Starting phenix.real_space_refine on Mon Nov 18 23:08:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/11_2024/8st3_40756_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/11_2024/8st3_40756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/11_2024/8st3_40756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/11_2024/8st3_40756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/11_2024/8st3_40756_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/11_2024/8st3_40756_trim.cif" } resolution = 2.93 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= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 S 135 5.16 5 Na 1 4.78 5 C 16377 2.51 5 N 4096 2.21 5 O 4753 1.98 5 H 24962 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 50327 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "B" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5937 Classifications: {'peptide': 363} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5937 Classifications: {'peptide': 363} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "E" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5937 Classifications: {'peptide': 363} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 340} Chain breaks: 1 Chain: "F" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "H" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "I" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "J" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "K" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Unusual residues: {' CA': 2, 'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 53 Unusual residues: {' CA': 1, 'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 23.57, per 1000 atoms: 0.47 Number of scatterers: 50327 At special positions: 0 Unit cell: (149.716, 198.908, 144.369, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 135 16.00 Na 1 11.00 O 4753 8.00 N 4096 7.00 C 16377 6.00 H 24962 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 199 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 147 " - pdb=" SG CYS K 202 " distance=2.03 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 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 701 " - " ASN A 31 " " NAG A 702 " - " ASN A 81 " " NAG A 703 " - " ASN A 148 " " NAG D 701 " - " ASN D 31 " " NAG D 702 " - " ASN D 81 " " NAG D 703 " - " ASN D 148 " " NAG L 1 " - " ASN B 143 " " NAG M 1 " - " ASN C 143 " " NAG N 1 " - " ASN E 143 " Time building additional restraints: 12.84 Conformation dependent library (CDL) restraints added in 3.7 seconds 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6014 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 50 sheets defined 27.5% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.37 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 75 through 80 removed outlier: 4.257A pdb=" N GLU A 80 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 217 through 234 removed outlier: 4.649A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.870A pdb=" N LEU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.439A pdb=" N VAL A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 268 Processing helix chain 'A' and resid 278 through 306 Processing helix chain 'A' and resid 315 through 330 removed outlier: 5.750A pdb=" N VAL A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 341 through 382 Proline residue: A 379 - end of helix Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.898A pdb=" N THR B 68 " --> pdb=" O TYR B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.102A pdb=" N ASP B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.368A pdb=" N ILE B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Proline residue: B 219 - end of helix removed outlier: 3.633A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 4.580A pdb=" N VAL B 230 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.631A pdb=" N GLY B 238 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 262 Processing helix chain 'B' and resid 270 through 298 Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 316 through 322 removed outlier: 3.955A pdb=" N ALA B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 364 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.504A pdb=" N LEU B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 70 through 75 removed outlier: 4.021A pdb=" N ASP C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 209 through 225 removed outlier: 4.550A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix Processing helix chain 'C' and resid 226 through 227 No H-bonds generated for 'chain 'C' and resid 226 through 227' Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.682A pdb=" N GLY C 238 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 262 Processing helix chain 'C' and resid 270 through 298 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 316 through 322 removed outlier: 3.931A pdb=" N ALA C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 363 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.935A pdb=" N GLY C 367 " --> pdb=" O PHE C 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 19 Processing helix chain 'D' and resid 75 through 80 removed outlier: 4.234A pdb=" N GLU D 80 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 234 removed outlier: 4.476A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.918A pdb=" N LEU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 removed outlier: 4.062A pdb=" N VAL D 238 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 268 Processing helix chain 'D' and resid 278 through 306 Processing helix chain 'D' and resid 315 through 330 removed outlier: 5.646A pdb=" N VAL D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Proline residue: D 327 - end of helix Processing helix chain 'D' and resid 341 through 382 Proline residue: D 379 - end of helix Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 65 through 68 removed outlier: 3.777A pdb=" N THR E 68 " --> pdb=" O TYR E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 68' Processing helix chain 'E' and resid 70 through 75 removed outlier: 3.785A pdb=" N ASP E 75 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.486A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix removed outlier: 3.677A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 4.374A pdb=" N VAL E 230 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 239 through 262 Processing helix chain 'E' and resid 270 through 298 Processing helix chain 'E' and resid 307 through 314 Processing helix chain 'E' and resid 316 through 322 removed outlier: 3.793A pdb=" N ALA E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 363 Processing helix chain 'E' and resid 364 through 366 No H-bonds generated for 'chain 'E' and resid 364 through 366' Processing helix chain 'F' and resid 84 through 88 Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 193 through 198 removed outlier: 3.980A pdb=" N SER G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 210 Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 188 through 192 removed outlier: 3.704A pdb=" N GLU H 192 " --> pdb=" O LYS H 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 188 through 192' Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.679A pdb=" N TYR I 33 " --> pdb=" O PHE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 removed outlier: 3.545A pdb=" N ARG I 66 " --> pdb=" O GLU I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 63 through 66' Processing helix chain 'J' and resid 84 through 88 Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 187 through 194 removed outlier: 4.381A pdb=" N HIS J 194 " --> pdb=" O GLU J 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 33 removed outlier: 3.521A pdb=" N TYR K 33 " --> pdb=" O PHE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 66 Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'K' and resid 193 through 198 removed outlier: 4.436A pdb=" N SER K 197 " --> pdb=" O SER K 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.868A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY A 121 " --> pdb=" O ASP A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.868A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY A 121 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET A 56 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP A 49 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 58 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.436A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 189 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.970A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.970A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 51 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 45 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR B 53 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP B 57 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU B 39 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B 59 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL B 37 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU B 61 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU B 35 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLU B 63 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL B 33 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.041A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 204 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.041A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 83 removed outlier: 3.921A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 83 removed outlier: 3.921A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER C 44 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.150A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.150A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.991A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.991A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN D 60 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU D 47 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N TRP D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA D 45 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS D 64 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N SER D 43 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLU D 66 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY D 41 " --> pdb=" O GLU D 66 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N HIS D 68 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ARG D 39 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.432A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 189 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 83 removed outlier: 3.932A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 83 removed outlier: 3.932A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN E 55 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU E 42 " --> pdb=" O ASN E 55 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TRP E 57 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA E 40 " --> pdb=" O TRP E 57 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR E 59 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER E 38 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLU E 61 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N MET E 36 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N GLU E 63 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N GLN E 34 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.215A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE E 204 " --> pdb=" O VAL E 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.215A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.780A pdb=" N GLU F 110 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP F 40 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.757A pdb=" N ASN F 142 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER F 179 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER F 167 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 149 through 152 removed outlier: 3.581A pdb=" N ASN F 150 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'F' and resid 196 through 198 Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.048A pdb=" N THR G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.406A pdb=" N ILE G 35 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU G 51 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 127 through 130 removed outlier: 3.534A pdb=" N CYS G 147 " --> pdb=" O SER G 186 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.678A pdb=" N VAL G 143 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 158 through 161 Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.054A pdb=" N GLY H 89 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TRP H 40 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.578A pdb=" N ASN H 142 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL H 138 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER H 179 " --> pdb=" O THR H 169 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER H 167 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR H 183 " --> pdb=" O LEU H 165 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 149 through 152 removed outlier: 3.756A pdb=" N LYS H 212 " --> pdb=" O CYS H 199 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 154 through 155 Processing sheet with id=AD8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.529A pdb=" N THR I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.440A pdb=" N ILE I 35 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU I 51 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 11 through 13 removed outlier: 7.058A pdb=" N CYS I 97 " --> pdb=" O TYR I 109 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR I 109 " --> pdb=" O CYS I 97 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG I 99 " --> pdb=" O MET I 107 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET I 107 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.507A pdb=" N LYS I 150 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR I 182 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL I 143 " --> pdb=" O VAL I 190 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.507A pdb=" N LYS I 150 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR I 182 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER I 187 " --> pdb=" O HIS I 171 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 158 through 161 removed outlier: 4.285A pdb=" N CYS I 202 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS I 215 " --> pdb=" O CYS I 202 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.786A pdb=" N GLY J 89 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU J 38 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR J 54 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TRP J 40 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 119 through 123 Processing sheet with id=AE8, first strand: chain 'J' and resid 119 through 123 removed outlier: 6.210A pdb=" N TYR J 178 " --> pdb=" O ASN J 143 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER J 179 " --> pdb=" O THR J 169 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 158 through 160 removed outlier: 4.455A pdb=" N TRP J 153 " --> pdb=" O ARG J 160 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS J 152 " --> pdb=" O GLU J 200 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS J 154 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR J 198 " --> pdb=" O LYS J 154 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS J 203 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER J 208 " --> pdb=" O HIS J 203 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.434A pdb=" N ILE K 35 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU K 51 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP K 37 " --> pdb=" O ILE K 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.979A pdb=" N GLY K 146 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS K 147 " --> pdb=" O SER K 186 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER K 186 " --> pdb=" O CYS K 147 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL K 149 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR K 182 " --> pdb=" O GLY K 151 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL K 143 " --> pdb=" O VAL K 190 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.979A pdb=" N GLY K 146 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS K 147 " --> pdb=" O SER K 186 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER K 186 " --> pdb=" O CYS K 147 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL K 149 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR K 182 " --> pdb=" O GLY K 151 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N SER K 185 " --> pdb=" O PRO K 174 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER K 187 " --> pdb=" O THR K 172 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR K 172 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR K 189 " --> pdb=" O VAL K 170 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL K 170 " --> pdb=" O THR K 189 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 202 through 206 removed outlier: 4.277A pdb=" N CYS K 202 " --> pdb=" O LYS K 215 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS K 215 " --> pdb=" O CYS K 202 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3264 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: 22.19 Time building geometry restraints manager: 15.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 24937 1.04 - 1.24: 2578 1.24 - 1.43: 8748 1.43 - 1.63: 14521 1.63 - 1.83: 207 Bond restraints: 50991 Sorted by residual: bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ASP J 1 " pdb=" CA ASP J 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" N ASP H 1 " pdb=" CA ASP H 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.59e+00 bond pdb=" N ASP H 1 " pdb=" H ASP H 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" N ASP F 1 " pdb=" H ASP F 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 ... (remaining 50986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 90280 1.46 - 2.91: 1655 2.91 - 4.37: 201 4.37 - 5.83: 21 5.83 - 7.29: 6 Bond angle restraints: 92163 Sorted by residual: angle pdb=" N SER I 179 " pdb=" CA SER I 179 " pdb=" C SER I 179 " ideal model delta sigma weight residual 112.72 108.96 3.76 1.28e+00 6.10e-01 8.64e+00 angle pdb=" C ASP B 193 " pdb=" N SER B 194 " pdb=" CA SER B 194 " ideal model delta sigma weight residual 121.54 127.09 -5.55 1.91e+00 2.74e-01 8.45e+00 angle pdb=" N SER K 179 " pdb=" CA SER K 179 " pdb=" C SER K 179 " ideal model delta sigma weight residual 112.93 109.43 3.50 1.33e+00 5.65e-01 6.94e+00 angle pdb=" N ASP A 104 " pdb=" CA ASP A 104 " pdb=" CB ASP A 104 " ideal model delta sigma weight residual 112.47 108.65 3.82 1.52e+00 4.33e-01 6.32e+00 angle pdb=" C PRO E 90 " pdb=" N ASP E 91 " pdb=" CA ASP E 91 " ideal model delta sigma weight residual 122.21 118.56 3.65 1.48e+00 4.57e-01 6.09e+00 ... (remaining 92158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 22771 21.90 - 43.80: 1356 43.80 - 65.69: 294 65.69 - 87.59: 67 87.59 - 109.49: 15 Dihedral angle restraints: 24503 sinusoidal: 13255 harmonic: 11248 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual -86.00 -173.56 87.56 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 93 " pdb=" CB CYS F 93 " ideal model delta sinusoidal sigma weight residual 93.00 147.72 -54.72 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS E 130 " pdb=" SG CYS E 130 " pdb=" SG CYS E 144 " pdb=" CB CYS E 144 " ideal model delta sinusoidal sigma weight residual 93.00 42.32 50.68 1 1.00e+01 1.00e-02 3.52e+01 ... (remaining 24500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3334 0.052 - 0.104: 627 0.104 - 0.156: 149 0.156 - 0.208: 0 0.208 - 0.261: 3 Chirality restraints: 4113 Sorted by residual: chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.51 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4110 not shown) Planarity restraints: 7357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 326 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO C 327 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 327 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 327 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 180 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ILE C 180 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE C 180 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL C 181 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 307 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO E 308 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 308 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 308 " -0.028 5.00e-02 4.00e+02 ... (remaining 7354 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 711 2.07 - 2.70: 79892 2.70 - 3.33: 145826 3.33 - 3.97: 193484 3.97 - 4.60: 300883 Nonbonded interactions: 720796 Sorted by model distance: nonbonded pdb="HD21 ASN H 166 " pdb=" HZ3 TRP H 168 " model vdw 1.432 2.100 nonbonded pdb=" OE1 GLU K 90 " pdb=" H GLU K 90 " model vdw 1.488 2.450 nonbonded pdb=" OE1 GLU F 86 " pdb=" H GLU F 86 " model vdw 1.536 2.450 nonbonded pdb=" O GLN J 129 " pdb="HE21 GLN J 129 " model vdw 1.552 2.450 nonbonded pdb=" HD2 TYR D 197 " pdb=" OD2 ASP E 171 " model vdw 1.566 2.450 ... (remaining 720791 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' and (resid 5 through 383 or resid 701 through 705)) selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 1 through 372) selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.440 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: 0.830 Extract box with map and model: 1.730 Check model and map are aligned: 0.350 Set scattering table: 0.470 Process input model: 102.570 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.280 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:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.005 0.044 26029 Z= 0.305 Angle : 0.554 7.287 35502 Z= 0.282 Chirality : 0.044 0.261 4113 Planarity : 0.004 0.075 4389 Dihedral : 15.963 109.490 9596 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.07 % Allowed : 14.55 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.15 (0.15), residues: 3127 helix: 1.74 (0.20), residues: 670 sheet: -0.14 (0.16), residues: 1016 loop : -0.41 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 101 HIS 0.005 0.001 HIS D 305 PHE 0.011 0.001 PHE B 278 TYR 0.032 0.001 TYR E 95 ARG 0.011 0.001 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 3.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.7336 (t0) cc_final: 0.7098 (t0) REVERT: B 368 MET cc_start: 0.3868 (tmm) cc_final: 0.3512 (mmp) REVERT: C 95 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8961 (m-80) REVERT: F 11 LEU cc_start: 0.7949 (tp) cc_final: 0.7633 (tt) REVERT: F 35 ASN cc_start: 0.6346 (m110) cc_final: 0.6086 (m-40) REVERT: F 66 ARG cc_start: 0.7902 (ptt-90) cc_final: 0.7471 (ptt-90) REVERT: F 84 GLU cc_start: 0.7464 (mp0) cc_final: 0.7086 (mp0) REVERT: F 178 TYR cc_start: 0.7413 (m-80) cc_final: 0.7171 (m-80) REVERT: G 158 THR cc_start: 0.8918 (m) cc_final: 0.8644 (p) REVERT: H 11 LEU cc_start: 0.8408 (tp) cc_final: 0.8066 (tt) REVERT: H 24 ARG cc_start: 0.6891 (mtp-110) cc_final: 0.6527 (ttm110) REVERT: I 155 GLU cc_start: 0.8976 (mp0) cc_final: 0.8672 (OUTLIER) REVERT: J 58 ASN cc_start: 0.8542 (m110) cc_final: 0.8316 (m-40) REVERT: J 84 GLU cc_start: 0.7231 (tt0) cc_final: 0.6403 (tm-30) outliers start: 2 outliers final: 3 residues processed: 340 average time/residue: 2.6570 time to fit residues: 1064.9888 Evaluate side-chains 261 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 258 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain F residue 65 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 8.9990 chunk 233 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 241 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN G 4 GLN G 6 GLN G 60 ASN H 43 GLN ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26029 Z= 0.282 Angle : 0.561 6.235 35502 Z= 0.293 Chirality : 0.045 0.156 4113 Planarity : 0.005 0.063 4389 Dihedral : 6.654 66.346 3724 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.18 % Allowed : 15.39 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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 (0.15), residues: 3127 helix: 1.87 (0.20), residues: 693 sheet: -0.20 (0.16), residues: 993 loop : -0.50 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 101 HIS 0.003 0.001 HIS A 305 PHE 0.013 0.001 PHE H 140 TYR 0.014 0.001 TYR E 95 ARG 0.010 0.001 ARG J 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 MET cc_start: 0.3972 (tmm) cc_final: 0.3506 (mmp) REVERT: C 95 TYR cc_start: 0.9340 (OUTLIER) cc_final: 0.8947 (m-80) REVERT: D 364 MET cc_start: 0.8129 (ttm) cc_final: 0.7839 (ttt) REVERT: E 95 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.6963 (m-10) REVERT: F 4 MET cc_start: 0.7456 (mmm) cc_final: 0.7116 (mmm) REVERT: F 66 ARG cc_start: 0.7909 (ptt-90) cc_final: 0.7625 (ptt-90) REVERT: F 82 ARG cc_start: 0.7725 (ttp-110) cc_final: 0.7490 (mpp80) REVERT: F 84 GLU cc_start: 0.7261 (mp0) cc_final: 0.6833 (mp0) REVERT: G 158 THR cc_start: 0.8939 (m) cc_final: 0.8666 (p) REVERT: H 11 LEU cc_start: 0.8280 (tp) cc_final: 0.7954 (tt) REVERT: H 24 ARG cc_start: 0.7167 (mtp-110) cc_final: 0.6629 (ttm110) REVERT: H 195 ASN cc_start: 0.7368 (p0) cc_final: 0.7167 (p0) REVERT: I 155 GLU cc_start: 0.8956 (mp0) cc_final: 0.8681 (mp0) REVERT: I 181 LEU cc_start: 0.9292 (mm) cc_final: 0.9072 (mm) outliers start: 34 outliers final: 16 residues processed: 287 average time/residue: 2.6297 time to fit residues: 892.8905 Evaluate side-chains 262 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 105 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 280 optimal weight: 9.9990 chunk 302 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 166 ASN J 195 ASN K 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26029 Z= 0.345 Angle : 0.558 6.236 35502 Z= 0.289 Chirality : 0.045 0.153 4113 Planarity : 0.005 0.074 4389 Dihedral : 5.482 51.605 3722 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 1.67 % Allowed : 15.18 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.00 (0.15), residues: 3127 helix: 1.76 (0.20), residues: 693 sheet: -0.31 (0.16), residues: 998 loop : -0.57 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 101 HIS 0.005 0.001 HIS A 305 PHE 0.019 0.001 PHE J 214 TYR 0.014 0.002 TYR E 95 ARG 0.007 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8585 (mp) REVERT: B 368 MET cc_start: 0.4068 (tmm) cc_final: 0.3505 (mmp) REVERT: C 95 TYR cc_start: 0.9337 (OUTLIER) cc_final: 0.8808 (m-80) REVERT: D 56 MET cc_start: 0.8928 (mtp) cc_final: 0.8360 (mtt) REVERT: D 364 MET cc_start: 0.8129 (ttm) cc_final: 0.7805 (ttt) REVERT: E 95 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.7078 (m-10) REVERT: F 4 MET cc_start: 0.7908 (mmm) cc_final: 0.7274 (mmm) REVERT: F 176 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8368 (p) REVERT: H 24 ARG cc_start: 0.7262 (mtp-110) cc_final: 0.6739 (ttm110) REVERT: H 149 ILE cc_start: 0.6643 (tt) cc_final: 0.6279 (tp) REVERT: I 155 GLU cc_start: 0.8942 (mp0) cc_final: 0.8657 (OUTLIER) REVERT: J 210 ILE cc_start: 0.7696 (tp) cc_final: 0.7105 (pp) REVERT: J 216 ARG cc_start: 0.6473 (ttp80) cc_final: 0.6037 (tpm170) outliers start: 48 outliers final: 26 residues processed: 285 average time/residue: 2.6471 time to fit residues: 891.7801 Evaluate side-chains 274 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 4.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain J residue 154 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 281 optimal weight: 6.9990 chunk 297 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 60 ASN H 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26029 Z= 0.229 Angle : 0.516 6.555 35502 Z= 0.266 Chirality : 0.044 0.157 4113 Planarity : 0.004 0.074 4389 Dihedral : 4.911 52.186 3722 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 1.46 % Allowed : 15.98 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.04 (0.15), residues: 3127 helix: 1.85 (0.20), residues: 693 sheet: -0.29 (0.16), residues: 987 loop : -0.57 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 101 HIS 0.003 0.001 HIS A 305 PHE 0.014 0.001 PHE H 140 TYR 0.016 0.001 TYR K 105 ARG 0.009 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 248 time to evaluate : 3.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.9109 (mtm) cc_final: 0.8883 (ttm) REVERT: B 286 SER cc_start: 0.9429 (OUTLIER) cc_final: 0.9194 (p) REVERT: B 321 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8548 (mp) REVERT: B 368 MET cc_start: 0.3993 (tmm) cc_final: 0.3426 (mmp) REVERT: C 36 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.7703 (tmm) REVERT: C 95 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8811 (m-80) REVERT: D 56 MET cc_start: 0.8900 (mtp) cc_final: 0.8342 (mtt) REVERT: D 364 MET cc_start: 0.8092 (ttm) cc_final: 0.7751 (ttt) REVERT: E 95 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.7055 (m-10) REVERT: F 4 MET cc_start: 0.7997 (mmm) cc_final: 0.7364 (mmm) REVERT: F 84 GLU cc_start: 0.7033 (mp0) cc_final: 0.6293 (mp0) REVERT: G 158 THR cc_start: 0.8994 (m) cc_final: 0.8729 (p) REVERT: H 24 ARG cc_start: 0.7255 (mtp-110) cc_final: 0.6751 (ttm110) REVERT: H 87 ASP cc_start: 0.7937 (m-30) cc_final: 0.7669 (m-30) REVERT: H 149 ILE cc_start: 0.6479 (tt) cc_final: 0.6189 (tp) REVERT: J 210 ILE cc_start: 0.7898 (tp) cc_final: 0.7263 (pp) REVERT: J 216 ARG cc_start: 0.6203 (ttp80) cc_final: 0.5767 (tpm170) outliers start: 42 outliers final: 22 residues processed: 276 average time/residue: 2.5557 time to fit residues: 842.1377 Evaluate side-chains 264 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 171 HIS Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain J residue 154 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 221 optimal weight: 30.0000 chunk 122 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 267 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8474 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26029 Z= 0.200 Angle : 0.501 6.515 35502 Z= 0.257 Chirality : 0.043 0.169 4113 Planarity : 0.004 0.073 4389 Dihedral : 4.659 52.698 3722 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 1.29 % Allowed : 16.26 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.12 (0.15), residues: 3127 helix: 2.05 (0.20), residues: 681 sheet: -0.29 (0.16), residues: 986 loop : -0.54 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 101 HIS 0.003 0.001 HIS B 297 PHE 0.010 0.001 PHE C 254 TYR 0.017 0.001 TYR H 145 ARG 0.010 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6753 (tt0) REVERT: B 286 SER cc_start: 0.9435 (OUTLIER) cc_final: 0.9206 (p) REVERT: B 321 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8549 (mp) REVERT: B 368 MET cc_start: 0.4027 (tmm) cc_final: 0.3444 (mmp) REVERT: C 36 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.7696 (tmm) REVERT: C 95 TYR cc_start: 0.9325 (OUTLIER) cc_final: 0.8826 (m-80) REVERT: D 56 MET cc_start: 0.8879 (mtp) cc_final: 0.8305 (mtt) REVERT: D 364 MET cc_start: 0.8117 (ttm) cc_final: 0.7792 (ttp) REVERT: E 95 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.7056 (m-10) REVERT: F 4 MET cc_start: 0.8050 (mmm) cc_final: 0.7442 (mmm) REVERT: F 168 TRP cc_start: 0.8901 (m-90) cc_final: 0.8457 (m-90) REVERT: F 180 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.5650 (tpp) REVERT: G 158 THR cc_start: 0.9021 (m) cc_final: 0.8749 (p) REVERT: H 24 ARG cc_start: 0.7187 (mtp-110) cc_final: 0.6693 (ttm110) REVERT: H 87 ASP cc_start: 0.7906 (m-30) cc_final: 0.7613 (m-30) REVERT: H 149 ILE cc_start: 0.6256 (tt) cc_final: 0.6010 (tp) REVERT: H 180 MET cc_start: 0.6890 (tpp) cc_final: 0.6462 (tpt) REVERT: J 210 ILE cc_start: 0.7897 (tp) cc_final: 0.7140 (pp) outliers start: 37 outliers final: 23 residues processed: 276 average time/residue: 2.5322 time to fit residues: 831.0893 Evaluate side-chains 270 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain G residue 171 HIS Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 105 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 174 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 chunk 247 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26029 Z= 0.182 Angle : 0.493 6.664 35502 Z= 0.253 Chirality : 0.043 0.169 4113 Planarity : 0.004 0.082 4389 Dihedral : 4.526 52.987 3722 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.51 % Rotamer: Outliers : 1.25 % Allowed : 16.57 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.19 (0.15), residues: 3127 helix: 2.20 (0.20), residues: 675 sheet: -0.27 (0.16), residues: 984 loop : -0.51 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 101 HIS 0.003 0.001 HIS B 297 PHE 0.011 0.001 PHE I 173 TYR 0.016 0.001 TYR F 145 ARG 0.011 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6800 (tt0) REVERT: A 344 ARG cc_start: 0.7491 (ttp-110) cc_final: 0.7259 (ttp-110) REVERT: B 77 MET cc_start: 0.9135 (mtm) cc_final: 0.8916 (ttm) REVERT: B 286 SER cc_start: 0.9434 (OUTLIER) cc_final: 0.9198 (p) REVERT: B 368 MET cc_start: 0.4018 (tmm) cc_final: 0.3500 (tpt) REVERT: C 36 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.7730 (tmm) REVERT: C 95 TYR cc_start: 0.9321 (OUTLIER) cc_final: 0.8691 (m-10) REVERT: D 56 MET cc_start: 0.8864 (mtp) cc_final: 0.8284 (mtt) REVERT: D 364 MET cc_start: 0.8124 (ttm) cc_final: 0.7794 (ttp) REVERT: E 95 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.7068 (m-10) REVERT: F 4 MET cc_start: 0.8097 (mmm) cc_final: 0.7522 (mmm) REVERT: G 158 THR cc_start: 0.9031 (m) cc_final: 0.8763 (p) REVERT: H 87 ASP cc_start: 0.7906 (m-30) cc_final: 0.7610 (m-30) REVERT: H 115 ASP cc_start: 0.8893 (p0) cc_final: 0.8115 (p0) REVERT: H 149 ILE cc_start: 0.6131 (tt) cc_final: 0.5879 (tp) REVERT: J 210 ILE cc_start: 0.7827 (tp) cc_final: 0.7302 (pp) outliers start: 36 outliers final: 17 residues processed: 276 average time/residue: 2.5485 time to fit residues: 836.8870 Evaluate side-chains 263 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 241 time to evaluate : 4.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 105 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 217 optimal weight: 30.0000 chunk 168 optimal weight: 0.6980 chunk 250 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 180 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26029 Z= 0.214 Angle : 0.501 7.486 35502 Z= 0.257 Chirality : 0.043 0.175 4113 Planarity : 0.004 0.089 4389 Dihedral : 4.516 53.161 3722 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 1.22 % Allowed : 16.75 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.13 (0.15), residues: 3127 helix: 2.05 (0.20), residues: 693 sheet: -0.22 (0.17), residues: 936 loop : -0.59 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 101 HIS 0.005 0.001 HIS K 171 PHE 0.011 0.001 PHE I 173 TYR 0.020 0.001 TYR H 145 ARG 0.011 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 4.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6814 (tt0) REVERT: B 286 SER cc_start: 0.9437 (OUTLIER) cc_final: 0.9203 (p) REVERT: B 368 MET cc_start: 0.3880 (tmm) cc_final: 0.3373 (tpt) REVERT: C 36 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.7738 (tmm) REVERT: C 95 TYR cc_start: 0.9324 (OUTLIER) cc_final: 0.8690 (m-10) REVERT: D 56 MET cc_start: 0.8873 (mtp) cc_final: 0.8304 (mtt) REVERT: D 364 MET cc_start: 0.8135 (ttm) cc_final: 0.7788 (ttp) REVERT: E 95 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.7104 (m-10) REVERT: F 4 MET cc_start: 0.8152 (mmm) cc_final: 0.7417 (mmm) REVERT: F 84 GLU cc_start: 0.6939 (mp0) cc_final: 0.6297 (mp0) REVERT: G 158 THR cc_start: 0.9028 (m) cc_final: 0.8751 (p) REVERT: H 24 ARG cc_start: 0.7204 (mtp-110) cc_final: 0.6598 (ttm110) REVERT: H 35 ASN cc_start: 0.6236 (m-40) cc_final: 0.5841 (m110) REVERT: H 87 ASP cc_start: 0.7951 (m-30) cc_final: 0.7650 (m-30) REVERT: H 115 ASP cc_start: 0.8846 (p0) cc_final: 0.8044 (p0) REVERT: H 149 ILE cc_start: 0.6175 (tt) cc_final: 0.5929 (tp) REVERT: I 155 GLU cc_start: 0.8923 (mp0) cc_final: 0.8653 (mm-30) REVERT: J 210 ILE cc_start: 0.7751 (tp) cc_final: 0.7242 (pp) REVERT: K 131 LEU cc_start: 0.5588 (OUTLIER) cc_final: 0.5345 (mt) outliers start: 35 outliers final: 24 residues processed: 278 average time/residue: 2.5782 time to fit residues: 864.9543 Evaluate side-chains 271 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 4.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 171 HIS Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 139 CYS Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 195 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 233 optimal weight: 4.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26029 Z= 0.223 Angle : 0.503 7.673 35502 Z= 0.257 Chirality : 0.043 0.176 4113 Planarity : 0.004 0.090 4389 Dihedral : 4.524 53.274 3722 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.29 % Allowed : 16.82 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.12 (0.15), residues: 3127 helix: 2.06 (0.20), residues: 693 sheet: -0.25 (0.16), residues: 938 loop : -0.59 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 101 HIS 0.003 0.001 HIS B 297 PHE 0.010 0.001 PHE C 254 TYR 0.017 0.001 TYR H 145 ARG 0.012 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6767 (tt0) REVERT: B 286 SER cc_start: 0.9436 (OUTLIER) cc_final: 0.9202 (p) REVERT: B 368 MET cc_start: 0.3883 (tmm) cc_final: 0.3368 (tpt) REVERT: C 36 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.7729 (tmm) REVERT: C 95 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.8689 (m-80) REVERT: D 56 MET cc_start: 0.8882 (mtp) cc_final: 0.8285 (mtt) REVERT: D 364 MET cc_start: 0.8149 (ttm) cc_final: 0.7785 (ttp) REVERT: E 95 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.7035 (m-10) REVERT: F 4 MET cc_start: 0.8239 (mmm) cc_final: 0.7517 (mmm) REVERT: F 72 SER cc_start: 0.7746 (t) cc_final: 0.7464 (p) REVERT: F 84 GLU cc_start: 0.6856 (mp0) cc_final: 0.6146 (mp0) REVERT: F 113 ARG cc_start: 0.6923 (pmt-80) cc_final: 0.6713 (pmt-80) REVERT: F 177 THR cc_start: 0.6957 (OUTLIER) cc_final: 0.6617 (p) REVERT: G 158 THR cc_start: 0.9037 (m) cc_final: 0.8763 (p) REVERT: H 24 ARG cc_start: 0.7125 (mtp-110) cc_final: 0.6565 (ttm110) REVERT: H 35 ASN cc_start: 0.6256 (m-40) cc_final: 0.5891 (m110) REVERT: H 87 ASP cc_start: 0.7964 (m-30) cc_final: 0.7667 (m-30) REVERT: H 115 ASP cc_start: 0.8894 (p0) cc_final: 0.8179 (p0) REVERT: H 149 ILE cc_start: 0.6222 (tt) cc_final: 0.6005 (tp) REVERT: I 155 GLU cc_start: 0.8911 (mp0) cc_final: 0.8627 (mm-30) REVERT: J 210 ILE cc_start: 0.7833 (tp) cc_final: 0.7308 (pp) outliers start: 37 outliers final: 22 residues processed: 273 average time/residue: 2.6275 time to fit residues: 852.7617 Evaluate side-chains 272 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 4.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 139 CYS Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.8980 chunk 284 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 275 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26029 Z= 0.286 Angle : 0.527 8.577 35502 Z= 0.270 Chirality : 0.044 0.175 4113 Planarity : 0.005 0.096 4389 Dihedral : 4.623 53.164 3722 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 1.18 % Allowed : 17.03 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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 (0.15), residues: 3127 helix: 2.00 (0.20), residues: 693 sheet: -0.29 (0.16), residues: 953 loop : -0.62 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 101 HIS 0.004 0.001 HIS A 305 PHE 0.011 0.001 PHE C 254 TYR 0.019 0.001 TYR F 191 ARG 0.012 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 4.058 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: A 343 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6757 (tt0) REVERT: B 286 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9205 (p) REVERT: B 368 MET cc_start: 0.3986 (tmm) cc_final: 0.3446 (tpt) REVERT: C 36 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.7768 (tmm) REVERT: C 95 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.8672 (m-10) REVERT: D 56 MET cc_start: 0.8947 (mtp) cc_final: 0.8365 (mtt) REVERT: D 364 MET cc_start: 0.8208 (ttm) cc_final: 0.7794 (ttt) REVERT: E 95 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.7123 (m-10) REVERT: F 4 MET cc_start: 0.8265 (mmm) cc_final: 0.7565 (mmm) REVERT: F 72 SER cc_start: 0.7821 (t) cc_final: 0.7548 (p) REVERT: F 84 GLU cc_start: 0.6787 (mp0) cc_final: 0.6094 (mp0) REVERT: F 113 ARG cc_start: 0.6945 (pmt-80) cc_final: 0.6707 (pmt-80) REVERT: F 177 THR cc_start: 0.6965 (OUTLIER) cc_final: 0.6598 (p) REVERT: G 158 THR cc_start: 0.9058 (m) cc_final: 0.8780 (p) REVERT: H 24 ARG cc_start: 0.7156 (mtp-110) cc_final: 0.6818 (ttm110) REVERT: H 35 ASN cc_start: 0.6333 (m-40) cc_final: 0.6091 (m110) REVERT: H 87 ASP cc_start: 0.7973 (m-30) cc_final: 0.7678 (m-30) REVERT: H 115 ASP cc_start: 0.8893 (p0) cc_final: 0.8178 (p0) REVERT: H 144 PHE cc_start: 0.7531 (p90) cc_final: 0.6990 (p90) REVERT: J 210 ILE cc_start: 0.7923 (tp) cc_final: 0.7405 (pp) outliers start: 34 outliers final: 24 residues processed: 280 average time/residue: 2.5547 time to fit residues: 860.2980 Evaluate side-chains 271 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 139 CYS Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 8.9990 chunk 292 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 306 optimal weight: 30.0000 chunk 282 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 25 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN ** K 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26029 Z= 0.270 Angle : 0.530 10.887 35502 Z= 0.271 Chirality : 0.044 0.177 4113 Planarity : 0.005 0.095 4389 Dihedral : 4.638 53.334 3722 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 1.04 % Allowed : 17.41 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.06 (0.15), residues: 3127 helix: 2.00 (0.20), residues: 693 sheet: -0.30 (0.16), residues: 951 loop : -0.62 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 101 HIS 0.004 0.001 HIS B 297 PHE 0.011 0.001 PHE C 254 TYR 0.019 0.001 TYR H 145 ARG 0.012 0.001 ARG B 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 3.860 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: A 343 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6762 (tt0) REVERT: B 77 MET cc_start: 0.9174 (mtm) cc_final: 0.8939 (ttm) REVERT: B 286 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9204 (p) REVERT: B 368 MET cc_start: 0.3857 (tmm) cc_final: 0.3345 (tpt) REVERT: C 36 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.7765 (tmm) REVERT: C 95 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.8670 (m-10) REVERT: D 56 MET cc_start: 0.8921 (mtp) cc_final: 0.8331 (mtt) REVERT: D 344 ARG cc_start: 0.7711 (ttp-170) cc_final: 0.7501 (ttp-110) REVERT: D 364 MET cc_start: 0.8210 (ttm) cc_final: 0.7790 (ttt) REVERT: E 95 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.7126 (m-10) REVERT: F 4 MET cc_start: 0.8331 (mmm) cc_final: 0.7667 (mmm) REVERT: F 72 SER cc_start: 0.7764 (t) cc_final: 0.7494 (p) REVERT: F 84 GLU cc_start: 0.6833 (mp0) cc_final: 0.6158 (mp0) REVERT: F 113 ARG cc_start: 0.6951 (pmt-80) cc_final: 0.6722 (pmt-80) REVERT: F 177 THR cc_start: 0.6968 (OUTLIER) cc_final: 0.6613 (p) REVERT: G 158 THR cc_start: 0.9038 (m) cc_final: 0.8752 (p) REVERT: H 24 ARG cc_start: 0.7119 (mtp-110) cc_final: 0.6772 (ttm110) REVERT: H 87 ASP cc_start: 0.7983 (m-30) cc_final: 0.7693 (m-30) REVERT: H 129 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8687 (tp-100) REVERT: H 144 PHE cc_start: 0.7549 (p90) cc_final: 0.7013 (p90) REVERT: J 210 ILE cc_start: 0.7823 (tp) cc_final: 0.7312 (pp) REVERT: J 215 ASN cc_start: 0.6217 (p0) cc_final: 0.6006 (p0) outliers start: 30 outliers final: 20 residues processed: 272 average time/residue: 2.2913 time to fit residues: 744.7000 Evaluate side-chains 269 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 139 CYS Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 105 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 20.0000 chunk 260 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 225 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100775 restraints weight = 94137.899| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.68 r_work: 0.2722 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26029 Z= 0.171 Angle : 0.505 10.176 35502 Z= 0.257 Chirality : 0.043 0.175 4113 Planarity : 0.004 0.096 4389 Dihedral : 4.473 53.719 3722 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 0.94 % Allowed : 17.51 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.15 (0.15), residues: 3127 helix: 2.05 (0.20), residues: 701 sheet: -0.29 (0.16), residues: 953 loop : -0.52 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 101 HIS 0.003 0.001 HIS D 111 PHE 0.009 0.001 PHE I 173 TYR 0.019 0.001 TYR H 145 ARG 0.012 0.000 ARG B 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14726.80 seconds wall clock time: 256 minutes 42.14 seconds (15402.14 seconds total)