A 109 GLU cc_start: 0.8892 (tp30) cc_final: 0.8042 (tt0) REVERT: A 110 GLU cc_start: 0.9127 (mp0) cc_final: 0.8891 (mp0) REVERT: A 128 GLU cc_start: 0.9506 (tp30) cc_final: 0.9221 (tp30) REVERT: A 164 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: A 180 MET cc_start: 0.9190 (mtp) cc_final: 0.8962 (mtm) REVERT: A 194 ASP cc_start: 0.8547 (m-30) cc_final: 0.7820 (m-30) REVERT: A 217 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8632 (mt-10) REVERT: B 20 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8857 (pm20) REVERT: B 128 GLU cc_start: 0.9509 (tp30) cc_final: 0.9277 (tp30) REVERT: B 164 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: B 175 ILE cc_start: 0.9547 (mt) cc_final: 0.9340 (mp) REVERT: B 180 MET cc_start: 0.9493 (mtm) cc_final: 0.9205 (mtm) REVERT: B 194 ASP cc_start: 0.8547 (m-30) cc_final: 0.7921 (m-30) REVERT: B 217 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8628 (mt-10) REVERT: C 20 GLN cc_start: 0.9377 (OUTLIER) cc_final: 0.8988 (pm20) REVERT: C 128 GLU cc_start: 0.9502 (tp30) cc_final: 0.9216 (tp30) REVERT: C 164 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: C 180 MET cc_start: 0.9214 (mtp) cc_final: 0.8973 (mtm) REVERT: C 194 ASP cc_start: 0.8581 (m-30) cc_final: 0.7899 (m-30) REVERT: D 20 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8950 (pm20) REVERT: D 128 GLU cc_start: 0.9493 (tp30) cc_final: 0.9202 (tp30) REVERT: D 164 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: D 194 ASP cc_start: 0.8546 (m-30) cc_final: 0.7790 (m-30) REVERT: G 18 ARG cc_start: 0.9129 (ppp80) cc_final: 0.8686 (ptm160) REVERT: G 49 TYR cc_start: 0.9209 (p90) cc_final: 0.8857 (p90) REVERT: G 50 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8858 (mp0) REVERT: G 67 SER cc_start: 0.9210 (m) cc_final: 0.8959 (p) REVERT: G 93 ASP cc_start: 0.9306 (t0) cc_final: 0.8972 (t70) REVERT: G 103 LYS cc_start: 0.9322 (mttt) cc_final: 0.8760 (mtpp) REVERT: G 185 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7612 (p0) REVERT: H 3 GLN cc_start: 0.9105 (pm20) cc_final: 0.8688 (pm20) REVERT: H 6 GLU cc_start: 0.8103 (mp0) cc_final: 0.7207 (mp0) REVERT: H 46 GLU cc_start: 0.8885 (tt0) cc_final: 0.8411 (tt0) REVERT: H 72 ASP cc_start: 0.8919 (t0) cc_final: 0.8489 (t0) REVERT: H 95 ASP cc_start: 0.9563 (t0) cc_final: 0.9159 (t0) REVERT: H 105 GLN cc_start: 0.9439 (mt0) cc_final: 0.9083 (pm20) REVERT: H 163 LEU cc_start: 0.9613 (mp) cc_final: 0.9379 (tm) REVERT: F 3 GLN cc_start: 0.9049 (pm20) cc_final: 0.8663 (pm20) REVERT: F 6 GLU cc_start: 0.8102 (mp0) cc_final: 0.7210 (mp0) REVERT: F 26 ARG cc_start: 0.8700 (tmm-80) cc_final: 0.8362 (tmm-80) REVERT: F 27 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: F 46 GLU cc_start: 0.8889 (tt0) cc_final: 0.8415 (tt0) REVERT: F 72 ASP cc_start: 0.8933 (t0) cc_final: 0.8481 (t0) REVERT: F 95 ASP cc_start: 0.9560 (t0) cc_final: 0.9151 (t0) REVERT: F 105 GLN cc_start: 0.9409 (mt0) cc_final: 0.9063 (pm20) REVERT: F 213 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7320 (tmmm) REVERT: J 3 GLN cc_start: 0.9070 (pm20) cc_final: 0.8714 (pm20) REVERT: J 6 GLU cc_start: 0.8102 (mp0) cc_final: 0.7229 (mp0) REVERT: J 46 GLU cc_start: 0.8869 (tt0) cc_final: 0.8393 (tt0) REVERT: J 72 ASP cc_start: 0.8914 (t0) cc_final: 0.8475 (t0) REVERT: J 95 ASP cc_start: 0.9536 (t0) cc_final: 0.9026 (t0) REVERT: J 100 LEU cc_start: 0.9477 (mt) cc_final: 0.9203 (mt) REVERT: J 105 GLN cc_start: 0.9429 (mt0) cc_final: 0.9053 (pm20) REVERT: J 163 LEU cc_start: 0.9611 (mp) cc_final: 0.9380 (tm) REVERT: J 199 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8541 (tp) REVERT: J 213 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7375 (ttpp) REVERT: K 3 GLN cc_start: 0.9079 (pm20) cc_final: 0.8723 (pm20) REVERT: K 6 GLU cc_start: 0.8107 (mp0) cc_final: 0.7226 (mp0) REVERT: K 46 GLU cc_start: 0.8878 (tt0) cc_final: 0.8403 (tt0) REVERT: K 72 ASP cc_start: 0.8920 (t0) cc_final: 0.8480 (t0) REVERT: K 95 ASP cc_start: 0.9543 (t0) cc_final: 0.9058 (t0) REVERT: K 100 LEU cc_start: 0.9475 (mt) cc_final: 0.9203 (mt) REVERT: K 105 GLN cc_start: 0.9412 (mt0) cc_final: 0.9059 (pm20) REVERT: K 213 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7294 (tmmm) REVERT: E 18 ARG cc_start: 0.9134 (ppp80) cc_final: 0.8702 (ptm160) REVERT: E 49 TYR cc_start: 0.9212 (p90) cc_final: 0.8855 (p90) REVERT: E 50 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8862 (mp0) REVERT: E 67 SER cc_start: 0.9198 (m) cc_final: 0.8945 (p) REVERT: E 93 ASP cc_start: 0.9288 (t0) cc_final: 0.8933 (t70) REVERT: E 103 LYS cc_start: 0.9350 (mttt) cc_final: 0.8790 (mtpp) REVERT: E 105 GLU cc_start: 0.8137 (tp30) cc_final: 0.7803 (tp30) REVERT: E 106 ILE cc_start: 0.8732 (mt) cc_final: 0.8185 (pp) REVERT: E 185 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7530 (p0) REVERT: E 196 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8772 (m) REVERT: I 18 ARG cc_start: 0.9122 (ppp80) cc_final: 0.8686 (ptm160) REVERT: I 49 TYR cc_start: 0.9303 (p90) cc_final: 0.8881 (p90) REVERT: I 50 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8924 (mp0) REVERT: I 67 SER cc_start: 0.9211 (m) cc_final: 0.8960 (p) REVERT: I 93 ASP cc_start: 0.9274 (t0) cc_final: 0.8935 (t70) REVERT: I 103 LYS cc_start: 0.9328 (mttt) cc_final: 0.8772 (mtpp) REVERT: I 185 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7571 (p0) REVERT: L 18 ARG cc_start: 0.9128 (ppp80) cc_final: 0.8693 (ptm160) REVERT: L 49 TYR cc_start: 0.9221 (p90) cc_final: 0.8866 (p90) REVERT: L 50 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8877 (mp0) REVERT: L 67 SER cc_start: 0.9204 (m) cc_final: 0.8955 (p) REVERT: L 93 ASP cc_start: 0.9267 (t0) cc_final: 0.8930 (t70) REVERT: L 103 LYS cc_start: 0.9329 (mttt) cc_final: 0.8776 (mtpp) REVERT: L 105 GLU cc_start: 0.8113 (tp30) cc_final: 0.7779 (tp30) REVERT: L 106 ILE cc_start: 0.8734 (mt) cc_final: 0.8195 (pp) REVERT: L 185 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7612 (p0) REVERT: L 196 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8766 (m) outliers start: 94 outliers final: 41 residues processed: 505 average time/residue: 1.0907 time to fit residues: 641.1866 Evaluate side-chains 468 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 408 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN D 146 ASN G 30 ASN H 208 ASN F 76 ASN F 208 ASN J 76 ASN J 208 ASN K 76 ASN K 208 ASN E 30 ASN E 124 GLN I 30 ASN L 30 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21016 Z= 0.241 Angle : 0.685 10.071 28688 Z= 0.352 Chirality : 0.046 0.197 3224 Planarity : 0.005 0.060 3668 Dihedral : 5.116 20.286 2860 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.67 % Allowed : 21.77 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.14 (0.16), residues: 2636 helix: -0.87 (0.43), residues: 144 sheet: 0.67 (0.17), residues: 825 loop : -0.39 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 158 HIS 0.003 0.001 HIS B 173 PHE 0.044 0.002 PHE E 209 TYR 0.013 0.001 TYR I 36 ARG 0.013 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 442 time to evaluate : 2.420 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: A 20 GLN cc_start: 0.9435 (OUTLIER) cc_final: 0.9091 (pm20) REVERT: A 109 GLU cc_start: 0.8909 (tp30) cc_final: 0.8313 (tt0) REVERT: A 128 GLU cc_start: 0.9487 (tp30) cc_final: 0.9267 (tp30) REVERT: A 164 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: A 194 ASP cc_start: 0.8554 (m-30) cc_final: 0.7795 (m-30) REVERT: A 217 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8629 (mt-10) REVERT: B 20 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.8916 (pm20) REVERT: B 109 GLU cc_start: 0.8826 (tt0) cc_final: 0.7801 (tt0) REVERT: B 128 GLU cc_start: 0.9499 (tp30) cc_final: 0.9262 (tp30) REVERT: B 164 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: B 180 MET cc_start: 0.9496 (mtm) cc_final: 0.9204 (mtm) REVERT: B 194 ASP cc_start: 0.8535 (m-30) cc_final: 0.7961 (m-30) REVERT: B 217 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8628 (mt-10) REVERT: C 20 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.9034 (pm20) REVERT: C 109 GLU cc_start: 0.8801 (tt0) cc_final: 0.7921 (tt0) REVERT: C 128 GLU cc_start: 0.9484 (tp30) cc_final: 0.9262 (tp30) REVERT: C 164 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: C 194 ASP cc_start: 0.8566 (m-30) cc_final: 0.7842 (m-30) REVERT: D 20 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.8987 (pm20) REVERT: D 109 GLU cc_start: 0.8860 (tt0) cc_final: 0.7905 (tt0) REVERT: D 128 GLU cc_start: 0.9476 (tp30) cc_final: 0.9248 (tp30) REVERT: D 164 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: D 180 MET cc_start: 0.9427 (mtm) cc_final: 0.9135 (mtm) REVERT: D 194 ASP cc_start: 0.8545 (m-30) cc_final: 0.7903 (m-30) REVERT: D 217 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8582 (mt-10) REVERT: G 24 GLN cc_start: 0.8660 (mt0) cc_final: 0.8430 (mp10) REVERT: G 49 TYR cc_start: 0.9187 (p90) cc_final: 0.8819 (p90) REVERT: G 50 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8903 (mp0) REVERT: G 67 SER cc_start: 0.9205 (m) cc_final: 0.8966 (p) REVERT: G 93 ASP cc_start: 0.9245 (t0) cc_final: 0.8941 (t70) REVERT: G 103 LYS cc_start: 0.9338 (mttt) cc_final: 0.8768 (mtpp) REVERT: G 185 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7632 (p0) REVERT: H 3 GLN cc_start: 0.9112 (pm20) cc_final: 0.8692 (pm20) REVERT: H 6 GLU cc_start: 0.8108 (mp0) cc_final: 0.7188 (mp0) REVERT: H 27 PHE cc_start: 0.7946 (t80) cc_final: 0.7649 (t80) REVERT: H 46 GLU cc_start: 0.8878 (tt0) cc_final: 0.8377 (tt0) REVERT: H 72 ASP cc_start: 0.8912 (t0) cc_final: 0.8477 (t0) REVERT: H 95 ASP cc_start: 0.9539 (t0) cc_final: 0.9130 (t0) REVERT: H 105 GLN cc_start: 0.9442 (mt0) cc_final: 0.9068 (pm20) REVERT: H 163 LEU cc_start: 0.9596 (mp) cc_final: 0.9375 (tm) REVERT: H 203 ASN cc_start: 0.8739 (m-40) cc_final: 0.8489 (t0) REVERT: H 213 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7239 (ttpp) REVERT: F 3 GLN cc_start: 0.9014 (pm20) cc_final: 0.8643 (pm20) REVERT: F 6 GLU cc_start: 0.8130 (mp0) cc_final: 0.7205 (mp0) REVERT: F 26 ARG cc_start: 0.8687 (tmm-80) cc_final: 0.8387 (tmm-80) REVERT: F 27 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: F 46 GLU cc_start: 0.8880 (tt0) cc_final: 0.8380 (tt0) REVERT: F 72 ASP cc_start: 0.8931 (t0) cc_final: 0.8496 (t0) REVERT: F 95 ASP cc_start: 0.9523 (t0) cc_final: 0.9064 (t0) REVERT: F 99 TYR cc_start: 0.9113 (m-10) cc_final: 0.8667 (m-80) REVERT: F 105 GLN cc_start: 0.9432 (mt0) cc_final: 0.9089 (pm20) REVERT: F 203 ASN cc_start: 0.8735 (m-40) cc_final: 0.8523 (t0) REVERT: J 3 GLN cc_start: 0.9019 (pm20) cc_final: 0.8648 (pm20) REVERT: J 6 GLU cc_start: 0.8151 (mp0) cc_final: 0.7236 (mp0) REVERT: J 16 GLU cc_start: 0.8126 (pm20) cc_final: 0.7898 (pm20) REVERT: J 26 ARG cc_start: 0.8608 (tmm-80) cc_final: 0.8327 (tmm-80) REVERT: J 27 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: J 46 GLU cc_start: 0.8862 (tt0) cc_final: 0.8361 (tt0) REVERT: J 72 ASP cc_start: 0.8912 (t0) cc_final: 0.8473 (t0) REVERT: J 95 ASP cc_start: 0.9477 (t0) cc_final: 0.8944 (t0) REVERT: J 99 TYR cc_start: 0.9090 (m-10) cc_final: 0.8629 (m-10) REVERT: J 100 LEU cc_start: 0.9471 (mt) cc_final: 0.9192 (mt) REVERT: J 105 GLN cc_start: 0.9430 (mt0) cc_final: 0.9049 (pm20) REVERT: J 163 LEU cc_start: 0.9613 (mp) cc_final: 0.9391 (tm) REVERT: J 199 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8548 (tp) REVERT: J 203 ASN cc_start: 0.8685 (m-40) cc_final: 0.8412 (t0) REVERT: J 213 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7459 (ttpp) REVERT: K 3 GLN cc_start: 0.9027 (pm20) cc_final: 0.8657 (pm20) REVERT: K 6 GLU cc_start: 0.8133 (mp0) cc_final: 0.7250 (mp0) REVERT: K 26 ARG cc_start: 0.8617 (tmm-80) cc_final: 0.8341 (tmm-80) REVERT: K 27 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: K 46 GLU cc_start: 0.8869 (tt0) cc_final: 0.8503 (pt0) REVERT: K 72 ASP cc_start: 0.8913 (t0) cc_final: 0.8481 (t0) REVERT: K 95 ASP cc_start: 0.9488 (t0) cc_final: 0.8971 (t0) REVERT: K 99 TYR cc_start: 0.9085 (m-10) cc_final: 0.8697 (m-10) REVERT: K 100 LEU cc_start: 0.9468 (mt) cc_final: 0.9190 (mt) REVERT: K 105 GLN cc_start: 0.9435 (mt0) cc_final: 0.9086 (pm20) REVERT: K 203 ASN cc_start: 0.8730 (m-40) cc_final: 0.8521 (t0) REVERT: K 213 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7294 (tmmm) REVERT: E 49 TYR cc_start: 0.9190 (p90) cc_final: 0.8817 (p90) REVERT: E 50 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8899 (mp0) REVERT: E 67 SER cc_start: 0.9191 (m) cc_final: 0.8952 (p) REVERT: E 93 ASP cc_start: 0.9291 (t0) cc_final: 0.8956 (t70) REVERT: E 103 LYS cc_start: 0.9345 (mttt) cc_final: 0.8781 (mtpp) REVERT: E 185 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7582 (p0) REVERT: E 195 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.5399 (tm-30) REVERT: I 24 GLN cc_start: 0.8674 (mt0) cc_final: 0.8441 (mp10) REVERT: I 49 TYR cc_start: 0.9267 (p90) cc_final: 0.8859 (p90) REVERT: I 50 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8901 (mp0) REVERT: I 67 SER cc_start: 0.9201 (m) cc_final: 0.8965 (p) REVERT: I 93 ASP cc_start: 0.9269 (t0) cc_final: 0.8950 (t70) REVERT: I 103 LYS cc_start: 0.9344 (mttt) cc_final: 0.8780 (mtpp) REVERT: I 185 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7568 (p0) REVERT: L 49 TYR cc_start: 0.9209 (p90) cc_final: 0.8878 (p90) REVERT: L 50 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8873 (mp0) REVERT: L 67 SER cc_start: 0.9198 (m) cc_final: 0.8961 (p) REVERT: L 93 ASP cc_start: 0.9267 (t0) cc_final: 0.8950 (t70) REVERT: L 103 LYS cc_start: 0.9345 (mttt) cc_final: 0.8786 (mtpp) REVERT: L 185 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7566 (p0) REVERT: L 195 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.5388 (tm-30) outliers start: 107 outliers final: 39 residues processed: 504 average time/residue: 1.0838 time to fit residues: 638.5370 Evaluate side-chains 465 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 405 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 213 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain L residue 195 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.0670 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 146 ASN D 146 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN F 76 ASN F 203 ASN J 76 ASN J 203 ASN K 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21016 Z= 0.251 Angle : 0.709 11.002 28688 Z= 0.357 Chirality : 0.046 0.153 3224 Planarity : 0.005 0.061 3668 Dihedral : 5.009 20.188 2860 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.84 % Allowed : 22.56 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.07 (0.16), residues: 2636 helix: -0.53 (0.45), residues: 144 sheet: 0.74 (0.17), residues: 830 loop : -0.39 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 158 HIS 0.003 0.001 HIS C 173 PHE 0.047 0.002 PHE G 209 TYR 0.012 0.001 TYR G 36 ARG 0.010 0.001 ARG E 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 445 time to evaluate : 2.363 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: A 20 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.9156 (pm20) REVERT: A 109 GLU cc_start: 0.8815 (tp30) cc_final: 0.8240 (tt0) REVERT: A 128 GLU cc_start: 0.9493 (tp30) cc_final: 0.9227 (tp30) REVERT: A 164 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: A 180 MET cc_start: 0.9421 (mtm) cc_final: 0.9146 (mtm) REVERT: A 194 ASP cc_start: 0.8573 (m-30) cc_final: 0.7854 (m-30) REVERT: A 217 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8595 (mt-10) REVERT: B 20 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8944 (pm20) REVERT: B 109 GLU cc_start: 0.8768 (tt0) cc_final: 0.8079 (tt0) REVERT: B 128 GLU cc_start: 0.9498 (tp30) cc_final: 0.9228 (tp30) REVERT: B 164 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: B 180 MET cc_start: 0.9494 (mtm) cc_final: 0.9201 (mtm) REVERT: B 217 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8602 (mt-10) REVERT: C 20 GLN cc_start: 0.9400 (OUTLIER) cc_final: 0.9030 (pm20) REVERT: C 109 GLU cc_start: 0.8751 (tt0) cc_final: 0.8048 (tt0) REVERT: C 128 GLU cc_start: 0.9490 (tp30) cc_final: 0.9220 (tp30) REVERT: C 164 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: C 180 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8787 (mtm) REVERT: C 194 ASP cc_start: 0.8585 (m-30) cc_final: 0.7838 (m-30) REVERT: D 20 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.9032 (pm20) REVERT: D 109 GLU cc_start: 0.8804 (tt0) cc_final: 0.8046 (tt0) REVERT: D 128 GLU cc_start: 0.9474 (tp30) cc_final: 0.9245 (tp30) REVERT: D 164 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: D 180 MET cc_start: 0.9419 (mtm) cc_final: 0.9124 (mtm) REVERT: D 217 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8547 (mt-10) REVERT: G 24 GLN cc_start: 0.8651 (mt0) cc_final: 0.8430 (mp10) REVERT: G 49 TYR cc_start: 0.9200 (p90) cc_final: 0.8850 (p90) REVERT: G 50 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8846 (mp0) REVERT: G 67 SER cc_start: 0.9205 (m) cc_final: 0.8962 (p) REVERT: G 75 ILE cc_start: 0.9412 (mt) cc_final: 0.8905 (tp) REVERT: G 93 ASP cc_start: 0.9255 (t0) cc_final: 0.8947 (t70) REVERT: G 103 LYS cc_start: 0.9324 (mttt) cc_final: 0.8751 (mtpp) REVERT: G 118 PHE cc_start: 0.7889 (m-80) cc_final: 0.7569 (m-80) REVERT: G 167 ASP cc_start: 0.8776 (t70) cc_final: 0.8363 (t70) REVERT: G 185 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7635 (p0) REVERT: H 3 GLN cc_start: 0.9096 (pm20) cc_final: 0.8681 (pm20) REVERT: H 6 GLU cc_start: 0.8086 (mp0) cc_final: 0.7161 (mp0) REVERT: H 16 GLU cc_start: 0.8190 (pm20) cc_final: 0.7832 (pm20) REVERT: H 46 GLU cc_start: 0.8884 (tt0) cc_final: 0.8397 (tt0) REVERT: H 72 ASP cc_start: 0.8915 (t0) cc_final: 0.8483 (t0) REVERT: H 76 ASN cc_start: 0.8718 (t0) cc_final: 0.8414 (t0) REVERT: H 95 ASP cc_start: 0.9519 (t0) cc_final: 0.9104 (t0) REVERT: H 100 LEU cc_start: 0.9667 (mt) cc_final: 0.9357 (mt) REVERT: H 105 GLN cc_start: 0.9457 (mt0) cc_final: 0.9091 (pm20) REVERT: H 108 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9141 (tm) REVERT: H 163 LEU cc_start: 0.9627 (mp) cc_final: 0.9409 (tm) REVERT: H 203 ASN cc_start: 0.8729 (m110) cc_final: 0.8482 (t0) REVERT: H 213 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7448 (ttpp) REVERT: F 3 GLN cc_start: 0.8982 (pm20) cc_final: 0.8611 (pm20) REVERT: F 6 GLU cc_start: 0.8092 (mp0) cc_final: 0.7193 (mp0) REVERT: F 16 GLU cc_start: 0.8172 (pm20) cc_final: 0.7961 (pm20) REVERT: F 26 ARG cc_start: 0.8649 (tmm-80) cc_final: 0.8158 (tmm-80) REVERT: F 27 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: F 46 GLU cc_start: 0.8885 (tt0) cc_final: 0.8395 (tt0) REVERT: F 72 ASP cc_start: 0.8934 (t0) cc_final: 0.8501 (t0) REVERT: F 76 ASN cc_start: 0.8832 (t0) cc_final: 0.8480 (t0) REVERT: F 95 ASP cc_start: 0.9524 (t0) cc_final: 0.9069 (t0) REVERT: F 105 GLN cc_start: 0.9444 (mt0) cc_final: 0.9110 (pm20) REVERT: F 108 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9152 (tm) REVERT: F 203 ASN cc_start: 0.8722 (m110) cc_final: 0.8478 (t0) REVERT: J 3 GLN cc_start: 0.8992 (pm20) cc_final: 0.8636 (pm20) REVERT: J 6 GLU cc_start: 0.8122 (mp0) cc_final: 0.7219 (mp0) REVERT: J 26 ARG cc_start: 0.8662 (tmm-80) cc_final: 0.8359 (tmm-80) REVERT: J 27 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: J 46 GLU cc_start: 0.8867 (tt0) cc_final: 0.8384 (tt0) REVERT: J 72 ASP cc_start: 0.8912 (t0) cc_final: 0.8476 (t0) REVERT: J 76 ASN cc_start: 0.8828 (t0) cc_final: 0.8481 (t0) REVERT: J 95 ASP cc_start: 0.9492 (t0) cc_final: 0.9017 (t0) REVERT: J 100 LEU cc_start: 0.9430 (mt) cc_final: 0.9151 (mt) REVERT: J 105 GLN cc_start: 0.9445 (mt0) cc_final: 0.9071 (pm20) REVERT: J 163 LEU cc_start: 0.9628 (mp) cc_final: 0.9411 (tm) REVERT: J 203 ASN cc_start: 0.8683 (m110) cc_final: 0.8399 (t0) REVERT: K 3 GLN cc_start: 0.8985 (pm20) cc_final: 0.8627 (pm20) REVERT: K 6 GLU cc_start: 0.8154 (mp0) cc_final: 0.7273 (mp0) REVERT: K 26 ARG cc_start: 0.8649 (tmm-80) cc_final: 0.8348 (tmm-80) REVERT: K 27 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: K 46 GLU cc_start: 0.8871 (tt0) cc_final: 0.8383 (tt0) REVERT: K 72 ASP cc_start: 0.8916 (t0) cc_final: 0.8482 (t0) REVERT: K 76 ASN cc_start: 0.8825 (t0) cc_final: 0.8476 (t0) REVERT: K 95 ASP cc_start: 0.9496 (t0) cc_final: 0.9038 (t0) REVERT: K 100 LEU cc_start: 0.9424 (mt) cc_final: 0.9150 (mt) REVERT: K 105 GLN cc_start: 0.9440 (mt0) cc_final: 0.9073 (pm20) REVERT: K 203 ASN cc_start: 0.8705 (m-40) cc_final: 0.8497 (t0) REVERT: E 24 GLN cc_start: 0.8636 (mt0) cc_final: 0.8420 (mp10) REVERT: E 49 TYR cc_start: 0.9202 (p90) cc_final: 0.8849 (p90) REVERT: E 50 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8845 (mp0) REVERT: E 67 SER cc_start: 0.9193 (m) cc_final: 0.8949 (p) REVERT: E 75 ILE cc_start: 0.9421 (mt) cc_final: 0.8918 (tp) REVERT: E 93 ASP cc_start: 0.9222 (t0) cc_final: 0.8897 (t70) REVERT: E 103 LYS cc_start: 0.9343 (mttt) cc_final: 0.8775 (mtpp) REVERT: E 118 PHE cc_start: 0.7880 (m-80) cc_final: 0.7578 (m-80) REVERT: E 167 ASP cc_start: 0.8786 (t70) cc_final: 0.8377 (t70) REVERT: E 185 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7549 (p0) REVERT: I 24 GLN cc_start: 0.8666 (mt0) cc_final: 0.8440 (mp10) REVERT: I 49 TYR cc_start: 0.9268 (p90) cc_final: 0.8909 (p90) REVERT: I 50 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8888 (mp0) REVERT: I 67 SER cc_start: 0.9203 (m) cc_final: 0.8964 (p) REVERT: I 75 ILE cc_start: 0.9416 (mt) cc_final: 0.8908 (tp) REVERT: I 93 ASP cc_start: 0.9224 (t0) cc_final: 0.8900 (t70) REVERT: I 103 LYS cc_start: 0.9328 (mttt) cc_final: 0.8761 (mtpp) REVERT: I 118 PHE cc_start: 0.7895 (m-80) cc_final: 0.7584 (m-80) REVERT: I 167 ASP cc_start: 0.8792 (t70) cc_final: 0.8382 (t70) REVERT: I 185 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7533 (p0) REVERT: L 24 GLN cc_start: 0.8661 (mt0) cc_final: 0.8441 (mp10) REVERT: L 49 TYR cc_start: 0.9211 (p90) cc_final: 0.8847 (p90) REVERT: L 50 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8915 (mp0) REVERT: L 67 SER cc_start: 0.9198 (m) cc_final: 0.8959 (p) REVERT: L 75 ILE cc_start: 0.9427 (mt) cc_final: 0.8923 (tp) REVERT: L 93 ASP cc_start: 0.9224 (t0) cc_final: 0.8900 (t70) REVERT: L 103 LYS cc_start: 0.9344 (mttt) cc_final: 0.8780 (mtpp) REVERT: L 118 PHE cc_start: 0.7864 (m-80) cc_final: 0.7569 (m-80) REVERT: L 167 ASP cc_start: 0.8801 (t70) cc_final: 0.8403 (t70) REVERT: L 185 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7552 (p0) outliers start: 88 outliers final: 35 residues processed: 501 average time/residue: 0.9472 time to fit residues: 554.1902 Evaluate side-chains 473 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 419 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.5980 chunk 222 optimal weight: 0.0980 chunk 237 optimal weight: 0.0870 chunk 142 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN D 146 ASN G 124 GLN H 208 ASN F 208 ASN J 208 ASN K 208 ASN E 79 GLN I 79 GLN L 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21016 Z= 0.210 Angle : 0.713 10.845 28688 Z= 0.357 Chirality : 0.046 0.209 3224 Planarity : 0.006 0.061 3668 Dihedral : 4.898 18.995 2860 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.88 % Allowed : 24.13 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.02 (0.16), residues: 2636 helix: -0.48 (0.45), residues: 144 sheet: 0.88 (0.18), residues: 832 loop : -0.37 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 158 HIS 0.003 0.001 HIS C 57 PHE 0.047 0.002 PHE I 209 TYR 0.013 0.001 TYR K 149 ARG 0.013 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 469 time to evaluate : 2.737 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: A 20 GLN cc_start: 0.9466 (OUTLIER) cc_final: 0.9079 (pm20) REVERT: A 109 GLU cc_start: 0.8881 (tp30) cc_final: 0.8243 (tt0) REVERT: A 128 GLU cc_start: 0.9467 (tp30) cc_final: 0.9211 (tp30) REVERT: A 164 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: A 175 ILE cc_start: 0.9475 (mt) cc_final: 0.9235 (mp) REVERT: A 180 MET cc_start: 0.9394 (mtm) cc_final: 0.9102 (mtm) REVERT: A 194 ASP cc_start: 0.8514 (m-30) cc_final: 0.7775 (m-30) REVERT: A 217 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 20 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.8990 (pm20) REVERT: B 109 GLU cc_start: 0.8737 (tt0) cc_final: 0.8033 (tt0) REVERT: B 128 GLU cc_start: 0.9473 (tp30) cc_final: 0.9219 (tp30) REVERT: B 164 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: B 175 ILE cc_start: 0.9498 (mt) cc_final: 0.9247 (mp) REVERT: B 180 MET cc_start: 0.9459 (mtm) cc_final: 0.9194 (mtm) REVERT: B 194 ASP cc_start: 0.8565 (m-30) cc_final: 0.7938 (m-30) REVERT: B 217 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8544 (mt-10) REVERT: C 109 GLU cc_start: 0.8758 (tt0) cc_final: 0.8132 (tt0) REVERT: C 128 GLU cc_start: 0.9463 (tp30) cc_final: 0.9207 (tp30) REVERT: C 164 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: C 180 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8765 (mtm) REVERT: C 194 ASP cc_start: 0.8540 (m-30) cc_final: 0.7784 (m-30) REVERT: C 217 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8527 (mt-10) REVERT: D 109 GLU cc_start: 0.8780 (tt0) cc_final: 0.8026 (tt0) REVERT: D 128 GLU cc_start: 0.9458 (tp30) cc_final: 0.9197 (tp30) REVERT: D 164 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: D 175 ILE cc_start: 0.9472 (mt) cc_final: 0.9233 (mp) REVERT: D 180 MET cc_start: 0.9382 (mtm) cc_final: 0.9064 (mtm) REVERT: D 194 ASP cc_start: 0.8544 (m-30) cc_final: 0.7913 (m-30) REVERT: D 217 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8567 (mt-10) REVERT: G 24 GLN cc_start: 0.8644 (mt0) cc_final: 0.8419 (mp10) REVERT: G 49 TYR cc_start: 0.9166 (p90) cc_final: 0.8840 (p90) REVERT: G 50 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8816 (mp0) REVERT: G 67 SER cc_start: 0.9205 (m) cc_final: 0.8968 (p) REVERT: G 93 ASP cc_start: 0.9211 (t0) cc_final: 0.8911 (t70) REVERT: G 103 LYS cc_start: 0.9314 (mttt) cc_final: 0.8743 (mtpp) REVERT: G 118 PHE cc_start: 0.8120 (m-80) cc_final: 0.7839 (m-80) REVERT: G 161 GLU cc_start: 0.9145 (pm20) cc_final: 0.8612 (pp20) REVERT: G 167 ASP cc_start: 0.8794 (t70) cc_final: 0.8360 (t0) REVERT: G 185 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7527 (p0) REVERT: H 3 GLN cc_start: 0.9064 (pm20) cc_final: 0.8670 (pm20) REVERT: H 6 GLU cc_start: 0.8020 (mp0) cc_final: 0.7096 (mp0) REVERT: H 30 ILE cc_start: 0.9685 (mm) cc_final: 0.9481 (pp) REVERT: H 46 GLU cc_start: 0.8911 (tt0) cc_final: 0.8421 (tt0) REVERT: H 72 ASP cc_start: 0.8956 (t0) cc_final: 0.8521 (t0) REVERT: H 76 ASN cc_start: 0.8732 (t0) cc_final: 0.8471 (t0) REVERT: H 95 ASP cc_start: 0.9459 (t0) cc_final: 0.8934 (t0) REVERT: H 100 LEU cc_start: 0.9449 (mt) cc_final: 0.9202 (mt) REVERT: H 105 GLN cc_start: 0.9455 (mt0) cc_final: 0.9099 (pm20) REVERT: H 203 ASN cc_start: 0.8691 (m110) cc_final: 0.8469 (t0) REVERT: F 3 GLN cc_start: 0.8976 (pm20) cc_final: 0.8613 (pm20) REVERT: F 6 GLU cc_start: 0.8020 (mp0) cc_final: 0.7101 (mp0) REVERT: F 46 GLU cc_start: 0.8910 (tt0) cc_final: 0.8421 (tt0) REVERT: F 72 ASP cc_start: 0.8950 (t0) cc_final: 0.8543 (t0) REVERT: F 76 ASN cc_start: 0.8739 (t0) cc_final: 0.8479 (t0) REVERT: F 77 GLN cc_start: 0.9062 (mt0) cc_final: 0.8831 (mt0) REVERT: F 95 ASP cc_start: 0.9473 (t0) cc_final: 0.9012 (t0) REVERT: F 99 TYR cc_start: 0.8991 (m-10) cc_final: 0.8634 (m-10) REVERT: F 100 LEU cc_start: 0.9444 (mt) cc_final: 0.9194 (mt) REVERT: F 105 GLN cc_start: 0.9450 (mt0) cc_final: 0.9118 (pm20) REVERT: F 186 VAL cc_start: 0.9415 (OUTLIER) cc_final: 0.9205 (m) REVERT: J 3 GLN cc_start: 0.8966 (pm20) cc_final: 0.8620 (pm20) REVERT: J 6 GLU cc_start: 0.8007 (mp0) cc_final: 0.7112 (mp0) REVERT: J 46 GLU cc_start: 0.8893 (tt0) cc_final: 0.8409 (tt0) REVERT: J 72 ASP cc_start: 0.8932 (t0) cc_final: 0.8521 (t0) REVERT: J 76 ASN cc_start: 0.8743 (t0) cc_final: 0.8479 (t0) REVERT: J 77 GLN cc_start: 0.9049 (mt0) cc_final: 0.8811 (mt0) REVERT: J 95 ASP cc_start: 0.9445 (t0) cc_final: 0.8991 (t0) REVERT: J 99 TYR cc_start: 0.8988 (m-10) cc_final: 0.8561 (m-10) REVERT: J 100 LEU cc_start: 0.9383 (mt) cc_final: 0.9124 (mt) REVERT: J 105 GLN cc_start: 0.9447 (mt0) cc_final: 0.9085 (pm20) REVERT: J 108 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9067 (tm) REVERT: J 203 ASN cc_start: 0.8719 (m110) cc_final: 0.8462 (t0) REVERT: K 3 GLN cc_start: 0.8966 (pm20) cc_final: 0.8618 (pm20) REVERT: K 6 GLU cc_start: 0.7998 (mp0) cc_final: 0.7139 (mp0) REVERT: K 46 GLU cc_start: 0.8881 (tt0) cc_final: 0.8401 (tt0) REVERT: K 72 ASP cc_start: 0.8933 (t0) cc_final: 0.8525 (t0) REVERT: K 76 ASN cc_start: 0.8734 (t0) cc_final: 0.8481 (t0) REVERT: K 77 GLN cc_start: 0.9038 (mt0) cc_final: 0.8812 (mt0) REVERT: K 95 ASP cc_start: 0.9468 (t0) cc_final: 0.9004 (t0) REVERT: K 99 TYR cc_start: 0.8996 (m-10) cc_final: 0.8547 (m-10) REVERT: K 100 LEU cc_start: 0.9380 (mt) cc_final: 0.9140 (mt) REVERT: K 105 GLN cc_start: 0.9456 (mt0) cc_final: 0.9117 (pm20) REVERT: K 108 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9108 (tm) REVERT: K 186 VAL cc_start: 0.9415 (OUTLIER) cc_final: 0.9207 (m) REVERT: K 203 ASN cc_start: 0.8744 (m-40) cc_final: 0.8537 (t0) REVERT: E 18 ARG cc_start: 0.9237 (ppp80) cc_final: 0.8898 (ptm160) REVERT: E 21 ILE cc_start: 0.9478 (mt) cc_final: 0.9273 (mp) REVERT: E 49 TYR cc_start: 0.9165 (p90) cc_final: 0.8840 (p90) REVERT: E 50 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8819 (mp0) REVERT: E 67 SER cc_start: 0.9193 (m) cc_final: 0.8954 (p) REVERT: E 93 ASP cc_start: 0.9189 (t0) cc_final: 0.8872 (t70) REVERT: E 103 LYS cc_start: 0.9328 (mttt) cc_final: 0.8769 (mtpp) REVERT: E 118 PHE cc_start: 0.7948 (m-80) cc_final: 0.7614 (m-80) REVERT: E 161 GLU cc_start: 0.9144 (pm20) cc_final: 0.8582 (pp20) REVERT: E 167 ASP cc_start: 0.8813 (t70) cc_final: 0.8396 (t0) REVERT: E 185 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7513 (p0) REVERT: I 21 ILE cc_start: 0.9479 (mt) cc_final: 0.9276 (mp) REVERT: I 49 TYR cc_start: 0.9236 (p90) cc_final: 0.8835 (p90) REVERT: I 50 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8817 (mp0) REVERT: I 67 SER cc_start: 0.9201 (m) cc_final: 0.8971 (p) REVERT: I 93 ASP cc_start: 0.9173 (t0) cc_final: 0.8871 (t70) REVERT: I 103 LYS cc_start: 0.9319 (mttt) cc_final: 0.8754 (mtpp) REVERT: I 118 PHE cc_start: 0.8165 (m-80) cc_final: 0.7918 (m-80) REVERT: I 161 GLU cc_start: 0.9142 (pm20) cc_final: 0.8615 (pp20) REVERT: I 167 ASP cc_start: 0.8801 (t70) cc_final: 0.8384 (t0) REVERT: I 185 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7579 (p0) REVERT: L 18 ARG cc_start: 0.9229 (ppp80) cc_final: 0.8884 (ptm160) REVERT: L 21 ILE cc_start: 0.9482 (mt) cc_final: 0.9276 (mp) REVERT: L 49 TYR cc_start: 0.9179 (p90) cc_final: 0.8836 (p90) REVERT: L 50 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8825 (mp0) REVERT: L 67 SER cc_start: 0.9196 (m) cc_final: 0.8966 (p) REVERT: L 93 ASP cc_start: 0.9173 (t0) cc_final: 0.8872 (t70) REVERT: L 103 LYS cc_start: 0.9328 (mttt) cc_final: 0.8774 (mtpp) REVERT: L 118 PHE cc_start: 0.7988 (m-80) cc_final: 0.7645 (m-80) REVERT: L 161 GLU cc_start: 0.9140 (pm20) cc_final: 0.8586 (pp20) REVERT: L 167 ASP cc_start: 0.8835 (t70) cc_final: 0.8445 (t70) REVERT: L 185 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7528 (p0) outliers start: 66 outliers final: 31 residues processed: 500 average time/residue: 1.0214 time to fit residues: 599.5177 Evaluate side-chains 488 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 442 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN D 146 ASN G 79 GLN E 124 GLN L 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21016 Z= 0.291 Angle : 0.737 10.461 28688 Z= 0.372 Chirality : 0.046 0.161 3224 Planarity : 0.006 0.062 3668 Dihedral : 4.904 20.113 2860 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.71 % Allowed : 24.91 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.05 (0.17), residues: 2636 helix: -0.46 (0.45), residues: 144 sheet: 0.94 (0.18), residues: 853 loop : -0.40 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP J 158 HIS 0.003 0.001 HIS A 91 PHE 0.045 0.002 PHE E 209 TYR 0.014 0.002 TYR H 99 ARG 0.014 0.001 ARG L 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 440 time to evaluate : 2.406 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: A 20 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.9161 (pm20) REVERT: A 109 GLU cc_start: 0.8919 (tp30) cc_final: 0.8335 (tt0) REVERT: A 128 GLU cc_start: 0.9497 (tp30) cc_final: 0.9262 (tp30) REVERT: A 164 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: A 175 ILE cc_start: 0.9482 (mt) cc_final: 0.9255 (mp) REVERT: A 180 MET cc_start: 0.9435 (mtm) cc_final: 0.9139 (mtm) REVERT: A 194 ASP cc_start: 0.8551 (m-30) cc_final: 0.7833 (m-30) REVERT: A 217 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8532 (mt-10) REVERT: B 20 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8989 (pm20) REVERT: B 109 GLU cc_start: 0.8734 (tt0) cc_final: 0.8328 (tt0) REVERT: B 128 GLU cc_start: 0.9503 (tp30) cc_final: 0.9264 (tp30) REVERT: B 164 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: B 175 ILE cc_start: 0.9517 (mt) cc_final: 0.9248 (mp) REVERT: B 180 MET cc_start: 0.9479 (mtm) cc_final: 0.9196 (mtm) REVERT: B 194 ASP cc_start: 0.8507 (m-30) cc_final: 0.7933 (m-30) REVERT: B 217 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8597 (mt-10) REVERT: C 109 GLU cc_start: 0.8799 (tt0) cc_final: 0.8243 (tt0) REVERT: C 128 GLU cc_start: 0.9496 (tp30) cc_final: 0.9257 (tp30) REVERT: C 164 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: C 180 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8848 (mtm) REVERT: C 194 ASP cc_start: 0.8605 (m-30) cc_final: 0.7879 (m-30) REVERT: D 109 GLU cc_start: 0.8763 (tt0) cc_final: 0.8188 (tt0) REVERT: D 128 GLU cc_start: 0.9488 (tp30) cc_final: 0.9246 (tp30) REVERT: D 164 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: D 180 MET cc_start: 0.9404 (mtm) cc_final: 0.9106 (mtm) REVERT: D 194 ASP cc_start: 0.8515 (m-30) cc_final: 0.7936 (m-30) REVERT: D 217 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8529 (mt-10) REVERT: G 49 TYR cc_start: 0.9213 (p90) cc_final: 0.8965 (p90) REVERT: G 50 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8858 (mp0) REVERT: G 67 SER cc_start: 0.9201 (m) cc_final: 0.8968 (p) REVERT: G 93 ASP cc_start: 0.9219 (t0) cc_final: 0.8902 (t70) REVERT: G 103 LYS cc_start: 0.9326 (mttt) cc_final: 0.8759 (mtpp) REVERT: G 118 PHE cc_start: 0.8082 (m-80) cc_final: 0.7829 (m-80) REVERT: G 161 GLU cc_start: 0.9163 (pm20) cc_final: 0.8642 (pp20) REVERT: G 167 ASP cc_start: 0.8797 (t70) cc_final: 0.8371 (t0) REVERT: G 185 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7539 (p0) REVERT: H 3 GLN cc_start: 0.9077 (pm20) cc_final: 0.8677 (pm20) REVERT: H 6 GLU cc_start: 0.7997 (mp0) cc_final: 0.7036 (mp0) REVERT: H 30 ILE cc_start: 0.9689 (mm) cc_final: 0.9481 (pp) REVERT: H 46 GLU cc_start: 0.8915 (tt0) cc_final: 0.8410 (tt0) REVERT: H 51 ILE cc_start: 0.9508 (tt) cc_final: 0.9213 (tp) REVERT: H 72 ASP cc_start: 0.8919 (t0) cc_final: 0.8484 (t0) REVERT: H 76 ASN cc_start: 0.8697 (t0) cc_final: 0.8454 (t0) REVERT: H 95 ASP cc_start: 0.9483 (t0) cc_final: 0.9033 (t0) REVERT: H 100 LEU cc_start: 0.9419 (mt) cc_final: 0.9155 (mt) REVERT: H 105 GLN cc_start: 0.9478 (mt0) cc_final: 0.9105 (pm20) REVERT: H 203 ASN cc_start: 0.8688 (m110) cc_final: 0.8471 (t0) REVERT: F 3 GLN cc_start: 0.8962 (pm20) cc_final: 0.8596 (pm20) REVERT: F 6 GLU cc_start: 0.8013 (mp0) cc_final: 0.7034 (mp0) REVERT: F 46 GLU cc_start: 0.8911 (tt0) cc_final: 0.8408 (tt0) REVERT: F 72 ASP cc_start: 0.8953 (t0) cc_final: 0.8506 (t0) REVERT: F 76 ASN cc_start: 0.8806 (t0) cc_final: 0.8503 (t0) REVERT: F 77 GLN cc_start: 0.9023 (mt0) cc_final: 0.8767 (mt0) REVERT: F 95 ASP cc_start: 0.9510 (t0) cc_final: 0.9061 (t0) REVERT: F 100 LEU cc_start: 0.9442 (mt) cc_final: 0.9155 (mt) REVERT: F 105 GLN cc_start: 0.9458 (mt0) cc_final: 0.9104 (pm20) REVERT: F 184 SER cc_start: 0.8980 (t) cc_final: 0.8772 (p) REVERT: F 186 VAL cc_start: 0.9410 (OUTLIER) cc_final: 0.9185 (m) REVERT: J 3 GLN cc_start: 0.8948 (pm20) cc_final: 0.8573 (pm20) REVERT: J 6 GLU cc_start: 0.8001 (mp0) cc_final: 0.7079 (mp0) REVERT: J 27 PHE cc_start: 0.8033 (t80) cc_final: 0.7671 (p90) REVERT: J 46 GLU cc_start: 0.8892 (tt0) cc_final: 0.8382 (tt0) REVERT: J 72 ASP cc_start: 0.8936 (t0) cc_final: 0.8507 (t0) REVERT: J 76 ASN cc_start: 0.8780 (t0) cc_final: 0.8481 (t0) REVERT: J 77 GLN cc_start: 0.9018 (mt0) cc_final: 0.8762 (mt0) REVERT: J 95 ASP cc_start: 0.9515 (t0) cc_final: 0.9076 (t0) REVERT: J 100 LEU cc_start: 0.9454 (mt) cc_final: 0.9138 (mt) REVERT: J 105 GLN cc_start: 0.9472 (mt0) cc_final: 0.9095 (pm20) REVERT: J 203 ASN cc_start: 0.8710 (m110) cc_final: 0.8485 (t0) REVERT: J 213 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7665 (ttpp) REVERT: K 3 GLN cc_start: 0.8959 (pm20) cc_final: 0.8579 (pm20) REVERT: K 6 GLU cc_start: 0.8012 (mp0) cc_final: 0.7091 (mp0) REVERT: K 27 PHE cc_start: 0.8031 (t80) cc_final: 0.7525 (p90) REVERT: K 46 GLU cc_start: 0.8896 (tt0) cc_final: 0.8393 (tt0) REVERT: K 72 ASP cc_start: 0.8936 (t0) cc_final: 0.8506 (t0) REVERT: K 76 ASN cc_start: 0.8783 (t0) cc_final: 0.8481 (t0) REVERT: K 77 GLN cc_start: 0.9024 (mt0) cc_final: 0.8772 (mt0) REVERT: K 95 ASP cc_start: 0.9506 (t0) cc_final: 0.9056 (t0) REVERT: K 100 LEU cc_start: 0.9453 (mt) cc_final: 0.9143 (mt) REVERT: K 105 GLN cc_start: 0.9467 (mt0) cc_final: 0.9098 (pm20) REVERT: K 184 SER cc_start: 0.8949 (t) cc_final: 0.8715 (p) REVERT: K 186 VAL cc_start: 0.9426 (OUTLIER) cc_final: 0.9210 (m) REVERT: K 203 ASN cc_start: 0.8698 (m-40) cc_final: 0.8477 (t0) REVERT: E 49 TYR cc_start: 0.9212 (p90) cc_final: 0.8959 (p90) REVERT: E 50 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8849 (mp0) REVERT: E 67 SER cc_start: 0.9191 (m) cc_final: 0.8955 (p) REVERT: E 93 ASP cc_start: 0.9168 (t0) cc_final: 0.8857 (t70) REVERT: E 103 LYS cc_start: 0.9334 (mttt) cc_final: 0.8780 (mtpp) REVERT: E 118 PHE cc_start: 0.7965 (m-80) cc_final: 0.7612 (m-80) REVERT: E 161 GLU cc_start: 0.9164 (pm20) cc_final: 0.8641 (pp20) REVERT: E 167 ASP cc_start: 0.8814 (t70) cc_final: 0.8384 (t0) REVERT: E 185 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7569 (p0) REVERT: I 49 TYR cc_start: 0.9248 (p90) cc_final: 0.8912 (p90) REVERT: I 50 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8846 (mp0) REVERT: I 67 SER cc_start: 0.9203 (m) cc_final: 0.8976 (p) REVERT: I 93 ASP cc_start: 0.9168 (t0) cc_final: 0.8875 (t70) REVERT: I 103 LYS cc_start: 0.9331 (mttt) cc_final: 0.8771 (mtpp) REVERT: I 118 PHE cc_start: 0.8129 (m-80) cc_final: 0.7879 (m-80) REVERT: I 161 GLU cc_start: 0.9158 (pm20) cc_final: 0.8645 (pp20) REVERT: I 167 ASP cc_start: 0.8814 (t70) cc_final: 0.8397 (t0) REVERT: I 185 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7496 (p0) REVERT: L 49 TYR cc_start: 0.9206 (p90) cc_final: 0.8973 (p90) REVERT: L 50 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8858 (mp0) REVERT: L 67 SER cc_start: 0.9198 (m) cc_final: 0.8971 (p) REVERT: L 93 ASP cc_start: 0.9170 (t0) cc_final: 0.8878 (t70) REVERT: L 103 LYS cc_start: 0.9334 (mttt) cc_final: 0.8784 (mtpp) REVERT: L 118 PHE cc_start: 0.8114 (m-80) cc_final: 0.7774 (m-80) REVERT: L 161 GLU cc_start: 0.9159 (pm20) cc_final: 0.8644 (pp20) REVERT: L 167 ASP cc_start: 0.8822 (t70) cc_final: 0.8426 (t70) REVERT: L 185 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7536 (p0) outliers start: 62 outliers final: 37 residues processed: 472 average time/residue: 0.9928 time to fit residues: 552.4313 Evaluate side-chains 481 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 430 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 194 CYS Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.0670 chunk 209 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN D 146 ASN H 208 ASN F 76 ASN F 208 ASN J 76 ASN J 208 ASN K 76 ASN K 208 ASN I 124 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.090993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.061924 restraints weight = 51186.267| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.06 r_work: 0.2778 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21016 Z= 0.221 Angle : 0.720 10.005 28688 Z= 0.363 Chirality : 0.045 0.161 3224 Planarity : 0.006 0.061 3668 Dihedral : 4.849 19.173 2860 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.57 % Allowed : 25.00 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.11 (0.17), residues: 2636 helix: -0.48 (0.44), residues: 144 sheet: 1.01 (0.18), residues: 853 loop : -0.37 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP J 158 HIS 0.003 0.001 HIS C 173 PHE 0.046 0.002 PHE G 209 TYR 0.015 0.001 TYR H 99 ARG 0.013 0.001 ARG E 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9375.03 seconds wall clock time: 261 minutes 47.89 seconds (15707.89 seconds total)