Starting phenix.real_space_refine on Wed Nov 20 00:25:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgi_43201/11_2024/8vgi_43201.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgi_43201/11_2024/8vgi_43201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgi_43201/11_2024/8vgi_43201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgi_43201/11_2024/8vgi_43201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgi_43201/11_2024/8vgi_43201.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgi_43201/11_2024/8vgi_43201.cif" } resolution = 2.7 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= -0.009 sd= 0.308 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 100 5.16 5 C 12960 2.51 5 N 3488 2.21 5 O 3934 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: 20482 Number of models: 1 Model: "" Number of chains: 16 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: "E" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "F" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1570 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 1 Chain: "G" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "H" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1570 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 1 Chain: "I" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "J" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1570 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 1 Chain: "K" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1570 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 1 Chain: "L" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 12.66, per 1000 atoms: 0.62 Number of scatterers: 20482 At special positions: 0 Unit cell: (111, 97, 183, 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 100 16.00 O 3934 8.00 N 3488 7.00 C 12960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.04 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 220 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 58 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 220 " distance=2.04 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 58 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 220 " distance=2.04 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 58 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 220 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 80 " - pdb=" SG CYS E 171 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 151 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 171 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS H 151 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 80 " - pdb=" SG CYS I 171 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 11 " - pdb=" SG CYS J 151 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.06 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 200 " distance=2.04 Simple disulfide: pdb=" SG CYS K 11 " - pdb=" SG CYS K 151 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.06 Simple disulfide: pdb=" SG CYS K 144 " - pdb=" SG CYS K 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 171 " 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: 4.84 Conformation dependent library (CDL) restraints added in 3.0 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 52 sheets defined 9.0% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 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 removed outlier: 3.571A pdb=" N LEU A 173A" --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 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 removed outlier: 3.510A pdb=" N HIS B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 173A" --> pdb=" O ALA B 170 " (cutoff:3.500A) 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 removed outlier: 3.554A pdb=" N LEU C 173A" --> pdb=" O ALA C 170 " (cutoff:3.500A) 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 removed outlier: 3.537A pdb=" N LEU D 173A" --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 183 through 187 Processing helix 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 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'F' and resid 205 through 208 Processing helix chain 'G' and resid 121 through 126 Processing helix chain 'G' and resid 183 through 187 Processing helix 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 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 189 through 193 Processing helix chain 'H' and resid 205 through 208 Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 183 through 187 Processing helix 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 160 through 162 No H-bonds generated for 'chain 'J' and resid 160 through 162' Processing helix chain 'J' and resid 189 through 193 Processing helix chain 'J' and resid 205 through 208 Processing helix 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 160 through 162 No H-bonds generated for 'chain 'K' and resid 160 through 162' Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'K' and resid 205 through 208 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 4.230A pdb=" N CYS A 136 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 199 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL A 213 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N THR A 229 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS A 182 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.767A pdb=" N CYS A 42 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 35 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS A 40 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 21 removed outlier: 4.234A pdb=" N CYS B 136 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR B 139 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 199 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL B 213 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N THR B 229 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS B 182 " --> pdb=" O MET B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 67 removed outlier: 3.798A pdb=" N CYS B 42 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 35 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS B 40 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 20 through 21 removed outlier: 4.219A pdb=" N CYS C 136 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 139 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU C 199 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL C 213 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N THR C 229 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N CYS C 182 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 64 through 67 removed outlier: 3.776A pdb=" N CYS C 42 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL C 35 " --> pdb=" O HIS C 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N HIS C 40 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 20 through 21 removed outlier: 4.235A pdb=" N CYS D 136 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR D 139 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU D 199 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL D 213 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N THR D 229 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS D 182 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 64 through 67 removed outlier: 3.780A pdb=" N CYS D 42 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL D 35 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS D 40 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP D 51 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 14 removed outlier: 3.504A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 14 removed outlier: 3.504A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.554A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 153 through 155 removed outlier: 4.522A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 205 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.836A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.832A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.849A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY F 143 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL F 186 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU F 145 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER F 184 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS F 147 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 182 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.849A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY F 143 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL F 186 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU F 145 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER F 184 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS F 147 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 182 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 155 through 158 Processing sheet with id=AC2, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 14 removed outlier: 3.506A pdb=" N LEU G 11 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 14 removed outlier: 3.506A pdb=" N LEU G 11 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 114 through 118 removed outlier: 3.550A pdb=" N VAL G 133 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 153 through 155 removed outlier: 4.526A pdb=" N TRP G 148 " --> pdb=" O GLN G 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 205 " --> pdb=" O VAL G 196 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.835A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.834A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.849A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.849A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AD4, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 14 removed outlier: 4.128A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 14 removed outlier: 4.128A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.552A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 153 through 155 removed outlier: 4.529A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.842A pdb=" N ALA J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.810A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.869A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY J 143 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL J 186 " --> pdb=" O GLY J 143 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU J 145 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER J 184 " --> pdb=" O LEU J 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS J 147 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU J 182 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.869A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY J 143 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL J 186 " --> pdb=" O GLY J 143 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU J 145 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER J 184 " --> pdb=" O LEU J 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS J 147 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU J 182 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 155 through 158 Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.838A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.807A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 124 through 128 removed outlier: 3.866A pdb=" N GLY K 143 " --> pdb=" O LEU K 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY K 143 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL K 186 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU K 145 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER K 184 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS K 147 " --> pdb=" O LEU K 182 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU K 182 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 124 through 128 removed outlier: 3.866A pdb=" N GLY K 143 " --> pdb=" O LEU K 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY K 143 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL K 186 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU K 145 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER K 184 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS K 147 " --> pdb=" O LEU K 182 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU K 182 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 155 through 158 Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.129A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.129A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.554A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.532A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 1935 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: 7.75 Time building geometry restraints manager: 5.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6378 1.34 - 1.46: 5247 1.46 - 1.59: 9247 1.59 - 1.71: 0 1.71 - 1.84: 120 Bond restraints: 20992 Sorted by residual: bond pdb=" CB PRO C 152A" pdb=" CG PRO C 152A" ideal model delta sigma weight residual 1.492 1.384 0.108 5.00e-02 4.00e+02 4.65e+00 bond pdb=" CB PRO B 152A" pdb=" CG PRO B 152A" ideal model delta sigma weight residual 1.492 1.385 0.107 5.00e-02 4.00e+02 4.54e+00 bond pdb=" CB PRO A 152A" pdb=" CG PRO A 152A" ideal model delta sigma weight residual 1.492 1.387 0.105 5.00e-02 4.00e+02 4.42e+00 bond pdb=" CA GLN A 81 " pdb=" CB GLN A 81 " ideal model delta sigma weight residual 1.539 1.437 0.103 4.88e-02 4.20e+02 4.42e+00 bond pdb=" CB PRO D 152A" pdb=" CG PRO D 152A" ideal model delta sigma weight residual 1.492 1.388 0.104 5.00e-02 4.00e+02 4.33e+00 ... (remaining 20987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 25426 1.75 - 3.51: 2709 3.51 - 5.26: 425 5.26 - 7.02: 64 7.02 - 8.77: 20 Bond angle restraints: 28644 Sorted by residual: angle pdb=" N PRO C 152A" pdb=" CA PRO C 152A" pdb=" C PRO C 152A" ideal model delta sigma weight residual 110.70 119.34 -8.64 1.22e+00 6.72e-01 5.01e+01 angle pdb=" N PRO B 152A" pdb=" CA PRO B 152A" pdb=" C PRO B 152A" ideal model delta sigma weight residual 110.70 119.07 -8.37 1.22e+00 6.72e-01 4.71e+01 angle pdb=" N PRO D 152A" pdb=" CA PRO D 152A" pdb=" C PRO D 152A" ideal model delta sigma weight residual 110.70 118.32 -7.62 1.22e+00 6.72e-01 3.90e+01 angle pdb=" N PRO A 152A" pdb=" CA PRO A 152A" pdb=" C PRO A 152A" ideal model delta sigma weight residual 110.70 118.23 -7.53 1.22e+00 6.72e-01 3.81e+01 angle pdb=" CA PRO B 152A" pdb=" C PRO B 152A" pdb=" N PRO B 152B" ideal model delta sigma weight residual 117.93 123.45 -5.52 1.20e+00 6.94e-01 2.11e+01 ... (remaining 28639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11615 18.00 - 36.00: 705 36.00 - 54.00: 131 54.00 - 71.99: 40 71.99 - 89.99: 29 Dihedral angle restraints: 12520 sinusoidal: 4856 harmonic: 7664 Sorted by residual: 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 -149.65 -30.35 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA SER C 25 " pdb=" C SER C 25 " pdb=" N LYS C 26 " pdb=" CA LYS C 26 " ideal model delta harmonic sigma weight residual 180.00 -149.72 -30.28 0 5.00e+00 4.00e-02 3.67e+01 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 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 12517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1887 0.057 - 0.115: 916 0.115 - 0.172: 364 0.172 - 0.229: 41 0.229 - 0.286: 12 Chirality restraints: 3220 Sorted by residual: chirality pdb=" CA PRO C 152A" pdb=" N PRO C 152A" pdb=" C PRO C 152A" pdb=" CB PRO C 152A" both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB VAL A 121 " pdb=" CA VAL A 121 " pdb=" CG1 VAL A 121 " pdb=" CG2 VAL A 121 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB VAL C 121 " pdb=" CA VAL C 121 " pdb=" CG1 VAL C 121 " pdb=" CG2 VAL C 121 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 3217 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 24 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C ARG C 24 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG C 24 " 0.019 2.00e-02 2.50e+03 pdb=" N SER C 25 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 24 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ARG D 24 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG D 24 " 0.019 2.00e-02 2.50e+03 pdb=" N SER D 25 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 24 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.35e+00 pdb=" C ARG B 24 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG B 24 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 25 " -0.017 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 201 2.60 - 3.18: 17790 3.18 - 3.75: 30420 3.75 - 4.33: 44853 4.33 - 4.90: 73539 Nonbonded interactions: 166803 Sorted by model distance: nonbonded pdb=" OH TYR A 95 " pdb=" OE2 GLU D 217 " model vdw 2.029 3.040 nonbonded pdb=" OH TYR B 95 " pdb=" OE2 GLU C 217 " model vdw 2.036 3.040 nonbonded pdb=" OE2 GLU A 217 " pdb=" OH TYR D 95 " model vdw 2.038 3.040 nonbonded pdb=" OE2 GLU B 217 " pdb=" OH TYR C 95 " model vdw 2.055 3.040 nonbonded pdb=" O MET B 163 " pdb=" O HOH B 301 " model vdw 2.124 3.040 ... (remaining 166798 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: 5.110 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: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.770 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.140 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:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 0.108 20992 Z= 0.753 Angle : 1.162 8.770 28644 Z= 0.641 Chirality : 0.074 0.286 3220 Planarity : 0.010 0.072 3660 Dihedral : 13.302 89.992 7496 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.53 % Favored : 93.21 % Rotamer: Outliers : 0.70 % Allowed : 2.14 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.80 (0.16), residues: 2636 helix: -2.14 (0.43), residues: 92 sheet: 0.07 (0.17), residues: 860 loop : -0.75 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP A 38 HIS 0.023 0.005 HIS C 72 PHE 0.033 0.005 PHE I 118 TYR 0.030 0.005 TYR C 234 ARG 0.019 0.004 ARG K 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 700 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 684 time to evaluate : 2.360 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: C 220 CYS cc_start: 0.6907 (m) cc_final: 0.6341 (m) REVERT: E 123 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.8840 (mm-30) REVERT: E 148 TRP cc_start: 0.8541 (m100) cc_final: 0.8278 (m100) REVERT: F 3 GLN cc_start: 0.8568 (pm20) cc_final: 0.8332 (pm20) REVERT: F 6 GLU cc_start: 0.7273 (mp0) cc_final: 0.6883 (mp0) REVERT: F 76 ASN cc_start: 0.8114 (t0) cc_final: 0.7561 (t0) REVERT: F 170 PHE cc_start: 0.9088 (m-80) cc_final: 0.8517 (m-80) REVERT: F 180 TYR cc_start: 0.8843 (m-80) cc_final: 0.8616 (m-80) REVERT: G 123 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8840 (mm-30) REVERT: G 140 TYR cc_start: 0.8429 (t80) cc_final: 0.8201 (t80) REVERT: G 148 TRP cc_start: 0.8541 (m100) cc_final: 0.8270 (m100) REVERT: H 3 GLN cc_start: 0.8566 (pm20) cc_final: 0.8323 (pm20) REVERT: H 6 GLU cc_start: 0.7243 (mp0) cc_final: 0.6763 (mp0) REVERT: H 76 ASN cc_start: 0.8111 (t0) cc_final: 0.7553 (t0) REVERT: H 170 PHE cc_start: 0.9092 (m-80) cc_final: 0.8630 (m-80) REVERT: H 180 TYR cc_start: 0.8852 (m-80) cc_final: 0.8620 (m-80) REVERT: I 123 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.8923 (mm-30) REVERT: I 148 TRP cc_start: 0.8545 (m100) cc_final: 0.8258 (m100) REVERT: J 6 GLU cc_start: 0.7236 (mp0) cc_final: 0.6816 (mp0) REVERT: J 76 ASN cc_start: 0.8203 (t0) cc_final: 0.7605 (t0) REVERT: J 170 PHE cc_start: 0.9119 (m-80) cc_final: 0.8763 (m-80) REVERT: J 180 TYR cc_start: 0.8819 (m-80) cc_final: 0.8146 (m-80) REVERT: K 6 GLU cc_start: 0.7215 (mp0) cc_final: 0.6798 (mp0) REVERT: K 76 ASN cc_start: 0.8173 (t0) cc_final: 0.7580 (t0) REVERT: K 170 PHE cc_start: 0.9118 (m-80) cc_final: 0.8502 (m-80) REVERT: K 180 TYR cc_start: 0.8813 (m-80) cc_final: 0.8149 (m-80) REVERT: L 123 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8920 (mm-30) REVERT: L 148 TRP cc_start: 0.8519 (m100) cc_final: 0.8243 (m100) outliers start: 16 outliers final: 8 residues processed: 696 average time/residue: 1.2715 time to fit residues: 1003.9226 Evaluate side-chains 465 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 453 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 123 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 165 ASN B 165 ASN B 192 GLN C 165 ASN D 20 GLN D 165 ASN D 192 GLN E 147 GLN E 158 ASN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN G 147 GLN G 158 ASN H 159 ASN H 203 ASN I 147 GLN I 158 ASN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN L 158 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20992 Z= 0.344 Angle : 0.841 9.762 28644 Z= 0.437 Chirality : 0.050 0.195 3220 Planarity : 0.006 0.068 3660 Dihedral : 8.233 118.593 2884 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.71 % Allowed : 15.58 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.25 (0.16), residues: 2636 helix: -1.27 (0.44), residues: 124 sheet: 0.22 (0.16), residues: 848 loop : -0.23 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 215 HIS 0.005 0.001 HIS G 189 PHE 0.023 0.003 PHE F 126 TYR 0.019 0.002 TYR L 29 ARG 0.010 0.001 ARG J 26 *********************** 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 586 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 524 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 142 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.7940 (ttm-80) REVERT: E 145 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8644 (pptt) REVERT: E 210 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8344 (t0) REVERT: F 6 GLU cc_start: 0.7294 (mp0) cc_final: 0.7084 (mp0) REVERT: F 76 ASN cc_start: 0.8215 (t0) cc_final: 0.7947 (t0) REVERT: F 78 PHE cc_start: 0.8560 (m-80) cc_final: 0.8314 (m-80) REVERT: F 147 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8608 (tmtm) REVERT: F 148 ASP cc_start: 0.7800 (p0) cc_final: 0.7549 (p0) REVERT: F 152 GLU cc_start: 0.8693 (pm20) cc_final: 0.8339 (pm20) REVERT: F 205 LYS cc_start: 0.9417 (tppt) cc_final: 0.9186 (mmmt) REVERT: G 145 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8642 (pptt) REVERT: G 210 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8331 (t0) REVERT: H 6 GLU cc_start: 0.7232 (mp0) cc_final: 0.6853 (mp0) REVERT: H 76 ASN cc_start: 0.8211 (t0) cc_final: 0.7950 (t0) REVERT: H 78 PHE cc_start: 0.8574 (m-80) cc_final: 0.8349 (m-80) REVERT: H 147 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8606 (tmtm) REVERT: H 148 ASP cc_start: 0.7772 (p0) cc_final: 0.7495 (p0) REVERT: H 152 GLU cc_start: 0.8699 (pm20) cc_final: 0.8342 (pm20) REVERT: H 205 LYS cc_start: 0.9428 (tppt) cc_final: 0.9193 (mmmt) REVERT: I 210 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8342 (t0) REVERT: J 76 ASN cc_start: 0.8335 (t0) cc_final: 0.8042 (t0) REVERT: J 147 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8557 (tmtm) REVERT: J 148 ASP cc_start: 0.7750 (p0) cc_final: 0.7488 (p0) REVERT: J 152 GLU cc_start: 0.8799 (pm20) cc_final: 0.8483 (pm20) REVERT: J 205 LYS cc_start: 0.9462 (tppt) cc_final: 0.9205 (mmmt) REVERT: J 210 LYS cc_start: 0.8819 (mptt) cc_final: 0.8530 (tptp) REVERT: K 76 ASN cc_start: 0.8307 (t0) cc_final: 0.8021 (t0) REVERT: K 147 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8502 (ttpp) REVERT: K 148 ASP cc_start: 0.7749 (p0) cc_final: 0.7153 (p0) REVERT: K 152 GLU cc_start: 0.8785 (pm20) cc_final: 0.8474 (pm20) REVERT: K 205 LYS cc_start: 0.9452 (tppt) cc_final: 0.9193 (mmmt) REVERT: K 210 LYS cc_start: 0.8819 (mptt) cc_final: 0.8530 (tptp) REVERT: L 210 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8338 (t0) outliers start: 62 outliers final: 27 residues processed: 546 average time/residue: 1.1998 time to fit residues: 749.5538 Evaluate side-chains 433 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 396 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 147 LYS Chi-restraints excluded: chain F residue 151 CYS Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain H residue 151 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 147 LYS Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 210 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 192 GLN B 20 GLN B 36 HIS C 20 GLN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN L 124 GLN L 147 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20992 Z= 0.249 Angle : 0.764 7.618 28644 Z= 0.393 Chirality : 0.048 0.160 3220 Planarity : 0.006 0.121 3660 Dihedral : 5.766 21.290 2860 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.97 % Allowed : 17.93 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.47 (0.49), residues: 124 sheet: 0.71 (0.17), residues: 776 loop : -0.10 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 137 HIS 0.003 0.001 HIS D 173 PHE 0.024 0.002 PHE L 139 TYR 0.022 0.002 TYR L 140 ARG 0.010 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 523 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 455 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 148 TRP cc_start: 0.8213 (m100) cc_final: 0.7493 (m100) REVERT: E 210 ASN cc_start: 0.8623 (p0) cc_final: 0.8419 (t0) REVERT: F 76 ASN cc_start: 0.8214 (t0) cc_final: 0.7992 (t0) REVERT: F 105 GLN cc_start: 0.8352 (pm20) cc_final: 0.7821 (pm20) REVERT: F 147 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8687 (tmtm) REVERT: F 148 ASP cc_start: 0.7707 (p0) cc_final: 0.7397 (p0) REVERT: F 152 GLU cc_start: 0.8611 (pm20) cc_final: 0.8327 (pm20) REVERT: F 180 TYR cc_start: 0.8886 (m-80) cc_final: 0.8559 (m-10) REVERT: G 145 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8661 (pptt) REVERT: G 148 TRP cc_start: 0.8187 (m100) cc_final: 0.7501 (m100) REVERT: G 210 ASN cc_start: 0.8686 (p0) cc_final: 0.8389 (t0) REVERT: H 6 GLU cc_start: 0.7187 (mp0) cc_final: 0.6900 (mp0) REVERT: H 76 ASN cc_start: 0.8213 (t0) cc_final: 0.7994 (t0) REVERT: H 105 GLN cc_start: 0.8268 (pm20) cc_final: 0.7806 (pm20) REVERT: H 147 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8689 (tmtm) REVERT: H 148 ASP cc_start: 0.7714 (p0) cc_final: 0.7406 (p0) REVERT: H 152 GLU cc_start: 0.8602 (pm20) cc_final: 0.8339 (pm20) REVERT: H 180 TYR cc_start: 0.8888 (m-80) cc_final: 0.8445 (m-80) REVERT: I 18 ARG cc_start: 0.7703 (ttm110) cc_final: 0.7040 (mmt90) REVERT: I 148 TRP cc_start: 0.8184 (m100) cc_final: 0.7397 (m100) REVERT: I 169 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8630 (mtmm) REVERT: I 210 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8452 (t0) REVERT: J 6 GLU cc_start: 0.7399 (mp0) cc_final: 0.7120 (mp0) REVERT: J 76 ASN cc_start: 0.8351 (t0) cc_final: 0.8063 (t0) REVERT: J 105 GLN cc_start: 0.8425 (pm20) cc_final: 0.8045 (pm20) REVERT: J 147 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8678 (tmtm) REVERT: J 148 ASP cc_start: 0.7731 (p0) cc_final: 0.7438 (p0) REVERT: J 152 GLU cc_start: 0.8703 (pm20) cc_final: 0.8482 (pm20) REVERT: J 180 TYR cc_start: 0.8900 (m-80) cc_final: 0.8549 (m-10) REVERT: K 76 ASN cc_start: 0.8321 (t0) cc_final: 0.8043 (t0) REVERT: K 105 GLN cc_start: 0.8398 (pm20) cc_final: 0.7918 (pm20) REVERT: K 147 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8691 (tmtm) REVERT: K 148 ASP cc_start: 0.7684 (p0) cc_final: 0.7385 (p0) REVERT: K 152 GLU cc_start: 0.8689 (pm20) cc_final: 0.8480 (pm20) REVERT: K 180 TYR cc_start: 0.8899 (m-80) cc_final: 0.8531 (m-10) REVERT: L 18 ARG cc_start: 0.7584 (ttm110) cc_final: 0.7011 (mmt90) REVERT: L 117 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8060 (mp) REVERT: L 148 TRP cc_start: 0.8165 (m100) cc_final: 0.7379 (m100) REVERT: L 169 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8616 (mtmm) REVERT: L 210 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8445 (t0) outliers start: 68 outliers final: 22 residues processed: 478 average time/residue: 1.1127 time to fit residues: 615.7144 Evaluate side-chains 438 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 406 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 147 LYS Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 147 LYS Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 210 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.2980 chunk 180 optimal weight: 5.9990 chunk 124 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 161 optimal weight: 0.0050 chunk 241 optimal weight: 0.9990 chunk 255 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN D 204 ASN E 158 ASN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 ASN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 ASN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20992 Z= 0.194 Angle : 0.734 8.194 28644 Z= 0.379 Chirality : 0.047 0.165 3220 Planarity : 0.006 0.065 3660 Dihedral : 5.454 19.462 2860 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.66 % Allowed : 19.33 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.16 (0.16), residues: 2636 helix: -0.33 (0.49), residues: 124 sheet: 0.86 (0.16), residues: 808 loop : -0.20 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 137 HIS 0.006 0.001 HIS B 166 PHE 0.016 0.002 PHE E 83 TYR 0.025 0.002 TYR L 140 ARG 0.011 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 554 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 493 time to evaluate : 2.456 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: E 148 TRP cc_start: 0.8164 (m100) cc_final: 0.7475 (m100) REVERT: F 6 GLU cc_start: 0.7328 (mp0) cc_final: 0.7104 (pm20) REVERT: F 105 GLN cc_start: 0.8444 (pm20) cc_final: 0.8062 (pm20) REVERT: F 148 ASP cc_start: 0.7540 (p0) cc_final: 0.7317 (p0) REVERT: F 152 GLU cc_start: 0.8634 (pm20) cc_final: 0.8332 (pm20) REVERT: F 180 TYR cc_start: 0.8865 (m-80) cc_final: 0.8532 (m-80) REVERT: G 142 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.8262 (ttm-80) REVERT: G 145 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8699 (pptt) REVERT: G 148 TRP cc_start: 0.8137 (m100) cc_final: 0.7385 (m100) REVERT: H 6 GLU cc_start: 0.7168 (mp0) cc_final: 0.6966 (mp0) REVERT: H 105 GLN cc_start: 0.8200 (pm20) cc_final: 0.7707 (pm20) REVERT: H 148 ASP cc_start: 0.7511 (p0) cc_final: 0.7309 (p0) REVERT: H 152 GLU cc_start: 0.8637 (pm20) cc_final: 0.8371 (pm20) REVERT: H 180 TYR cc_start: 0.8872 (m-80) cc_final: 0.8539 (m-80) REVERT: I 18 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7209 (mmt90) REVERT: I 148 TRP cc_start: 0.8150 (m100) cc_final: 0.7469 (m100) REVERT: I 169 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8327 (mppt) REVERT: J 6 GLU cc_start: 0.7415 (mp0) cc_final: 0.7155 (mp0) REVERT: J 76 ASN cc_start: 0.8233 (t0) cc_final: 0.8019 (t0) REVERT: J 105 GLN cc_start: 0.8393 (pm20) cc_final: 0.7995 (pm20) REVERT: J 148 ASP cc_start: 0.7551 (p0) cc_final: 0.7326 (p0) REVERT: J 152 GLU cc_start: 0.8731 (pm20) cc_final: 0.8432 (pm20) REVERT: J 170 PHE cc_start: 0.9085 (m-80) cc_final: 0.8646 (m-80) REVERT: J 180 TYR cc_start: 0.8848 (m-80) cc_final: 0.8546 (m-80) REVERT: J 201 ASN cc_start: 0.8826 (t0) cc_final: 0.8111 (m110) REVERT: K 76 ASN cc_start: 0.8203 (t0) cc_final: 0.7990 (t0) REVERT: K 148 ASP cc_start: 0.7568 (p0) cc_final: 0.7345 (p0) REVERT: K 152 GLU cc_start: 0.8719 (pm20) cc_final: 0.8419 (pm20) REVERT: K 180 TYR cc_start: 0.8848 (m-80) cc_final: 0.8548 (m-80) REVERT: K 201 ASN cc_start: 0.8820 (t0) cc_final: 0.8111 (m110) REVERT: L 18 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7171 (mmt90) REVERT: L 148 TRP cc_start: 0.8086 (m100) cc_final: 0.7360 (m100) REVERT: L 169 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8322 (mppt) outliers start: 61 outliers final: 26 residues processed: 518 average time/residue: 1.1360 time to fit residues: 677.4252 Evaluate side-chains 467 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 438 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 169 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 229 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN B 20 GLN C 20 GLN C 192 GLN C 204 ASN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 GLN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN J 175 GLN K 175 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20992 Z= 0.241 Angle : 0.723 9.412 28644 Z= 0.372 Chirality : 0.048 0.305 3220 Planarity : 0.006 0.066 3660 Dihedral : 5.244 22.744 2860 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.05 % Allowed : 20.64 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.17 (0.16), residues: 2636 helix: -0.03 (0.51), residues: 124 sheet: 0.87 (0.16), residues: 844 loop : -0.24 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 141 HIS 0.005 0.001 HIS B 166 PHE 0.012 0.002 PHE A 153 TYR 0.026 0.002 TYR I 140 ARG 0.011 0.001 ARG G 18 *********************** 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 522 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 452 time to evaluate : 2.257 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: E 148 TRP cc_start: 0.8155 (m100) cc_final: 0.7362 (m100) REVERT: F 6 GLU cc_start: 0.7260 (mp0) cc_final: 0.6888 (mp0) REVERT: F 27 PHE cc_start: 0.7680 (m-80) cc_final: 0.6139 (m-80) REVERT: F 147 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8524 (tmtm) REVERT: F 148 ASP cc_start: 0.7656 (p0) cc_final: 0.7219 (p0) REVERT: F 152 GLU cc_start: 0.8823 (pm20) cc_final: 0.8516 (pm20) REVERT: F 180 TYR cc_start: 0.8860 (m-80) cc_final: 0.8402 (m-80) REVERT: G 148 TRP cc_start: 0.8163 (m100) cc_final: 0.7450 (m100) REVERT: H 6 GLU cc_start: 0.7035 (mp0) cc_final: 0.6779 (mp0) REVERT: H 105 GLN cc_start: 0.8199 (pm20) cc_final: 0.7693 (pm20) REVERT: H 147 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8527 (tmtm) REVERT: H 148 ASP cc_start: 0.7651 (p0) cc_final: 0.7260 (p0) REVERT: H 152 GLU cc_start: 0.8829 (pm20) cc_final: 0.8510 (pm20) REVERT: H 180 TYR cc_start: 0.8869 (m-80) cc_final: 0.8405 (m-80) REVERT: I 18 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7212 (mmt90) REVERT: I 117 ILE cc_start: 0.9103 (pp) cc_final: 0.8657 (mp) REVERT: I 148 TRP cc_start: 0.8117 (m100) cc_final: 0.7444 (m100) REVERT: J 27 PHE cc_start: 0.7670 (m-80) cc_final: 0.6126 (m-80) REVERT: J 78 PHE cc_start: 0.8588 (m-80) cc_final: 0.8304 (m-80) REVERT: J 152 GLU cc_start: 0.8856 (pm20) cc_final: 0.8607 (pm20) REVERT: J 180 TYR cc_start: 0.8826 (m-80) cc_final: 0.8358 (m-80) REVERT: J 201 ASN cc_start: 0.8859 (t0) cc_final: 0.8231 (m110) REVERT: K 27 PHE cc_start: 0.7665 (m-80) cc_final: 0.6066 (m-80) REVERT: K 78 PHE cc_start: 0.8594 (m-80) cc_final: 0.8303 (m-80) REVERT: K 148 ASP cc_start: 0.7640 (p0) cc_final: 0.7439 (p0) REVERT: K 152 GLU cc_start: 0.8841 (pm20) cc_final: 0.8595 (pm20) REVERT: K 180 TYR cc_start: 0.8818 (m-80) cc_final: 0.8337 (m-80) REVERT: K 201 ASN cc_start: 0.8876 (t0) cc_final: 0.8200 (m110) REVERT: L 18 ARG cc_start: 0.7840 (ttm110) cc_final: 0.7339 (mmt90) REVERT: L 148 TRP cc_start: 0.8132 (m100) cc_final: 0.7529 (m100) outliers start: 70 outliers final: 38 residues processed: 490 average time/residue: 1.1263 time to fit residues: 636.1967 Evaluate side-chains 460 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 420 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 147 LYS Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 221AGLN E 158 ASN ** G 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20992 Z= 0.227 Angle : 0.719 8.095 28644 Z= 0.377 Chirality : 0.047 0.172 3220 Planarity : 0.006 0.064 3660 Dihedral : 5.135 21.261 2860 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.27 % Allowed : 21.90 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.24 (0.16), residues: 2636 helix: -0.02 (0.50), residues: 124 sheet: 0.75 (0.16), residues: 908 loop : -0.12 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 137 HIS 0.005 0.001 HIS D 166 PHE 0.025 0.002 PHE I 139 TYR 0.023 0.002 TYR I 140 ARG 0.014 0.001 ARG I 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 532 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 457 time to evaluate : 2.238 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: E 125 LEU cc_start: 0.9378 (pp) cc_final: 0.9129 (mm) REVERT: E 140 TYR cc_start: 0.8152 (t80) cc_final: 0.7455 (t80) REVERT: E 142 ARG cc_start: 0.8541 (tpp80) cc_final: 0.8256 (ttm-80) REVERT: E 148 TRP cc_start: 0.8185 (m100) cc_final: 0.7428 (m100) REVERT: F 152 GLU cc_start: 0.8855 (pm20) cc_final: 0.8560 (pm20) REVERT: F 180 TYR cc_start: 0.8844 (m-80) cc_final: 0.8511 (m-80) REVERT: G 125 LEU cc_start: 0.9382 (pp) cc_final: 0.9136 (mm) REVERT: G 148 TRP cc_start: 0.8117 (m100) cc_final: 0.7413 (m100) REVERT: H 6 GLU cc_start: 0.7050 (mp0) cc_final: 0.6766 (mp0) REVERT: H 105 GLN cc_start: 0.8230 (pm20) cc_final: 0.7747 (pm20) REVERT: H 147 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8603 (tmtm) REVERT: H 148 ASP cc_start: 0.7699 (p0) cc_final: 0.7314 (p0) REVERT: H 152 GLU cc_start: 0.8858 (pm20) cc_final: 0.8602 (pm20) REVERT: H 180 TYR cc_start: 0.8817 (m-80) cc_final: 0.8592 (m-80) REVERT: I 117 ILE cc_start: 0.9117 (pp) cc_final: 0.8693 (mp) REVERT: I 125 LEU cc_start: 0.9299 (pp) cc_final: 0.9067 (mm) REVERT: I 142 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7761 (ttm-80) REVERT: I 148 TRP cc_start: 0.8133 (m100) cc_final: 0.7451 (m100) REVERT: I 173 TYR cc_start: 0.8484 (m-10) cc_final: 0.7872 (m-10) REVERT: J 147 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8575 (tmmt) REVERT: J 152 GLU cc_start: 0.8826 (pm20) cc_final: 0.8595 (pm20) REVERT: J 180 TYR cc_start: 0.8890 (m-80) cc_final: 0.8604 (m-80) REVERT: J 201 ASN cc_start: 0.8890 (t0) cc_final: 0.8279 (m110) REVERT: K 147 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8516 (tmtm) REVERT: K 148 ASP cc_start: 0.7692 (p0) cc_final: 0.7251 (p0) REVERT: K 152 GLU cc_start: 0.8826 (pm20) cc_final: 0.8604 (pm20) REVERT: K 180 TYR cc_start: 0.8883 (m-80) cc_final: 0.8573 (m-80) REVERT: K 201 ASN cc_start: 0.8882 (t0) cc_final: 0.8263 (m110) REVERT: L 125 LEU cc_start: 0.9285 (pp) cc_final: 0.9060 (mm) REVERT: L 142 ARG cc_start: 0.8698 (tpp80) cc_final: 0.8066 (ttm-80) REVERT: L 148 TRP cc_start: 0.8125 (m100) cc_final: 0.7532 (m100) outliers start: 75 outliers final: 43 residues processed: 499 average time/residue: 1.0893 time to fit residues: 630.7739 Evaluate side-chains 473 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 427 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 147 LYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 117 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221AGLN B 221AGLN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20992 Z= 0.245 Angle : 0.742 8.834 28644 Z= 0.382 Chirality : 0.048 0.272 3220 Planarity : 0.006 0.064 3660 Dihedral : 5.077 18.820 2860 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.01 % Allowed : 22.56 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2636 helix: 0.03 (0.50), residues: 124 sheet: 0.97 (0.17), residues: 824 loop : -0.26 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 47 HIS 0.007 0.001 HIS A 166 PHE 0.018 0.002 PHE G 62 TYR 0.026 0.002 TYR I 140 ARG 0.014 0.001 ARG L 142 *********************** 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 507 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 438 time to evaluate : 2.364 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: E 148 TRP cc_start: 0.8150 (m100) cc_final: 0.7442 (m100) REVERT: F 147 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8526 (tmtm) REVERT: F 152 GLU cc_start: 0.8857 (pm20) cc_final: 0.8602 (pm20) REVERT: F 180 TYR cc_start: 0.8834 (m-80) cc_final: 0.8627 (m-80) REVERT: G 148 TRP cc_start: 0.8138 (m100) cc_final: 0.7436 (m100) REVERT: H 6 GLU cc_start: 0.7065 (mp0) cc_final: 0.6767 (mp0) REVERT: H 105 GLN cc_start: 0.8221 (pm20) cc_final: 0.7749 (pm20) REVERT: H 152 GLU cc_start: 0.8861 (pm20) cc_final: 0.8603 (pm20) REVERT: I 117 ILE cc_start: 0.9154 (pp) cc_final: 0.8731 (mt) REVERT: I 125 LEU cc_start: 0.9320 (pp) cc_final: 0.9110 (mm) REVERT: I 148 TRP cc_start: 0.8080 (m100) cc_final: 0.7431 (m100) REVERT: J 78 PHE cc_start: 0.8448 (m-80) cc_final: 0.8195 (m-80) REVERT: J 105 GLN cc_start: 0.8524 (pm20) cc_final: 0.8254 (pm20) REVERT: J 147 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8505 (tmtm) REVERT: J 148 ASP cc_start: 0.7765 (p0) cc_final: 0.7486 (p0) REVERT: J 152 GLU cc_start: 0.8893 (pm20) cc_final: 0.8569 (pm20) REVERT: J 201 ASN cc_start: 0.8911 (t0) cc_final: 0.8340 (m110) REVERT: K 78 PHE cc_start: 0.8451 (m-80) cc_final: 0.8206 (m-80) REVERT: K 147 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8595 (tmtm) REVERT: K 148 ASP cc_start: 0.7733 (p0) cc_final: 0.7344 (p0) REVERT: K 152 GLU cc_start: 0.8877 (pm20) cc_final: 0.8558 (pm20) REVERT: K 180 TYR cc_start: 0.8859 (m-80) cc_final: 0.8658 (m-10) REVERT: K 201 ASN cc_start: 0.8872 (t0) cc_final: 0.8295 (m110) REVERT: L 142 ARG cc_start: 0.8565 (tpp80) cc_final: 0.8362 (ttm-80) REVERT: L 148 TRP cc_start: 0.8120 (m100) cc_final: 0.7529 (m100) outliers start: 69 outliers final: 51 residues processed: 476 average time/residue: 1.1300 time to fit residues: 620.8023 Evaluate side-chains 469 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 415 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 147 LYS Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 147 LYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.8980 chunk 101 optimal weight: 0.0050 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN D 50 GLN D 221AGLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20992 Z= 0.227 Angle : 0.762 9.052 28644 Z= 0.395 Chirality : 0.048 0.194 3220 Planarity : 0.006 0.064 3660 Dihedral : 5.019 22.134 2860 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.97 % Allowed : 23.52 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.05 (0.50), residues: 124 sheet: 1.00 (0.17), residues: 848 loop : -0.27 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 137 HIS 0.008 0.001 HIS D 166 PHE 0.026 0.002 PHE G 139 TYR 0.029 0.002 TYR I 140 ARG 0.013 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 519 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 451 time to evaluate : 2.489 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: E 125 LEU cc_start: 0.9373 (pp) cc_final: 0.9100 (mm) REVERT: E 148 TRP cc_start: 0.8134 (m100) cc_final: 0.7483 (m100) REVERT: F 147 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8593 (ttpp) REVERT: F 152 GLU cc_start: 0.8845 (pm20) cc_final: 0.8612 (pm20) REVERT: G 125 LEU cc_start: 0.9377 (pp) cc_final: 0.9108 (mm) REVERT: G 148 TRP cc_start: 0.8123 (m100) cc_final: 0.7396 (m100) REVERT: H 6 GLU cc_start: 0.7046 (mp0) cc_final: 0.6737 (mp0) REVERT: H 105 GLN cc_start: 0.8201 (pm20) cc_final: 0.7725 (pm20) REVERT: H 147 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8581 (tmtm) REVERT: H 148 ASP cc_start: 0.7773 (p0) cc_final: 0.7477 (p0) REVERT: H 152 GLU cc_start: 0.8825 (pm20) cc_final: 0.8581 (pm20) REVERT: I 18 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7148 (mmt90) REVERT: I 117 ILE cc_start: 0.9145 (pp) cc_final: 0.8774 (mt) REVERT: I 148 TRP cc_start: 0.8074 (m100) cc_final: 0.7492 (m100) REVERT: J 147 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8564 (tmtm) REVERT: J 148 ASP cc_start: 0.7722 (p0) cc_final: 0.7411 (p0) REVERT: J 201 ASN cc_start: 0.8897 (t0) cc_final: 0.8358 (m110) REVERT: K 147 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8590 (tmtm) REVERT: K 148 ASP cc_start: 0.7767 (p0) cc_final: 0.7392 (p0) REVERT: K 152 GLU cc_start: 0.8872 (pm20) cc_final: 0.8565 (pm20) REVERT: K 201 ASN cc_start: 0.8897 (t0) cc_final: 0.8358 (m110) REVERT: L 18 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7129 (mmt90) REVERT: L 148 TRP cc_start: 0.8067 (m100) cc_final: 0.7413 (m100) outliers start: 68 outliers final: 53 residues processed: 487 average time/residue: 1.1479 time to fit residues: 645.8940 Evaluate side-chains 482 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 425 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 147 LYS Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 147 LYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 117 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 142 optimal weight: 0.0050 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 236 optimal weight: 0.3980 chunk 155 optimal weight: 9.9990 overall best weight: 2.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 79 GLN B 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 20992 Z= 0.498 Angle : 0.851 8.854 28644 Z= 0.445 Chirality : 0.051 0.194 3220 Planarity : 0.006 0.066 3660 Dihedral : 5.343 20.405 2860 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.88 % Allowed : 24.43 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.07 (0.48), residues: 128 sheet: 0.79 (0.17), residues: 840 loop : -0.31 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 158 HIS 0.008 0.001 HIS D 166 PHE 0.026 0.002 PHE H 27 TYR 0.038 0.003 TYR D 75 ARG 0.015 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 486 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 420 time to evaluate : 2.417 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: E 211 ARG cc_start: 0.7307 (ttp-170) cc_final: 0.6943 (ptm160) REVERT: F 152 GLU cc_start: 0.8920 (pm20) cc_final: 0.8680 (pm20) REVERT: H 6 GLU cc_start: 0.7185 (mp0) cc_final: 0.6880 (mp0) REVERT: H 105 GLN cc_start: 0.8285 (pm20) cc_final: 0.7770 (pm20) REVERT: H 147 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8680 (tmtm) REVERT: I 18 ARG cc_start: 0.7937 (ttm110) cc_final: 0.7377 (mmt90) REVERT: I 117 ILE cc_start: 0.9232 (pp) cc_final: 0.8871 (mt) REVERT: I 148 TRP cc_start: 0.8140 (m100) cc_final: 0.7526 (m100) REVERT: J 78 PHE cc_start: 0.8578 (m-80) cc_final: 0.8320 (m-80) REVERT: J 147 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8629 (tmtm) REVERT: J 201 ASN cc_start: 0.8920 (t0) cc_final: 0.8408 (m110) REVERT: K 78 PHE cc_start: 0.8597 (m-80) cc_final: 0.8331 (m-80) REVERT: K 147 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8686 (tmtm) REVERT: K 148 ASP cc_start: 0.7813 (p0) cc_final: 0.7450 (p0) REVERT: K 201 ASN cc_start: 0.8931 (t0) cc_final: 0.8408 (m110) REVERT: L 18 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7352 (mmt90) REVERT: L 148 TRP cc_start: 0.8121 (m100) cc_final: 0.7465 (m100) outliers start: 66 outliers final: 59 residues processed: 454 average time/residue: 1.1875 time to fit residues: 623.7171 Evaluate side-chains 464 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 402 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 147 LYS Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 26 ARG Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 147 LYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 117 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 263 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20992 Z= 0.261 Angle : 0.848 9.215 28644 Z= 0.443 Chirality : 0.049 0.200 3220 Planarity : 0.006 0.064 3660 Dihedral : 5.404 28.797 2860 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.23 % Allowed : 26.05 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.16), residues: 2636 helix: 0.01 (0.49), residues: 128 sheet: 1.00 (0.17), residues: 800 loop : -0.37 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 148 HIS 0.009 0.001 HIS D 166 PHE 0.028 0.002 PHE L 139 TYR 0.029 0.002 TYR L 140 ARG 0.017 0.001 ARG I 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 482 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 431 time to evaluate : 2.434 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: E 125 LEU cc_start: 0.9386 (pp) cc_final: 0.9068 (mm) REVERT: E 148 TRP cc_start: 0.8145 (m100) cc_final: 0.7619 (m100) REVERT: G 125 LEU cc_start: 0.9389 (pp) cc_final: 0.9074 (mm) REVERT: G 148 TRP cc_start: 0.8138 (m100) cc_final: 0.7636 (m100) REVERT: H 6 GLU cc_start: 0.7072 (mp0) cc_final: 0.6818 (mp0) REVERT: H 105 GLN cc_start: 0.8262 (pm20) cc_final: 0.7725 (pm20) REVERT: H 147 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8743 (tmtm) REVERT: I 18 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7292 (mmt90) REVERT: I 117 ILE cc_start: 0.9207 (pp) cc_final: 0.8903 (mt) REVERT: I 148 TRP cc_start: 0.8083 (m100) cc_final: 0.7465 (m100) REVERT: J 147 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8623 (tmtm) REVERT: J 201 ASN cc_start: 0.8942 (t0) cc_final: 0.8429 (m110) REVERT: K 3 GLN cc_start: 0.7323 (pm20) cc_final: 0.6650 (pm20) REVERT: K 147 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8685 (tmtm) REVERT: K 148 ASP cc_start: 0.7755 (p0) cc_final: 0.7387 (p0) REVERT: K 201 ASN cc_start: 0.8938 (t0) cc_final: 0.8432 (m110) REVERT: L 18 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7264 (mmt90) REVERT: L 148 TRP cc_start: 0.8056 (m100) cc_final: 0.7379 (m100) outliers start: 51 outliers final: 45 residues processed: 457 average time/residue: 1.1436 time to fit residues: 602.9293 Evaluate side-chains 466 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 418 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 147 LYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 147 LYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 193 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 87 optimal weight: 0.0870 chunk 215 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.0050 chunk 184 optimal weight: 0.0870 overall best weight: 0.3150 ------------------------------------------------------------------------------- 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 K 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.101823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.062976 restraints weight = 42219.624| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.42 r_work: 0.2628 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20992 Z= 0.223 Angle : 0.832 10.780 28644 Z= 0.432 Chirality : 0.049 0.206 3220 Planarity : 0.006 0.062 3660 Dihedral : 5.316 29.011 2860 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.31 % Allowed : 26.35 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.03 (0.49), residues: 128 sheet: 1.15 (0.17), residues: 804 loop : -0.43 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 158 HIS 0.009 0.001 HIS C 166 PHE 0.036 0.002 PHE H 27 TYR 0.027 0.002 TYR K 180 ARG 0.014 0.001 ARG L 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9713.27 seconds wall clock time: 175 minutes 26.96 seconds (10526.96 seconds total)