Starting phenix.real_space_refine (version: dev) on Tue Oct 5 07:48:44 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/10_2021/7s67_24852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/10_2021/7s67_24852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/10_2021/7s67_24852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/10_2021/7s67_24852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/10_2021/7s67_24852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/10_2021/7s67_24852_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 193": "NH1" <-> "NH2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 193": "NH1" <-> "NH2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F GLU 214": "OE1" <-> "OE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4376/modules/chem_data/mon_lib" Total number of atoms: 23058 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {' MG': 3, 'ADP': 1, 'ATP': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.49, per 1000 atoms: 0.50 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 497) selection = (chain 'B' and resid 16 through 497) selection = (chain 'C' and resid 16 through 497) selection = (chain 'D' and resid 16 through 497) selection = (chain 'E' and resid 16 through 497) selection = (chain 'F' and resid 16 through 497) } Number of scatterers: 23058 At special positions: 0 Unit cell: (118.45, 118.45, 109.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 30 15.00 Mg 12 11.99 O 4440 8.00 N 4056 7.00 C 14430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.22 Conformation dependent library (CDL) restraints added in 3.3 seconds 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 18 sheets defined 34.9% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 28 through 31 No H-bonds generated for 'chain 'A' and resid 28 through 31' Processing helix chain 'A' and resid 52 through 66 Processing helix chain 'A' and resid 80 through 90 removed outlier: 4.216A pdb=" N SER A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 120 through 136 removed outlier: 3.605A pdb=" N ALA A 125 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 157 through 174 Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 370 Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.653A pdb=" N GLY A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'B' and resid 28 through 31 No H-bonds generated for 'chain 'B' and resid 28 through 31' Processing helix chain 'B' and resid 52 through 66 Processing helix chain 'B' and resid 80 through 90 removed outlier: 4.216A pdb=" N SER B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 120 through 136 removed outlier: 3.605A pdb=" N ALA B 125 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 157 through 174 Processing helix chain 'B' and resid 197 through 200 No H-bonds generated for 'chain 'B' and resid 197 through 200' Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 356 through 370 Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.654A pdb=" N GLY B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 405 Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'C' and resid 28 through 31 No H-bonds generated for 'chain 'C' and resid 28 through 31' Processing helix chain 'C' and resid 52 through 66 Processing helix chain 'C' and resid 80 through 90 removed outlier: 4.217A pdb=" N SER C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 120 through 136 removed outlier: 3.605A pdb=" N ALA C 125 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 157 through 174 Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'C' and resid 294 through 308 Processing helix chain 'C' and resid 321 through 331 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 356 through 370 Processing helix chain 'C' and resid 380 through 386 removed outlier: 4.653A pdb=" N GLY C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 405 Processing helix chain 'C' and resid 430 through 432 No H-bonds generated for 'chain 'C' and resid 430 through 432' Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 52 through 66 Processing helix chain 'D' and resid 80 through 90 removed outlier: 4.216A pdb=" N SER D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE D 90 " --> pdb=" O ASN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 120 through 136 removed outlier: 3.604A pdb=" N ALA D 125 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 157 through 174 Processing helix chain 'D' and resid 197 through 200 No H-bonds generated for 'chain 'D' and resid 197 through 200' Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 268 through 273 Processing helix chain 'D' and resid 294 through 308 Processing helix chain 'D' and resid 321 through 331 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 356 through 370 Processing helix chain 'D' and resid 380 through 386 removed outlier: 4.653A pdb=" N GLY D 386 " --> pdb=" O ALA D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 405 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'E' and resid 28 through 31 No H-bonds generated for 'chain 'E' and resid 28 through 31' Processing helix chain 'E' and resid 52 through 66 Processing helix chain 'E' and resid 80 through 90 removed outlier: 4.216A pdb=" N SER E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE E 90 " --> pdb=" O ASN E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 120 through 136 removed outlier: 3.605A pdb=" N ALA E 125 " --> pdb=" O ASP E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 150 Processing helix chain 'E' and resid 157 through 174 Processing helix chain 'E' and resid 197 through 200 No H-bonds generated for 'chain 'E' and resid 197 through 200' Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 268 through 273 Processing helix chain 'E' and resid 294 through 308 Processing helix chain 'E' and resid 321 through 331 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 356 through 370 Processing helix chain 'E' and resid 380 through 386 removed outlier: 4.653A pdb=" N GLY E 386 " --> pdb=" O ALA E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 405 Processing helix chain 'E' and resid 430 through 432 No H-bonds generated for 'chain 'E' and resid 430 through 432' Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'F' and resid 28 through 31 No H-bonds generated for 'chain 'F' and resid 28 through 31' Processing helix chain 'F' and resid 52 through 66 Processing helix chain 'F' and resid 80 through 90 removed outlier: 4.216A pdb=" N SER F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 Processing helix chain 'F' and resid 120 through 136 removed outlier: 3.606A pdb=" N ALA F 125 " --> pdb=" O ASP F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 150 Processing helix chain 'F' and resid 157 through 174 Processing helix chain 'F' and resid 197 through 200 No H-bonds generated for 'chain 'F' and resid 197 through 200' Processing helix chain 'F' and resid 249 through 251 No H-bonds generated for 'chain 'F' and resid 249 through 251' Processing helix chain 'F' and resid 268 through 273 Processing helix chain 'F' and resid 294 through 308 Processing helix chain 'F' and resid 321 through 331 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 356 through 370 Processing helix chain 'F' and resid 380 through 386 removed outlier: 4.654A pdb=" N GLY F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 405 Processing helix chain 'F' and resid 430 through 432 No H-bonds generated for 'chain 'F' and resid 430 through 432' Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing sheet with id= A, first strand: chain 'A' and resid 215 through 225 removed outlier: 6.544A pdb=" N VAL A 204 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER A 41 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL A 205 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU A 43 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU A 207 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER A 45 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN A 209 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR A 178 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL A 44 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET A 180 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLY A 46 " --> pdb=" O MET A 180 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= C, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.887A pdb=" N ARG A 451 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE A 472 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET A 449 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 289 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR A 442 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 410 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA A 286 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE A 412 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLY A 288 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN A 414 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 413 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 215 through 225 removed outlier: 6.543A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER B 41 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL B 205 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU B 43 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 207 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER B 45 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN B 209 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR B 178 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL B 44 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET B 180 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLY B 46 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= F, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.887A pdb=" N ARG B 451 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE B 472 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET B 449 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 289 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR B 442 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY B 410 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA B 286 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 412 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLY B 288 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN B 414 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 413 " --> pdb=" O ILE B 377 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 215 through 225 removed outlier: 6.544A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER C 41 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL C 205 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU C 43 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU C 207 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER C 45 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASN C 209 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR C 178 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL C 44 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET C 180 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLY C 46 " --> pdb=" O MET C 180 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= I, first strand: chain 'C' and resid 476 through 479 removed outlier: 3.887A pdb=" N ARG C 451 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE C 472 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET C 449 " --> pdb=" O ILE C 472 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 289 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR C 442 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY C 410 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA C 286 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE C 412 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLY C 288 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN C 414 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 413 " --> pdb=" O ILE C 377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 215 through 225 removed outlier: 6.544A pdb=" N VAL D 204 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER D 41 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL D 205 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU D 43 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU D 207 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER D 45 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN D 209 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR D 178 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL D 44 " --> pdb=" O THR D 178 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET D 180 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLY D 46 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 237 through 240 Processing sheet with id= L, first strand: chain 'D' and resid 476 through 479 removed outlier: 3.887A pdb=" N ARG D 451 " --> pdb=" O PHE D 470 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N ILE D 472 " --> pdb=" O MET D 449 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N MET D 449 " --> pdb=" O ILE D 472 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA D 289 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR D 442 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY D 410 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA D 286 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE D 412 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N GLY D 288 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN D 414 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR D 413 " --> pdb=" O ILE D 377 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 215 through 225 removed outlier: 6.544A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER E 41 " --> pdb=" O ASN E 203 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL E 205 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU E 43 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU E 207 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER E 45 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASN E 209 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR E 178 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL E 44 " --> pdb=" O THR E 178 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET E 180 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLY E 46 " --> pdb=" O MET E 180 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 237 through 240 Processing sheet with id= O, first strand: chain 'E' and resid 476 through 479 removed outlier: 3.887A pdb=" N ARG E 451 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N ILE E 472 " --> pdb=" O MET E 449 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET E 449 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA E 289 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR E 442 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY E 410 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA E 286 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE E 412 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLY E 288 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN E 414 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR E 413 " --> pdb=" O ILE E 377 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 215 through 225 removed outlier: 6.544A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER F 41 " --> pdb=" O ASN F 203 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL F 205 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU F 43 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU F 207 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER F 45 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN F 209 " --> pdb=" O SER F 45 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR F 178 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL F 44 " --> pdb=" O THR F 178 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET F 180 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLY F 46 " --> pdb=" O MET F 180 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 237 through 240 Processing sheet with id= R, first strand: chain 'F' and resid 476 through 479 removed outlier: 3.886A pdb=" N ARG F 451 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE F 472 " --> pdb=" O MET F 449 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET F 449 " --> pdb=" O ILE F 472 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA F 289 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR F 442 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY F 410 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA F 286 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE F 412 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N GLY F 288 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN F 414 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR F 413 " --> pdb=" O ILE F 377 " (cutoff:3.500A) 894 hydrogen bonds defined for protein. 2322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 8.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4061 1.31 - 1.44: 5983 1.44 - 1.56: 13200 1.56 - 1.69: 42 1.69 - 1.81: 162 Bond restraints: 23448 Sorted by residual: bond pdb=" C4 ADP F 602 " pdb=" C5 ADP F 602 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C4 ADP D 603 " pdb=" C5 ADP D 603 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 ADP C 603 " pdb=" C5 ADP C 603 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 ADP A 603 " pdb=" C5 ADP A 603 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 23443 not shown) Histogram of bond angle deviations from ideal: 96.23 - 103.76: 292 103.76 - 111.28: 9442 111.28 - 118.81: 9223 118.81 - 126.34: 12529 126.34 - 133.87: 194 Bond angle restraints: 31680 Sorted by residual: angle pdb=" PA ATP F 601 " pdb=" O3A ATP F 601 " pdb=" PB ATP F 601 " ideal model delta sigma weight residual 136.83 116.10 20.73 1.00e+00 1.00e+00 4.30e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 116.11 20.72 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 116.11 20.72 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 116.13 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 116.13 20.70 1.00e+00 1.00e+00 4.29e+02 ... (remaining 31675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.18: 13738 29.18 - 58.36: 224 58.36 - 87.54: 30 87.54 - 116.72: 6 116.72 - 145.90: 6 Dihedral angle restraints: 14004 sinusoidal: 5742 harmonic: 8262 Sorted by residual: dihedral pdb=" C5' ADP B 603 " pdb=" O5' ADP B 603 " pdb=" PA ADP B 603 " pdb=" O2A ADP B 603 " ideal model delta sinusoidal sigma weight residual 300.00 154.10 145.90 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual 300.00 154.15 145.85 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP A 603 " pdb=" O5' ADP A 603 " pdb=" PA ADP A 603 " pdb=" O2A ADP A 603 " ideal model delta sinusoidal sigma weight residual 300.00 154.15 145.85 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 14001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2513 0.064 - 0.128: 813 0.128 - 0.191: 176 0.191 - 0.255: 20 0.255 - 0.319: 12 Chirality restraints: 3534 Sorted by residual: chirality pdb=" CA HIS D 429 " pdb=" N HIS D 429 " pdb=" C HIS D 429 " pdb=" CB HIS D 429 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA HIS A 429 " pdb=" N HIS A 429 " pdb=" C HIS A 429 " pdb=" CB HIS A 429 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA HIS E 429 " pdb=" N HIS E 429 " pdb=" C HIS E 429 " pdb=" CB HIS E 429 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 3531 not shown) Planarity restraints: 4062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP C 603 " -0.175 2.00e-02 2.50e+03 7.17e-02 1.41e+02 pdb=" C2 ADP C 603 " 0.024 2.00e-02 2.50e+03 pdb=" C4 ADP C 603 " 0.065 2.00e-02 2.50e+03 pdb=" C5 ADP C 603 " 0.028 2.00e-02 2.50e+03 pdb=" C6 ADP C 603 " -0.016 2.00e-02 2.50e+03 pdb=" C8 ADP C 603 " 0.066 2.00e-02 2.50e+03 pdb=" N1 ADP C 603 " -0.029 2.00e-02 2.50e+03 pdb=" N3 ADP C 603 " 0.063 2.00e-02 2.50e+03 pdb=" N6 ADP C 603 " -0.092 2.00e-02 2.50e+03 pdb=" N7 ADP C 603 " 0.023 2.00e-02 2.50e+03 pdb=" N9 ADP C 603 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP E 902 " 0.175 2.00e-02 2.50e+03 7.16e-02 1.41e+02 pdb=" C2 ADP E 902 " -0.024 2.00e-02 2.50e+03 pdb=" C4 ADP E 902 " -0.065 2.00e-02 2.50e+03 pdb=" C5 ADP E 902 " -0.028 2.00e-02 2.50e+03 pdb=" C6 ADP E 902 " 0.016 2.00e-02 2.50e+03 pdb=" C8 ADP E 902 " -0.066 2.00e-02 2.50e+03 pdb=" N1 ADP E 902 " 0.028 2.00e-02 2.50e+03 pdb=" N3 ADP E 902 " -0.063 2.00e-02 2.50e+03 pdb=" N6 ADP E 902 " 0.092 2.00e-02 2.50e+03 pdb=" N7 ADP E 902 " -0.023 2.00e-02 2.50e+03 pdb=" N9 ADP E 902 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 603 " -0.175 2.00e-02 2.50e+03 7.16e-02 1.41e+02 pdb=" C2 ADP B 603 " 0.024 2.00e-02 2.50e+03 pdb=" C4 ADP B 603 " 0.064 2.00e-02 2.50e+03 pdb=" C5 ADP B 603 " 0.028 2.00e-02 2.50e+03 pdb=" C6 ADP B 603 " -0.016 2.00e-02 2.50e+03 pdb=" C8 ADP B 603 " 0.066 2.00e-02 2.50e+03 pdb=" N1 ADP B 603 " -0.029 2.00e-02 2.50e+03 pdb=" N3 ADP B 603 " 0.063 2.00e-02 2.50e+03 pdb=" N6 ADP B 603 " -0.092 2.00e-02 2.50e+03 pdb=" N7 ADP B 603 " 0.023 2.00e-02 2.50e+03 pdb=" N9 ADP B 603 " 0.043 2.00e-02 2.50e+03 ... (remaining 4059 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 64 2.43 - 3.05: 15423 3.05 - 3.67: 34585 3.67 - 4.28: 57360 4.28 - 4.90: 89937 Nonbonded interactions: 197369 Sorted by model distance: nonbonded pdb=" NH1 ARG F 226 " pdb=" O2G ATP F 601 " model vdw 1.815 2.520 nonbonded pdb=" NH1 ARG C 226 " pdb=" O2G ATP B 601 " model vdw 1.887 2.520 nonbonded pdb=" NH1 ARG E 226 " pdb=" O2G ATP D 601 " model vdw 1.912 2.520 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 1.917 2.230 nonbonded pdb=" O2G ATP A 605 " pdb="MG MG A 606 " model vdw 1.918 2.230 ... (remaining 197364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 12 5.21 5 S 90 5.16 5 C 14430 2.51 5 N 4056 2.21 5 O 4440 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.650 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.160 Process input model: 54.760 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Internal consistency checks: 0.000 Total: 61.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.013 0.143 23448 Z= 0.857 Angle : 1.395 21.283 31680 Z= 0.953 Chirality : 0.067 0.319 3534 Planarity : 0.011 0.072 4062 Dihedral : 11.904 145.899 8700 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 2880 helix: -0.43 (0.13), residues: 1038 sheet: 0.76 (0.21), residues: 696 loop : 0.65 (0.18), residues: 1146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1032 time to evaluate : 2.581 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 outliers start: 0 outliers final: 0 residues processed: 1032 average time/residue: 0.3977 time to fit residues: 599.8182 Evaluate side-chains 564 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 304 ASN A 327 ASN A 341 GLN A 368 ASN B 260 ASN B 341 GLN B 342 ASN B 423 HIS ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN C 308 ASN C 341 GLN C 342 ASN C 368 ASN C 423 HIS D 260 ASN D 304 ASN D 341 GLN D 368 ASN E 260 ASN E 304 ASN E 308 ASN E 341 GLN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN F 308 ASN F 341 GLN F 342 ASN F 368 ASN ** F 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 23448 Z= 0.255 Angle : 0.612 7.144 31680 Z= 0.318 Chirality : 0.046 0.195 3534 Planarity : 0.005 0.044 4062 Dihedral : 9.181 116.742 3270 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 2880 helix: 0.20 (0.15), residues: 1050 sheet: 0.35 (0.19), residues: 798 loop : 0.50 (0.18), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 684 time to evaluate : 2.782 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 outliers start: 58 outliers final: 41 residues processed: 718 average time/residue: 0.3597 time to fit residues: 393.5716 Evaluate side-chains 594 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 553 time to evaluate : 2.876 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2086 time to fit residues: 19.9623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 217 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 304 ASN E 304 ASN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 23448 Z= 0.315 Angle : 0.640 7.235 31680 Z= 0.328 Chirality : 0.046 0.148 3534 Planarity : 0.004 0.041 4062 Dihedral : 8.710 113.526 3270 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2880 helix: 0.37 (0.15), residues: 1050 sheet: 0.15 (0.18), residues: 798 loop : 0.02 (0.19), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 632 time to evaluate : 2.670 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 outliers start: 51 outliers final: 35 residues processed: 654 average time/residue: 0.3457 time to fit residues: 350.5681 Evaluate side-chains 575 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 540 time to evaluate : 2.847 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2305 time to fit residues: 18.1931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 175 optimal weight: 30.0000 chunk 262 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN C 131 ASN ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN E 304 ASN F 131 ASN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 HIS ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.115 23448 Z= 0.335 Angle : 0.642 8.776 31680 Z= 0.326 Chirality : 0.046 0.149 3534 Planarity : 0.005 0.140 4062 Dihedral : 8.584 115.532 3270 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2880 helix: 0.51 (0.16), residues: 1020 sheet: 0.34 (0.19), residues: 720 loop : -0.51 (0.17), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 602 time to evaluate : 2.774 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 outliers start: 59 outliers final: 40 residues processed: 638 average time/residue: 0.3304 time to fit residues: 333.4222 Evaluate side-chains 586 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 546 time to evaluate : 2.693 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2092 time to fit residues: 19.7407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 HIS ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.114 23448 Z= 0.327 Angle : 0.638 8.292 31680 Z= 0.324 Chirality : 0.045 0.148 3534 Planarity : 0.005 0.127 4062 Dihedral : 8.423 118.865 3270 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 2880 helix: 0.48 (0.16), residues: 1026 sheet: 0.18 (0.19), residues: 720 loop : -0.64 (0.18), residues: 1134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 602 time to evaluate : 2.879 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 outliers start: 46 outliers final: 27 residues processed: 621 average time/residue: 0.3322 time to fit residues: 323.9095 Evaluate side-chains 584 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 557 time to evaluate : 2.676 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2076 time to fit residues: 14.3393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 10.0000 chunk 250 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 163 optimal weight: 0.4980 chunk 68 optimal weight: 8.9990 chunk 278 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.149 23448 Z= 0.296 Angle : 0.622 7.770 31680 Z= 0.316 Chirality : 0.045 0.146 3534 Planarity : 0.005 0.136 4062 Dihedral : 8.161 117.899 3270 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2880 helix: 0.56 (0.16), residues: 1026 sheet: 0.03 (0.18), residues: 744 loop : -0.51 (0.18), residues: 1110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 585 time to evaluate : 2.820 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 outliers start: 38 outliers final: 30 residues processed: 600 average time/residue: 0.3311 time to fit residues: 317.1174 Evaluate side-chains 571 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 541 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2101 time to fit residues: 16.0352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 277 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.155 23448 Z= 0.308 Angle : 0.641 8.172 31680 Z= 0.325 Chirality : 0.045 0.174 3534 Planarity : 0.005 0.138 4062 Dihedral : 7.965 117.412 3270 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 2880 helix: 0.56 (0.16), residues: 1026 sheet: -0.01 (0.18), residues: 744 loop : -0.60 (0.18), residues: 1110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 580 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 27 residues processed: 591 average time/residue: 0.3412 time to fit residues: 318.9861 Evaluate side-chains 567 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 540 time to evaluate : 2.746 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2315 time to fit residues: 15.3827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 54 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 overall best weight: 4.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.104 23448 Z= 0.397 Angle : 0.701 10.308 31680 Z= 0.359 Chirality : 0.047 0.177 3534 Planarity : 0.006 0.150 4062 Dihedral : 8.099 115.357 3270 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2880 helix: 0.25 (0.16), residues: 1050 sheet: -0.14 (0.18), residues: 744 loop : -0.83 (0.18), residues: 1086 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 555 time to evaluate : 2.740 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 outliers start: 39 outliers final: 34 residues processed: 572 average time/residue: 0.3502 time to fit residues: 314.8345 Evaluate side-chains 561 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 527 time to evaluate : 2.747 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2178 time to fit residues: 17.7227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 9.9990 chunk 265 optimal weight: 0.7980 chunk 242 optimal weight: 8.9990 chunk 258 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 257 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.175 23448 Z= 0.261 Angle : 0.650 12.221 31680 Z= 0.335 Chirality : 0.045 0.170 3534 Planarity : 0.005 0.107 4062 Dihedral : 7.446 111.264 3270 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 2880 helix: 0.48 (0.16), residues: 1020 sheet: 0.11 (0.19), residues: 720 loop : -0.78 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 614 time to evaluate : 2.717 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 outliers start: 10 outliers final: 6 residues processed: 615 average time/residue: 0.3364 time to fit residues: 325.6131 Evaluate side-chains 575 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 569 time to evaluate : 2.671 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2038 time to fit residues: 6.0428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 0.0070 chunk 190 optimal weight: 0.9980 chunk 286 optimal weight: 9.9990 chunk 264 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 176 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 ASN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.210 23448 Z= 0.315 Angle : 0.697 18.150 31680 Z= 0.363 Chirality : 0.046 0.224 3534 Planarity : 0.006 0.175 4062 Dihedral : 7.351 108.925 3270 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 2880 helix: 0.52 (0.16), residues: 1014 sheet: 0.18 (0.19), residues: 714 loop : -0.80 (0.18), residues: 1152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 580 time to evaluate : 2.655 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 outliers start: 8 outliers final: 2 residues processed: 585 average time/residue: 0.3292 time to fit residues: 301.2538 Evaluate side-chains 550 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 548 time to evaluate : 2.654 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2196 time to fit residues: 4.4330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 210 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 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 = 0.3703 r_free = 0.3703 target = 0.148552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119531 restraints weight = 39243.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122902 restraints weight = 22166.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125261 restraints weight = 15232.041| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES. BOND : 0.004 0.163 23448 Z= 0.273 ANGLE : 0.680 19.278 31680 Z= 0.349 CHIRALITY : 0.045 0.235 3534 PLANARITY : 0.005 0.182 4062 DIHEDRAL : 6.968 98.970 3270 MIN NONBONDED DISTANCE : 1.977 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 14.59 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.53 % FAVORED : 97.47 % ROTAMER OUTLIERS : 0.74 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -0.13 (0.15), RESIDUES: 2880 HELIX: 0.49 (0.16), RESIDUES: 1020 SHEET: 0.32 (0.20), RESIDUES: 654 LOOP : -0.73 (0.17), RESIDUES: 1206 ------------------------------------------------------------------------------- Occupancy refinement ******************** GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES. BOND : 0.004 0.163 23448 Z= 0.273 ANGLE : 0.680 19.278 31680 Z= 0.349 CHIRALITY : 0.045 0.235 3534 PLANARITY : 0.005 0.182 4062 DIHEDRAL : 6.968 98.970 3270 MIN NONBONDED DISTANCE : 1.977 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 14.59 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.53 % FAVORED : 97.47 % ROTAMER OUTLIERS : 0.74 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -0.13 (0.15), RESIDUES: 2880 HELIX: 0.49 (0.16), RESIDUES: 1020 SHEET: 0.32 (0.20), RESIDUES: 654 LOOP : -0.73 (0.17), RESIDUES: 1206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.163 23448 Z= 0.273 Angle : 0.680 19.278 31680 Z= 0.349 Chirality : 0.045 0.235 3534 Planarity : 0.005 0.182 4062 Dihedral : 6.968 98.970 3270 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2880 helix: 0.49 (0.16), residues: 1020 sheet: 0.32 (0.20), residues: 654 loop : -0.73 (0.17), residues: 1206 =============================================================================== Job complete usr+sys time: 5818.92 seconds wall clock time: 106 minutes 24.68 seconds (6384.68 seconds total)