Starting phenix.real_space_refine on Tue Mar 19 03:49:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/03_2024/7s67_24852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/03_2024/7s67_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_24852/03_2024/7s67_24852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/03_2024/7s67_24852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/03_2024/7s67_24852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/03_2024/7s67_24852_updated.pdb" } resolution = 3.8 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= 0.002 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: 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. 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-5265/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: 11.79, per 1000 atoms: 0.51 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 Amino 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: 9.03 Conformation dependent library (CDL) restraints added in 4.3 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: 4.62 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: 7.50 Time building geometry restraints manager: 9.72 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: 13864 29.18 - 58.36: 272 58.36 - 87.54: 42 87.54 - 116.72: 6 116.72 - 145.90: 6 Dihedral angle restraints: 14190 sinusoidal: 5928 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 14187 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 2.170 nonbonded pdb=" O2G ATP A 605 " pdb="MG MG A 606 " model vdw 1.918 2.170 ... (remaining 197364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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) } 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 group one per residue 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: 0.350 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: 0.010 Extract box with map and model: 3.070 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 60.620 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.130 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 12.758 145.899 8886 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.018 TRP E 92 HIS 0.009 0.003 HIS F 423 PHE 0.037 0.008 PHE E 237 TYR 0.109 0.015 TYR D 442 ARG 0.011 0.001 ARG C 451 *********************** 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 : 2.555 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: A 82 ASP cc_start: 0.7257 (m-30) cc_final: 0.6775 (m-30) REVERT: A 234 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7822 (mt-10) REVERT: A 235 TYR cc_start: 0.8591 (m-80) cc_final: 0.8121 (m-80) REVERT: A 247 PHE cc_start: 0.8559 (m-80) cc_final: 0.8331 (m-10) REVERT: A 442 TYR cc_start: 0.6837 (m-80) cc_final: 0.6562 (m-80) REVERT: B 82 ASP cc_start: 0.7607 (m-30) cc_final: 0.7201 (m-30) REVERT: B 234 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 235 TYR cc_start: 0.8637 (m-80) cc_final: 0.8246 (m-80) REVERT: B 247 PHE cc_start: 0.8546 (m-80) cc_final: 0.8275 (m-10) REVERT: B 357 GLU cc_start: 0.8395 (mp0) cc_final: 0.8018 (mp0) REVERT: C 82 ASP cc_start: 0.7449 (m-30) cc_final: 0.7186 (m-30) REVERT: C 247 PHE cc_start: 0.8547 (m-80) cc_final: 0.8335 (m-10) REVERT: C 357 GLU cc_start: 0.8516 (mp0) cc_final: 0.8194 (mp0) REVERT: D 82 ASP cc_start: 0.7021 (m-30) cc_final: 0.6820 (m-30) REVERT: D 235 TYR cc_start: 0.8608 (m-80) cc_final: 0.8276 (m-80) REVERT: D 357 GLU cc_start: 0.8587 (mp0) cc_final: 0.8249 (mp0) REVERT: D 442 TYR cc_start: 0.6727 (m-80) cc_final: 0.6490 (m-80) REVERT: E 82 ASP cc_start: 0.7681 (m-30) cc_final: 0.7254 (m-30) REVERT: E 188 TYR cc_start: 0.8332 (m-80) cc_final: 0.8128 (m-80) REVERT: E 234 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7534 (mt-10) REVERT: E 235 TYR cc_start: 0.8673 (m-80) cc_final: 0.8276 (m-80) REVERT: E 247 PHE cc_start: 0.8608 (m-80) cc_final: 0.8219 (m-10) REVERT: E 357 GLU cc_start: 0.8517 (mp0) cc_final: 0.8194 (mp0) REVERT: F 82 ASP cc_start: 0.7450 (m-30) cc_final: 0.7063 (m-30) REVERT: F 234 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7922 (mt-10) REVERT: F 247 PHE cc_start: 0.8586 (m-80) cc_final: 0.8320 (m-10) REVERT: F 357 GLU cc_start: 0.8448 (mp0) cc_final: 0.8143 (mp0) outliers start: 0 outliers final: 0 residues processed: 1032 average time/residue: 0.4126 time to fit residues: 615.6126 Evaluate side-chains 580 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 580 time to evaluate : 2.687 ------------------------------------------------------------------------------- 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: 0.8980 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: 1.9990 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: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 A 463 HIS B 260 ASN B 341 GLN B 342 ASN ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN C 341 GLN C 342 ASN C 368 ASN ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN D 304 ASN D 368 ASN D 463 HIS 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** F 463 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23448 Z= 0.278 Angle : 0.644 6.954 31680 Z= 0.340 Chirality : 0.046 0.169 3534 Planarity : 0.005 0.038 4062 Dihedral : 11.981 126.051 3456 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.43 % Allowed : 12.35 % Favored : 85.23 % 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: 0.39 (0.15), residues: 2880 helix: 0.23 (0.15), residues: 1008 sheet: 0.58 (0.20), residues: 702 loop : 0.30 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 331 HIS 0.018 0.003 HIS B 429 PHE 0.022 0.002 PHE D 199 TYR 0.026 0.002 TYR C 442 ARG 0.007 0.001 ARG E 217 *********************** 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 702 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 643 time to evaluate : 2.903 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 234 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 235 TYR cc_start: 0.8582 (m-80) cc_final: 0.7981 (m-80) REVERT: A 281 ASP cc_start: 0.6707 (p0) cc_final: 0.6450 (p0) REVERT: A 393 ARG cc_start: 0.7321 (ptt-90) cc_final: 0.7118 (ptt-90) REVERT: A 420 MET cc_start: 0.5767 (tpp) cc_final: 0.5355 (tpp) REVERT: B 170 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6975 (mtp85) REVERT: B 191 ILE cc_start: 0.7874 (mp) cc_final: 0.7629 (mt) REVERT: B 234 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7587 (mt-10) REVERT: B 235 TYR cc_start: 0.8625 (m-80) cc_final: 0.8260 (m-80) REVERT: B 247 PHE cc_start: 0.8518 (m-80) cc_final: 0.8171 (m-10) REVERT: B 357 GLU cc_start: 0.8263 (mp0) cc_final: 0.8053 (mp0) REVERT: B 394 GLN cc_start: 0.7776 (mt0) cc_final: 0.7495 (mp10) REVERT: B 469 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6811 (tm-30) REVERT: C 86 ASN cc_start: 0.8145 (m-40) cc_final: 0.7937 (m-40) REVERT: C 216 ARG cc_start: 0.8351 (mmt180) cc_final: 0.8139 (mmt-90) REVERT: C 247 PHE cc_start: 0.8515 (m-80) cc_final: 0.8213 (m-10) REVERT: C 273 MET cc_start: 0.6429 (mtp) cc_final: 0.6083 (mtp) REVERT: C 442 TYR cc_start: 0.7139 (m-80) cc_final: 0.6799 (m-80) REVERT: C 489 ILE cc_start: 0.7893 (mt) cc_final: 0.7693 (mt) REVERT: D 162 ARG cc_start: 0.7356 (mmm160) cc_final: 0.7006 (mmm160) REVERT: D 234 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7612 (mt-10) REVERT: D 235 TYR cc_start: 0.8631 (m-80) cc_final: 0.8094 (m-80) REVERT: D 281 ASP cc_start: 0.6700 (p0) cc_final: 0.6398 (p0) REVERT: D 420 MET cc_start: 0.5906 (tpp) cc_final: 0.5662 (tpp) REVERT: D 457 LYS cc_start: 0.8540 (ptmm) cc_final: 0.8107 (pttp) REVERT: E 170 ARG cc_start: 0.7423 (mtt180) cc_final: 0.7023 (mtp85) REVERT: E 234 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7717 (mt-10) REVERT: E 235 TYR cc_start: 0.8603 (m-80) cc_final: 0.8304 (m-80) REVERT: E 247 PHE cc_start: 0.8533 (m-80) cc_final: 0.8252 (m-80) REVERT: E 357 GLU cc_start: 0.8258 (mp0) cc_final: 0.8009 (mp0) REVERT: E 394 GLN cc_start: 0.7601 (mt0) cc_final: 0.7381 (mp10) REVERT: E 474 ASP cc_start: 0.7074 (m-30) cc_final: 0.6864 (m-30) REVERT: F 86 ASN cc_start: 0.8285 (m-40) cc_final: 0.8023 (m-40) REVERT: F 216 ARG cc_start: 0.8334 (mmt180) cc_final: 0.7984 (mmt180) REVERT: F 273 MET cc_start: 0.6375 (mtp) cc_final: 0.5954 (mtp) outliers start: 59 outliers final: 43 residues processed: 679 average time/residue: 0.3527 time to fit residues: 367.7726 Evaluate side-chains 579 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 536 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 436 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.5980 chunk 81 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN C 308 ASN D 304 ASN D 341 GLN D 463 HIS E 304 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23448 Z= 0.297 Angle : 0.624 12.262 31680 Z= 0.321 Chirality : 0.045 0.163 3534 Planarity : 0.004 0.043 4062 Dihedral : 11.703 113.540 3456 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.84 % Allowed : 14.86 % Favored : 82.30 % 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: 0.15 (0.15), residues: 2880 helix: 0.31 (0.16), residues: 1014 sheet: 0.13 (0.18), residues: 786 loop : 0.12 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 331 HIS 0.016 0.003 HIS B 429 PHE 0.019 0.002 PHE D 199 TYR 0.030 0.002 TYR F 442 ARG 0.008 0.001 ARG A 162 *********************** 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 657 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 588 time to evaluate : 2.699 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: A 76 PHE cc_start: 0.8038 (m-80) cc_final: 0.7657 (m-10) REVERT: A 194 TYR cc_start: 0.7195 (m-80) cc_final: 0.6836 (m-80) REVERT: A 234 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 235 TYR cc_start: 0.8530 (m-80) cc_final: 0.7865 (m-80) REVERT: A 302 VAL cc_start: 0.9072 (m) cc_final: 0.8776 (t) REVERT: A 420 MET cc_start: 0.5921 (tpp) cc_final: 0.5507 (tpp) REVERT: B 194 TYR cc_start: 0.7243 (m-80) cc_final: 0.6874 (m-80) REVERT: B 234 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 235 TYR cc_start: 0.8601 (m-80) cc_final: 0.8154 (m-80) REVERT: B 247 PHE cc_start: 0.8572 (m-80) cc_final: 0.8361 (m-80) REVERT: B 394 GLN cc_start: 0.7608 (mt0) cc_final: 0.7370 (mp10) REVERT: B 420 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.5871 (tpp) REVERT: C 86 ASN cc_start: 0.8113 (m-40) cc_final: 0.7871 (m-40) REVERT: C 191 ILE cc_start: 0.8000 (mp) cc_final: 0.7534 (mt) REVERT: C 194 TYR cc_start: 0.7325 (m-80) cc_final: 0.6772 (m-80) REVERT: C 247 PHE cc_start: 0.8480 (m-80) cc_final: 0.8147 (m-10) REVERT: D 76 PHE cc_start: 0.7912 (m-80) cc_final: 0.7646 (m-10) REVERT: D 194 TYR cc_start: 0.7218 (m-80) cc_final: 0.6884 (m-80) REVERT: D 234 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7618 (mt-10) REVERT: D 235 TYR cc_start: 0.8546 (m-80) cc_final: 0.8030 (m-80) REVERT: D 302 VAL cc_start: 0.9045 (m) cc_final: 0.8744 (t) REVERT: D 420 MET cc_start: 0.5794 (tpp) cc_final: 0.5351 (tpp) REVERT: D 457 LYS cc_start: 0.8569 (ptmm) cc_final: 0.8167 (pttp) REVERT: E 194 TYR cc_start: 0.7238 (m-80) cc_final: 0.6936 (m-80) REVERT: E 234 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7542 (mt-10) REVERT: E 235 TYR cc_start: 0.8621 (m-80) cc_final: 0.8174 (m-80) REVERT: E 247 PHE cc_start: 0.8581 (m-80) cc_final: 0.8334 (m-80) REVERT: F 86 ASN cc_start: 0.8270 (m-40) cc_final: 0.7942 (m-40) REVERT: F 170 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7254 (mtp85) REVERT: F 194 TYR cc_start: 0.7385 (m-80) cc_final: 0.7049 (m-80) REVERT: F 442 TYR cc_start: 0.7303 (m-80) cc_final: 0.6980 (m-10) outliers start: 69 outliers final: 58 residues processed: 626 average time/residue: 0.3452 time to fit residues: 333.4089 Evaluate side-chains 586 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 527 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 436 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 chunk 278 optimal weight: 2.9990 chunk 137 optimal weight: 0.0370 chunk 249 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 HIS D 131 ASN ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 HIS F 423 HIS F 463 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23448 Z= 0.316 Angle : 0.626 9.981 31680 Z= 0.317 Chirality : 0.045 0.147 3534 Planarity : 0.004 0.043 4062 Dihedral : 11.203 113.406 3456 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.70 % Allowed : 15.02 % Favored : 81.28 % 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: -0.09 (0.15), residues: 2880 helix: 0.24 (0.16), residues: 1050 sheet: -0.04 (0.18), residues: 786 loop : -0.13 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 331 HIS 0.012 0.003 HIS E 423 PHE 0.018 0.002 PHE D 59 TYR 0.026 0.002 TYR D 402 ARG 0.005 0.001 ARG C 217 *********************** 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 663 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 573 time to evaluate : 2.675 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: A 194 TYR cc_start: 0.7408 (m-80) cc_final: 0.7099 (m-80) REVERT: A 235 TYR cc_start: 0.8470 (m-80) cc_final: 0.7899 (m-80) REVERT: A 247 PHE cc_start: 0.8457 (m-80) cc_final: 0.8092 (m-10) REVERT: A 302 VAL cc_start: 0.9130 (m) cc_final: 0.8837 (t) REVERT: B 234 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7611 (mt-10) REVERT: B 235 TYR cc_start: 0.8515 (m-80) cc_final: 0.8110 (m-80) REVERT: B 247 PHE cc_start: 0.8573 (m-80) cc_final: 0.8323 (m-80) REVERT: B 358 ASP cc_start: 0.7000 (m-30) cc_final: 0.6758 (m-30) REVERT: B 420 MET cc_start: 0.6198 (OUTLIER) cc_final: 0.5664 (tpp) REVERT: C 170 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.7234 (mtp85) REVERT: C 194 TYR cc_start: 0.7253 (m-80) cc_final: 0.6940 (m-80) REVERT: D 162 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7840 (tpt90) REVERT: D 166 ARG cc_start: 0.7544 (mtm180) cc_final: 0.7314 (mtt180) REVERT: D 194 TYR cc_start: 0.7304 (m-80) cc_final: 0.6991 (m-80) REVERT: D 235 TYR cc_start: 0.8508 (m-80) cc_final: 0.8005 (m-80) REVERT: D 247 PHE cc_start: 0.8230 (m-80) cc_final: 0.7937 (m-10) REVERT: D 302 VAL cc_start: 0.9080 (m) cc_final: 0.8780 (t) REVERT: D 457 LYS cc_start: 0.8351 (ptmm) cc_final: 0.7972 (pttp) REVERT: E 170 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7306 (mtp85) REVERT: E 234 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7611 (mt-10) REVERT: E 235 TYR cc_start: 0.8564 (m-80) cc_final: 0.8066 (m-80) REVERT: F 86 ASN cc_start: 0.8170 (m-40) cc_final: 0.7884 (m-40) REVERT: F 170 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.7293 (mtp85) REVERT: F 191 ILE cc_start: 0.7933 (mp) cc_final: 0.7409 (mt) REVERT: F 194 TYR cc_start: 0.7382 (m-80) cc_final: 0.7020 (m-80) outliers start: 90 outliers final: 75 residues processed: 627 average time/residue: 0.3375 time to fit residues: 328.8923 Evaluate side-chains 599 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 523 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 249 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN E 304 ASN ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23448 Z= 0.267 Angle : 0.605 8.062 31680 Z= 0.305 Chirality : 0.045 0.152 3534 Planarity : 0.004 0.042 4062 Dihedral : 10.577 114.207 3456 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.91 % Allowed : 17.08 % Favored : 79.01 % 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: -0.00 (0.15), residues: 2880 helix: 0.47 (0.16), residues: 1008 sheet: -0.09 (0.18), residues: 786 loop : -0.16 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 331 HIS 0.011 0.002 HIS F 429 PHE 0.016 0.002 PHE D 59 TYR 0.030 0.002 TYR C 402 ARG 0.005 0.001 ARG A 162 *********************** 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 673 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 578 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 THR cc_start: 0.8966 (m) cc_final: 0.8734 (m) REVERT: A 194 TYR cc_start: 0.7529 (m-80) cc_final: 0.7149 (m-80) REVERT: A 235 TYR cc_start: 0.8486 (m-80) cc_final: 0.7876 (m-80) REVERT: A 247 PHE cc_start: 0.8542 (m-80) cc_final: 0.8337 (m-80) REVERT: A 302 VAL cc_start: 0.9072 (m) cc_final: 0.8842 (t) REVERT: B 170 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7294 (mtp85) REVERT: B 234 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7668 (mt-10) REVERT: B 235 TYR cc_start: 0.8464 (m-80) cc_final: 0.7928 (m-80) REVERT: B 358 ASP cc_start: 0.6994 (m-30) cc_final: 0.6746 (m-30) REVERT: B 392 PHE cc_start: 0.8482 (t80) cc_final: 0.8221 (t80) REVERT: B 420 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5633 (tpp) REVERT: B 469 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7069 (tm-30) REVERT: C 170 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7173 (mtp85) REVERT: C 185 ILE cc_start: 0.9048 (mt) cc_final: 0.8813 (mm) REVERT: C 194 TYR cc_start: 0.7366 (m-80) cc_final: 0.7108 (m-80) REVERT: C 234 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7713 (mt-10) REVERT: D 181 THR cc_start: 0.8993 (m) cc_final: 0.8781 (m) REVERT: D 194 TYR cc_start: 0.7347 (m-80) cc_final: 0.6975 (m-80) REVERT: D 235 TYR cc_start: 0.8495 (m-80) cc_final: 0.7972 (m-80) REVERT: D 247 PHE cc_start: 0.8428 (m-80) cc_final: 0.8133 (m-10) REVERT: D 302 VAL cc_start: 0.9071 (m) cc_final: 0.8830 (t) REVERT: D 457 LYS cc_start: 0.8315 (ptmm) cc_final: 0.7989 (pttp) REVERT: E 170 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7301 (mtp85) REVERT: E 234 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7626 (mt-10) REVERT: E 235 TYR cc_start: 0.8454 (m-80) cc_final: 0.7966 (m-80) REVERT: E 420 MET cc_start: 0.5556 (OUTLIER) cc_final: 0.4882 (ttp) REVERT: E 456 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7844 (t80) REVERT: E 471 MET cc_start: 0.7045 (mpp) cc_final: 0.6737 (mpp) REVERT: F 86 ASN cc_start: 0.8152 (m-40) cc_final: 0.7945 (m-40) REVERT: F 170 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.7230 (mtp85) REVERT: F 181 THR cc_start: 0.8948 (m) cc_final: 0.8747 (m) REVERT: F 194 TYR cc_start: 0.7433 (m-80) cc_final: 0.7163 (m-80) REVERT: F 221 GLU cc_start: 0.7261 (tt0) cc_final: 0.6894 (tt0) REVERT: F 469 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6415 (tt0) outliers start: 95 outliers final: 78 residues processed: 632 average time/residue: 0.3471 time to fit residues: 340.0157 Evaluate side-chains 624 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 543 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 23 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 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** ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23448 Z= 0.231 Angle : 0.599 7.400 31680 Z= 0.299 Chirality : 0.044 0.165 3534 Planarity : 0.004 0.041 4062 Dihedral : 10.110 114.665 3456 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.99 % Allowed : 18.60 % Favored : 77.41 % 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: 0.04 (0.15), residues: 2880 helix: 0.51 (0.16), residues: 1002 sheet: 0.07 (0.19), residues: 756 loop : -0.25 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 331 HIS 0.012 0.002 HIS B 423 PHE 0.026 0.002 PHE E 392 TYR 0.032 0.002 TYR F 402 ARG 0.005 0.000 ARG A 393 *********************** 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 685 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 588 time to evaluate : 2.321 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: A 181 THR cc_start: 0.8937 (m) cc_final: 0.8737 (m) REVERT: A 194 TYR cc_start: 0.7524 (m-80) cc_final: 0.7149 (m-80) REVERT: A 235 TYR cc_start: 0.8403 (m-80) cc_final: 0.7870 (m-80) REVERT: A 457 LYS cc_start: 0.8376 (ptmm) cc_final: 0.8162 (pttp) REVERT: B 234 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7667 (mt-10) REVERT: B 235 TYR cc_start: 0.8399 (m-80) cc_final: 0.7922 (m-80) REVERT: B 392 PHE cc_start: 0.8451 (t80) cc_final: 0.8199 (t80) REVERT: B 402 TYR cc_start: 0.7770 (t80) cc_final: 0.7307 (t80) REVERT: B 420 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5773 (tpp) REVERT: B 461 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7723 (t) REVERT: B 469 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7102 (tm-30) REVERT: C 170 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7171 (mtp85) REVERT: C 194 TYR cc_start: 0.7377 (m-80) cc_final: 0.7106 (m-80) REVERT: C 234 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7752 (mt-10) REVERT: D 194 TYR cc_start: 0.7359 (m-80) cc_final: 0.7073 (m-80) REVERT: D 235 TYR cc_start: 0.8451 (m-80) cc_final: 0.7916 (m-80) REVERT: D 457 LYS cc_start: 0.8292 (ptmm) cc_final: 0.7955 (pttp) REVERT: E 234 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7644 (mt-10) REVERT: E 235 TYR cc_start: 0.8387 (m-80) cc_final: 0.7919 (m-80) REVERT: E 302 VAL cc_start: 0.8850 (m) cc_final: 0.8506 (t) REVERT: E 402 TYR cc_start: 0.7816 (t80) cc_final: 0.7420 (t80) REVERT: E 456 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7860 (t80) REVERT: E 471 MET cc_start: 0.7026 (mpp) cc_final: 0.6788 (mpp) REVERT: F 86 ASN cc_start: 0.8116 (m-40) cc_final: 0.7790 (m-40) REVERT: F 170 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7121 (mtp85) REVERT: F 194 TYR cc_start: 0.7424 (m-80) cc_final: 0.7201 (m-80) REVERT: F 392 PHE cc_start: 0.8272 (t80) cc_final: 0.8060 (t80) REVERT: F 435 ASP cc_start: 0.6793 (t0) cc_final: 0.6526 (t0) REVERT: F 469 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7178 (tm-30) outliers start: 97 outliers final: 81 residues processed: 643 average time/residue: 0.3386 time to fit residues: 339.7355 Evaluate side-chains 640 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 556 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 158 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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** ** B 429 HIS ** 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 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN ** E 361 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 23448 Z= 0.608 Angle : 0.833 10.773 31680 Z= 0.422 Chirality : 0.051 0.193 3534 Planarity : 0.006 0.055 4062 Dihedral : 10.546 115.329 3456 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.02 % Allowed : 18.81 % Favored : 76.17 % 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: -0.71 (0.15), residues: 2880 helix: 0.18 (0.16), residues: 990 sheet: -0.49 (0.18), residues: 780 loop : -0.88 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 331 HIS 0.011 0.003 HIS D 463 PHE 0.026 0.003 PHE A 59 TYR 0.032 0.003 TYR F 402 ARG 0.007 0.001 ARG C 216 *********************** 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 664 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 542 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8259 (p0) cc_final: 0.7980 (p0) REVERT: A 235 TYR cc_start: 0.8455 (m-80) cc_final: 0.7941 (m-80) REVERT: A 319 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: B 166 ARG cc_start: 0.7333 (ptt180) cc_final: 0.6745 (ptp-170) REVERT: B 234 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7496 (mt-10) REVERT: B 235 TYR cc_start: 0.8446 (m-80) cc_final: 0.8026 (m-80) REVERT: B 247 PHE cc_start: 0.8710 (m-80) cc_final: 0.8498 (m-10) REVERT: B 420 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5837 (tpp) REVERT: C 194 TYR cc_start: 0.7586 (m-80) cc_final: 0.7308 (m-80) REVERT: C 234 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7812 (mt-10) REVERT: D 194 TYR cc_start: 0.7725 (m-80) cc_final: 0.7305 (m-80) REVERT: D 234 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7633 (mt-10) REVERT: D 235 TYR cc_start: 0.8527 (m-80) cc_final: 0.8032 (m-80) REVERT: D 319 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6677 (mt-10) REVERT: D 457 LYS cc_start: 0.8381 (ptmm) cc_final: 0.8100 (pttp) REVERT: E 106 LEU cc_start: 0.8351 (tt) cc_final: 0.8135 (tt) REVERT: E 170 ARG cc_start: 0.7617 (mtm-85) cc_final: 0.7284 (mtm180) REVERT: E 234 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7484 (mt-10) REVERT: E 235 TYR cc_start: 0.8476 (m-80) cc_final: 0.8026 (m-80) REVERT: E 456 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8056 (t80) REVERT: F 106 LEU cc_start: 0.8526 (tt) cc_final: 0.8319 (tt) REVERT: F 166 ARG cc_start: 0.7964 (mtt90) cc_final: 0.7537 (mtt180) REVERT: F 170 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7110 (mtp85) REVERT: F 191 ILE cc_start: 0.8106 (mp) cc_final: 0.7840 (mt) REVERT: F 194 TYR cc_start: 0.7552 (m-80) cc_final: 0.7157 (m-80) REVERT: F 234 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7819 (mt-10) REVERT: F 385 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7415 (ttm170) outliers start: 122 outliers final: 102 residues processed: 611 average time/residue: 0.3426 time to fit residues: 326.0073 Evaluate side-chains 621 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 515 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 423 HIS Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 429 HIS Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 474 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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** ** C 361 GLN ** 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 361 GLN ** 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: 0.7638 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23448 Z= 0.206 Angle : 0.625 8.303 31680 Z= 0.314 Chirality : 0.045 0.171 3534 Planarity : 0.004 0.041 4062 Dihedral : 9.684 117.789 3456 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.00 % Allowed : 22.39 % Favored : 74.61 % 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: -0.17 (0.15), residues: 2880 helix: 0.55 (0.16), residues: 984 sheet: -0.12 (0.18), residues: 756 loop : -0.54 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 331 HIS 0.011 0.002 HIS C 429 PHE 0.017 0.002 PHE B 59 TYR 0.031 0.002 TYR D 402 ARG 0.006 0.000 ARG F 217 *********************** 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 664 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 591 time to evaluate : 2.754 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: A 194 TYR cc_start: 0.7513 (m-80) cc_final: 0.7227 (m-80) REVERT: A 319 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6505 (mt-10) REVERT: B 166 ARG cc_start: 0.7191 (ptt180) cc_final: 0.6849 (ptp-170) REVERT: B 234 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 235 TYR cc_start: 0.8444 (m-80) cc_final: 0.7912 (m-80) REVERT: B 358 ASP cc_start: 0.6936 (m-30) cc_final: 0.6676 (m-30) REVERT: B 392 PHE cc_start: 0.8428 (t80) cc_final: 0.8140 (t80) REVERT: B 420 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5858 (tpp) REVERT: C 106 LEU cc_start: 0.8466 (tt) cc_final: 0.8261 (tt) REVERT: C 170 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.7165 (mtp85) REVERT: C 194 TYR cc_start: 0.7536 (m-80) cc_final: 0.7290 (m-80) REVERT: C 234 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7886 (mt-10) REVERT: D 185 ILE cc_start: 0.9129 (mm) cc_final: 0.8882 (mt) REVERT: D 194 TYR cc_start: 0.7682 (m-80) cc_final: 0.7371 (m-80) REVERT: D 235 TYR cc_start: 0.8328 (m-80) cc_final: 0.7772 (m-80) REVERT: D 319 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6577 (mt-10) REVERT: D 457 LYS cc_start: 0.8315 (ptmm) cc_final: 0.8051 (pttp) REVERT: E 234 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7672 (mt-10) REVERT: E 235 TYR cc_start: 0.8460 (m-80) cc_final: 0.7913 (m-80) REVERT: E 302 VAL cc_start: 0.8846 (m) cc_final: 0.8530 (t) REVERT: E 456 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.8079 (t80) REVERT: F 106 LEU cc_start: 0.8435 (tt) cc_final: 0.8224 (tt) REVERT: F 166 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7491 (mtt180) REVERT: F 170 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7182 (mtp85) REVERT: F 185 ILE cc_start: 0.9087 (mt) cc_final: 0.8875 (mm) REVERT: F 194 TYR cc_start: 0.7485 (m-80) cc_final: 0.7178 (m-80) REVERT: F 234 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7845 (mt-10) REVERT: F 385 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7395 (ttm170) outliers start: 73 outliers final: 51 residues processed: 624 average time/residue: 0.3440 time to fit residues: 332.3312 Evaluate side-chains 608 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 553 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 444 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.6980 chunk 265 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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** ** C 423 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** E 361 GLN F 245 ASN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23448 Z= 0.219 Angle : 0.637 11.013 31680 Z= 0.317 Chirality : 0.045 0.216 3534 Planarity : 0.004 0.068 4062 Dihedral : 9.447 117.968 3456 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.80 % Allowed : 23.09 % Favored : 74.12 % 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: -0.09 (0.16), residues: 2880 helix: 0.59 (0.16), residues: 984 sheet: -0.03 (0.19), residues: 756 loop : -0.50 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 331 HIS 0.013 0.002 HIS E 429 PHE 0.040 0.002 PHE F 392 TYR 0.031 0.002 TYR E 402 ARG 0.014 0.000 ARG B 170 *********************** 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 645 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 577 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 THR cc_start: 0.8840 (m) cc_final: 0.8589 (m) REVERT: A 194 TYR cc_start: 0.7439 (m-80) cc_final: 0.7183 (m-80) REVERT: A 319 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6429 (mt-10) REVERT: B 127 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7728 (mt) REVERT: B 166 ARG cc_start: 0.7149 (ptt180) cc_final: 0.6760 (ptp-170) REVERT: B 234 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7605 (mt-10) REVERT: B 235 TYR cc_start: 0.8482 (m-80) cc_final: 0.7933 (m-80) REVERT: B 358 ASP cc_start: 0.7005 (m-30) cc_final: 0.6674 (m-30) REVERT: B 392 PHE cc_start: 0.8470 (t80) cc_final: 0.8122 (t80) REVERT: B 420 MET cc_start: 0.6207 (OUTLIER) cc_final: 0.5841 (tpp) REVERT: B 469 GLU cc_start: 0.7601 (tm-30) cc_final: 0.6912 (tt0) REVERT: C 106 LEU cc_start: 0.8457 (tt) cc_final: 0.8242 (tt) REVERT: C 170 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.7220 (mtp85) REVERT: C 185 ILE cc_start: 0.9034 (mt) cc_final: 0.8818 (mm) REVERT: C 194 TYR cc_start: 0.7541 (m-80) cc_final: 0.7301 (m-80) REVERT: C 234 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7888 (mt-10) REVERT: D 194 TYR cc_start: 0.7687 (m-80) cc_final: 0.7353 (m-80) REVERT: D 235 TYR cc_start: 0.8334 (m-80) cc_final: 0.7874 (m-80) REVERT: D 319 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: D 457 LYS cc_start: 0.8307 (ptmm) cc_final: 0.8043 (pttp) REVERT: E 234 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7680 (mt-10) REVERT: E 235 TYR cc_start: 0.8489 (m-80) cc_final: 0.7941 (m-80) REVERT: E 402 TYR cc_start: 0.8183 (t80) cc_final: 0.7938 (t80) REVERT: E 418 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7759 (mm-40) REVERT: F 106 LEU cc_start: 0.8435 (tt) cc_final: 0.8211 (tt) REVERT: F 166 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7472 (mtt180) REVERT: F 170 ARG cc_start: 0.7381 (mtm-85) cc_final: 0.7043 (mtp85) REVERT: F 185 ILE cc_start: 0.9077 (mt) cc_final: 0.8857 (mm) REVERT: F 194 TYR cc_start: 0.7495 (m-80) cc_final: 0.7191 (m-80) outliers start: 68 outliers final: 53 residues processed: 611 average time/residue: 0.3470 time to fit residues: 330.4266 Evaluate side-chains 610 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 553 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 444 GLU 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: 7.9990 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 264 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** ** D 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** ** F 423 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: 0.7668 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23448 Z= 0.306 Angle : 0.664 10.268 31680 Z= 0.332 Chirality : 0.046 0.183 3534 Planarity : 0.004 0.041 4062 Dihedral : 9.443 119.287 3456 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.76 % Allowed : 23.42 % Favored : 73.83 % 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: -0.17 (0.15), residues: 2880 helix: 0.60 (0.16), residues: 984 sheet: 0.02 (0.19), residues: 744 loop : -0.71 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 331 HIS 0.013 0.002 HIS E 429 PHE 0.021 0.002 PHE E 278 TYR 0.032 0.002 TYR F 402 ARG 0.008 0.000 ARG B 468 ********************** 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 626 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 559 time to evaluate : 2.812 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: A 181 THR cc_start: 0.8923 (m) cc_final: 0.8688 (m) REVERT: A 319 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6404 (mt-10) REVERT: B 21 MET cc_start: 0.8153 (ptm) cc_final: 0.7845 (ptm) REVERT: B 127 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7842 (mt) REVERT: B 166 ARG cc_start: 0.7274 (ptt180) cc_final: 0.7003 (ptp-170) REVERT: B 234 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7560 (mt-10) REVERT: B 235 TYR cc_start: 0.8515 (m-80) cc_final: 0.7930 (m-80) REVERT: B 420 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5851 (tpp) REVERT: B 457 LYS cc_start: 0.8062 (pttp) cc_final: 0.7816 (pttp) REVERT: C 106 LEU cc_start: 0.8481 (tt) cc_final: 0.8270 (tt) REVERT: C 170 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7211 (mtp85) REVERT: C 185 ILE cc_start: 0.9121 (mt) cc_final: 0.8861 (mm) REVERT: C 194 TYR cc_start: 0.7545 (m-80) cc_final: 0.7291 (m-80) REVERT: C 234 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7859 (mt-10) REVERT: D 194 TYR cc_start: 0.7696 (m-80) cc_final: 0.7358 (m-80) REVERT: D 235 TYR cc_start: 0.8343 (m-80) cc_final: 0.7858 (m-80) REVERT: D 319 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6528 (mt-10) REVERT: D 457 LYS cc_start: 0.8314 (ptmm) cc_final: 0.8060 (pttp) REVERT: E 21 MET cc_start: 0.8073 (ptm) cc_final: 0.7793 (ptm) REVERT: E 234 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7614 (mt-10) REVERT: E 235 TYR cc_start: 0.8550 (m-80) cc_final: 0.7976 (m-80) REVERT: E 418 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7799 (mm-40) REVERT: E 457 LYS cc_start: 0.8100 (pttp) cc_final: 0.7826 (pttp) REVERT: F 106 LEU cc_start: 0.8448 (tt) cc_final: 0.8227 (tt) REVERT: F 166 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7532 (mtt180) REVERT: F 185 ILE cc_start: 0.9079 (mt) cc_final: 0.8875 (mm) REVERT: F 191 ILE cc_start: 0.7870 (mp) cc_final: 0.7616 (mt) REVERT: F 194 TYR cc_start: 0.7421 (m-80) cc_final: 0.7108 (m-80) outliers start: 67 outliers final: 58 residues processed: 590 average time/residue: 0.3380 time to fit residues: 311.2324 Evaluate side-chains 607 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 545 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 444 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 228 optimal weight: 0.1980 chunk 95 optimal weight: 8.9990 chunk 234 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN E 361 GLN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118722 restraints weight = 38668.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122356 restraints weight = 21943.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124824 restraints weight = 15093.793| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23448 Z= 0.227 Angle : 0.638 10.453 31680 Z= 0.317 Chirality : 0.045 0.185 3534 Planarity : 0.004 0.041 4062 Dihedral : 9.161 120.302 3456 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.55 % Allowed : 23.66 % Favored : 73.79 % 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: -0.09 (0.16), residues: 2880 helix: 0.63 (0.16), residues: 984 sheet: 0.17 (0.19), residues: 732 loop : -0.69 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 331 HIS 0.013 0.002 HIS E 429 PHE 0.028 0.002 PHE B 392 TYR 0.031 0.001 TYR F 402 ARG 0.008 0.000 ARG B 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5924.45 seconds wall clock time: 106 minutes 58.00 seconds (6418.00 seconds total)