Starting phenix.real_space_refine on Tue Jun 24 21:33:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c77_45277/06_2025/9c77_45277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c77_45277/06_2025/9c77_45277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c77_45277/06_2025/9c77_45277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c77_45277/06_2025/9c77_45277.map" model { file = "/net/cci-nas-00/data/ceres_data/9c77_45277/06_2025/9c77_45277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c77_45277/06_2025/9c77_45277.cif" } resolution = 3.2 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= 0.011 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 48 5.49 5 Mg 6 5.21 5 S 162 5.16 5 C 18170 2.51 5 N 4970 2.21 5 O 5436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28792 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4666 Classifications: {'peptide': 592} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 564} Chain breaks: 1 Chain: "B" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4720 Classifications: {'peptide': 600} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 572} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4666 Classifications: {'peptide': 592} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 564} Chain breaks: 1 Chain: "D" Number of atoms: 4712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4712 Classifications: {'peptide': 599} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 571} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4666 Classifications: {'peptide': 592} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 564} Chain breaks: 1 Chain: "F" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4720 Classifications: {'peptide': 600} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 572} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 2} Link IDs: {'rna2p': 2, 'rna3p': 1} Chain: "H" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 3} Chain: "I" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 24.06, per 1000 atoms: 0.84 Number of scatterers: 28792 At special positions: 0 Unit cell: (103.675, 199.375, 204.45, 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 162 16.00 P 48 15.00 Mg 6 11.99 O 5436 8.00 N 4970 7.00 C 18170 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.64 Conformation dependent library (CDL) restraints added in 3.4 seconds 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6730 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 13 sheets defined 53.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.973A pdb=" N GLU A 18 " --> pdb=" O MET A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 removed outlier: 4.077A pdb=" N LEU A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.569A pdb=" N MET A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 removed outlier: 3.597A pdb=" N LYS A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 removed outlier: 3.870A pdb=" N SER A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.743A pdb=" N GLY A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 347 through 369 Processing helix chain 'A' and resid 390 through 405 removed outlier: 4.119A pdb=" N SER A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 405 " --> pdb=" O ILE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.750A pdb=" N THR A 426 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 427 " --> pdb=" O LYS A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 427' Processing helix chain 'A' and resid 431 through 442 removed outlier: 4.404A pdb=" N ALA A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 575 through 596 Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.549A pdb=" N GLU B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 removed outlier: 4.604A pdb=" N LEU B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 180 through 199 Processing helix chain 'B' and resid 215 through 224 Processing helix chain 'B' and resid 230 through 236 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.711A pdb=" N LEU B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 Processing helix chain 'B' and resid 307 through 325 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.786A pdb=" N TYR B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 369 removed outlier: 3.627A pdb=" N LYS B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 405 removed outlier: 3.737A pdb=" N GLN B 405 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 431 through 442 removed outlier: 4.642A pdb=" N ALA B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.901A pdb=" N LEU B 476 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 473 through 477' Processing helix chain 'B' and resid 479 through 490 Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 517 through 525 Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 557 through 571 Processing helix chain 'B' and resid 575 through 600 Processing helix chain 'C' and resid 14 through 21 removed outlier: 4.144A pdb=" N GLU C 18 " --> pdb=" O MET C 14 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 19 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 removed outlier: 4.333A pdb=" N LEU C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 89 Processing helix chain 'C' and resid 103 through 118 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'C' and resid 161 through 167 removed outlier: 3.735A pdb=" N LYS C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 215 through 222 Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 253 through 261 Processing helix chain 'C' and resid 289 through 298 Processing helix chain 'C' and resid 307 through 325 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.652A pdb=" N ALA C 340 " --> pdb=" O ASN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 removed outlier: 3.927A pdb=" N LYS C 344 " --> pdb=" O ASP C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 369 Processing helix chain 'C' and resid 390 through 404 removed outlier: 4.009A pdb=" N SER C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 423 through 427 Processing helix chain 'C' and resid 434 through 441 removed outlier: 4.209A pdb=" N VAL C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 475 through 478 Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 496 through 504 Processing helix chain 'C' and resid 517 through 525 Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 557 through 572 Processing helix chain 'C' and resid 575 through 598 Processing helix chain 'D' and resid 14 through 23 removed outlier: 3.945A pdb=" N GLU D 18 " --> pdb=" O MET D 14 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 removed outlier: 4.459A pdb=" N LEU D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 87 Processing helix chain 'D' and resid 103 through 118 Processing helix chain 'D' and resid 133 through 144 removed outlier: 3.566A pdb=" N MET D 137 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 163 removed outlier: 3.524A pdb=" N LEU D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 Processing helix chain 'D' and resid 182 through 199 removed outlier: 3.662A pdb=" N ILE D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.714A pdb=" N LEU D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 297 removed outlier: 3.877A pdb=" N GLY D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 325 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.778A pdb=" N TYR D 339 " --> pdb=" O SER D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 369 removed outlier: 3.584A pdb=" N LYS D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.776A pdb=" N GLN D 405 " --> pdb=" O ILE D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 4.021A pdb=" N ARG D 427 " --> pdb=" O LYS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 442 removed outlier: 4.582A pdb=" N ALA D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 475 through 478 removed outlier: 3.584A pdb=" N GLU D 478 " --> pdb=" O ASN D 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 475 through 478' Processing helix chain 'D' and resid 479 through 489 Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'D' and resid 517 through 525 Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 541 through 548 Processing helix chain 'D' and resid 548 through 553 Processing helix chain 'D' and resid 557 through 572 Processing helix chain 'D' and resid 575 through 591 Processing helix chain 'D' and resid 594 through 600 Processing helix chain 'E' and resid 14 through 21 removed outlier: 4.122A pdb=" N HIS E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 51 removed outlier: 3.556A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 88 Processing helix chain 'E' and resid 103 through 118 Processing helix chain 'E' and resid 133 through 144 Processing helix chain 'E' and resid 161 through 167 removed outlier: 3.839A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 208 through 214 Processing helix chain 'E' and resid 215 through 224 Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 253 through 261 Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.885A pdb=" N GLY E 297 " --> pdb=" O TYR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 347 through 369 Processing helix chain 'E' and resid 390 through 404 removed outlier: 4.557A pdb=" N SER E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 434 through 441 removed outlier: 4.422A pdb=" N VAL E 438 " --> pdb=" O ASP E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 464 removed outlier: 3.588A pdb=" N ILE E 458 " --> pdb=" O ASP E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 489 Processing helix chain 'E' and resid 496 through 504 Processing helix chain 'E' and resid 517 through 525 Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 541 through 548 Processing helix chain 'E' and resid 548 through 553 Processing helix chain 'E' and resid 557 through 572 Processing helix chain 'E' and resid 575 through 596 removed outlier: 3.614A pdb=" N GLU E 581 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 41 through 50 removed outlier: 4.492A pdb=" N LEU F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 87 Processing helix chain 'F' and resid 103 through 118 Processing helix chain 'F' and resid 136 through 144 Processing helix chain 'F' and resid 157 through 162 Processing helix chain 'F' and resid 163 through 166 Processing helix chain 'F' and resid 180 through 199 Processing helix chain 'F' and resid 215 through 224 Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 230 through 237 Processing helix chain 'F' and resid 253 through 262 removed outlier: 3.630A pdb=" N ALA F 262 " --> pdb=" O GLN F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 297 removed outlier: 3.646A pdb=" N GLY F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 307 through 325 Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.753A pdb=" N TYR F 339 " --> pdb=" O SER F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 347 through 369 removed outlier: 3.673A pdb=" N LYS F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 404 removed outlier: 4.258A pdb=" N SER F 394 " --> pdb=" O LEU F 390 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET F 404 " --> pdb=" O ALA F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 423 through 427 removed outlier: 3.672A pdb=" N ARG F 427 " --> pdb=" O LYS F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.682A pdb=" N GLU F 432 " --> pdb=" O SER F 429 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS F 433 " --> pdb=" O TYR F 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 433' Processing helix chain 'F' and resid 434 through 441 removed outlier: 4.378A pdb=" N VAL F 438 " --> pdb=" O ASP F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 464 Processing helix chain 'F' and resid 475 through 478 Processing helix chain 'F' and resid 479 through 489 Processing helix chain 'F' and resid 496 through 504 Processing helix chain 'F' and resid 517 through 525 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 541 through 553 removed outlier: 3.895A pdb=" N LEU F 549 " --> pdb=" O ASN F 545 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA F 550 " --> pdb=" O LEU F 546 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 572 Processing helix chain 'F' and resid 575 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 61 removed outlier: 5.917A pdb=" N LEU A 5 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 33 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N CYS A 7 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL A 4 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N CYS A 98 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU A 6 " --> pdb=" O CYS A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 245 removed outlier: 4.335A pdb=" N VAL A 240 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU A 331 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU A 242 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ARG A 333 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N CYS A 244 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA A 328 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN A 377 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 330 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 379 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 332 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE A 381 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS A 334 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N SER A 383 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 413 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 378 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A 415 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA A 419 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 445 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLY A 471 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA A 447 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU A 470 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 62 removed outlier: 5.809A pdb=" N LEU B 5 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE B 33 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS B 7 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N THR B 35 " --> pdb=" O CYS B 7 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 6 " --> pdb=" O CYS B 98 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER B 121 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY B 152 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE B 123 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU B 150 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 125 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE B 148 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 245 removed outlier: 5.918A pdb=" N LYS B 239 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR B 329 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N HIS B 243 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG B 333 " --> pdb=" O HIS B 243 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS B 245 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 375 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL B 414 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU B 378 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 416 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL B 380 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU B 418 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 445 " --> pdb=" O ARG B 469 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLY B 471 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ALA B 447 " --> pdb=" O GLY B 471 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 493 " --> pdb=" O SER B 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 61 removed outlier: 3.925A pdb=" N SER C 58 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C 60 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LEU C 5 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE C 33 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N CYS C 7 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL C 4 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS C 98 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 6 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 97 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL C 125 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 239 through 245 removed outlier: 4.438A pdb=" N VAL C 240 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLU C 331 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU C 242 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG C 333 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS C 244 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 413 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 378 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 415 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA C 419 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL C 445 " --> pdb=" O ARG C 469 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLY C 471 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA C 447 " --> pdb=" O GLY C 471 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 56 through 62 removed outlier: 5.922A pdb=" N LEU D 5 " --> pdb=" O HIS D 31 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE D 33 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS D 7 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N THR D 35 " --> pdb=" O CYS D 7 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL D 4 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N CYS D 98 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU D 6 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 123 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL D 122 " --> pdb=" O MET D 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 239 through 245 removed outlier: 5.926A pdb=" N LYS D 239 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR D 329 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS D 243 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ARG D 333 " --> pdb=" O HIS D 243 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS D 245 " --> pdb=" O ARG D 333 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL D 414 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU D 378 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL D 416 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL D 380 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU D 418 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL D 445 " --> pdb=" O ARG D 469 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLY D 471 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA D 447 " --> pdb=" O GLY D 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.227A pdb=" N LEU E 5 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE E 33 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS E 7 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N THR E 35 " --> pdb=" O CYS E 7 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER E 58 " --> pdb=" O VAL E 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.691A pdb=" N LEU E 126 " --> pdb=" O HIS E 147 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS E 147 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 239 through 245 removed outlier: 5.910A pdb=" N LYS E 239 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR E 329 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N HIS E 243 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG E 333 " --> pdb=" O HIS E 243 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N HIS E 245 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE E 413 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU E 378 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY E 415 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA E 419 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL E 445 " --> pdb=" O ARG E 469 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLY E 471 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA E 447 " --> pdb=" O GLY E 471 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU E 470 " --> pdb=" O GLU E 494 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL E 493 " --> pdb=" O SER E 529 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 56 through 62 removed outlier: 6.715A pdb=" N VAL F 30 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR F 60 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 32 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N CYS F 62 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR F 34 " --> pdb=" O CYS F 62 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU F 5 " --> pdb=" O HIS F 31 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE F 33 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS F 7 " --> pdb=" O PHE F 33 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N THR F 35 " --> pdb=" O CYS F 7 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL F 4 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N CYS F 98 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU F 6 " --> pdb=" O CYS F 98 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL F 97 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL F 125 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN F 120 " --> pdb=" O TYR F 153 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR F 153 " --> pdb=" O GLN F 120 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL F 122 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 239 through 245 removed outlier: 6.026A pdb=" N LYS F 239 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR F 329 " --> pdb=" O LYS F 239 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N HIS F 243 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ARG F 333 " --> pdb=" O HIS F 243 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS F 245 " --> pdb=" O ARG F 333 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA F 328 " --> pdb=" O HIS F 375 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASN F 377 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA F 330 " --> pdb=" O ASN F 377 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU F 379 " --> pdb=" O ALA F 330 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE F 332 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE F 381 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS F 334 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL F 414 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU F 378 " --> pdb=" O VAL F 414 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL F 416 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL F 380 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU F 418 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS F 448 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG F 469 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU F 470 " --> pdb=" O GLU F 494 " (cutoff:3.500A) 1284 hydrogen bonds defined for protein. 3699 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: 11.76 Time building geometry restraints manager: 8.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9489 1.34 - 1.46: 6660 1.46 - 1.58: 12978 1.58 - 1.70: 93 1.70 - 1.82: 246 Bond restraints: 29466 Sorted by residual: bond pdb=" C1' ATP E 701 " pdb=" C2' ATP E 701 " ideal model delta sigma weight residual 1.531 1.302 0.229 1.20e-02 6.94e+03 3.64e+02 bond pdb=" C1' ATP D 701 " pdb=" C2' ATP D 701 " ideal model delta sigma weight residual 1.531 1.302 0.229 1.20e-02 6.94e+03 3.63e+02 bond pdb=" C1' ATP C 701 " pdb=" C2' ATP C 701 " ideal model delta sigma weight residual 1.531 1.303 0.228 1.20e-02 6.94e+03 3.62e+02 bond pdb=" C1' ATP F 701 " pdb=" C2' ATP F 701 " ideal model delta sigma weight residual 1.531 1.303 0.228 1.20e-02 6.94e+03 3.62e+02 bond pdb=" C1' ATP A 701 " pdb=" C2' ATP A 701 " ideal model delta sigma weight residual 1.531 1.303 0.228 1.20e-02 6.94e+03 3.61e+02 ... (remaining 29461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 39681 3.54 - 7.07: 264 7.07 - 10.61: 84 10.61 - 14.14: 16 14.14 - 17.68: 12 Bond angle restraints: 40057 Sorted by residual: angle pdb=" PB ATP C 702 " pdb=" O3B ATP C 702 " pdb=" PG ATP C 702 " ideal model delta sigma weight residual 139.87 122.19 17.68 1.00e+00 1.00e+00 3.13e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 123.04 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PB ATP F 701 " pdb=" O3B ATP F 701 " pdb=" PG ATP F 701 " ideal model delta sigma weight residual 139.87 123.10 16.77 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 123.12 16.75 1.00e+00 1.00e+00 2.80e+02 angle pdb=" PB ATP C 701 " pdb=" O3B ATP C 701 " pdb=" PG ATP C 701 " ideal model delta sigma weight residual 139.87 123.15 16.72 1.00e+00 1.00e+00 2.79e+02 ... (remaining 40052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 15944 24.48 - 48.95: 1584 48.95 - 73.43: 319 73.43 - 97.90: 39 97.90 - 122.38: 3 Dihedral angle restraints: 17889 sinusoidal: 7492 harmonic: 10397 Sorted by residual: dihedral pdb=" CA LYS E 143 " pdb=" C LYS E 143 " pdb=" N GLY E 144 " pdb=" CA GLY E 144 " ideal model delta harmonic sigma weight residual 180.00 151.57 28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA LEU B 211 " pdb=" C LEU B 211 " pdb=" N ALA B 212 " pdb=" CA ALA B 212 " ideal model delta harmonic sigma weight residual 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASP E 434 " pdb=" C ASP E 434 " pdb=" N PHE E 435 " pdb=" CA PHE E 435 " ideal model delta harmonic sigma weight residual 180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 17886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3910 0.067 - 0.133: 495 0.133 - 0.200: 16 0.200 - 0.266: 0 0.266 - 0.333: 12 Chirality restraints: 4433 Sorted by residual: chirality pdb=" C2' ATP C 702 " pdb=" C1' ATP C 702 " pdb=" C3' ATP C 702 " pdb=" O2' ATP C 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.35 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C2' ATP F 702 " pdb=" C1' ATP F 702 " pdb=" C3' ATP F 702 " pdb=" O2' ATP F 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.36 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C2' ATP A 702 " pdb=" C1' ATP A 702 " pdb=" C3' ATP A 702 " pdb=" O2' ATP A 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 4430 not shown) Planarity restraints: 5082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 157 " -0.011 2.00e-02 2.50e+03 1.68e-02 7.05e+00 pdb=" CG TRP E 157 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP E 157 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 157 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 157 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 157 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 157 " -0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 157 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 157 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 157 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 157 " -0.009 2.00e-02 2.50e+03 1.51e-02 5.73e+00 pdb=" CG TRP C 157 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 157 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 157 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 157 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 157 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 157 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 157 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 157 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 206 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 207 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " 0.029 5.00e-02 4.00e+02 ... (remaining 5079 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 20 2.17 - 2.85: 10524 2.85 - 3.53: 43515 3.53 - 4.22: 68763 4.22 - 4.90: 121775 Nonbonded interactions: 244597 Sorted by model distance: nonbonded pdb=" O GLY C 297 " pdb=" O3G ATP C 702 " model vdw 1.487 3.040 nonbonded pdb=" C GLY C 297 " pdb=" O3G ATP C 702 " model vdw 1.711 3.270 nonbonded pdb=" OD1 ASP B 533 " pdb="MG MG B 703 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP F 533 " pdb="MG MG F 703 " model vdw 2.030 2.170 nonbonded pdb=" NE2 HIS D 243 " pdb="MG MG D 703 " model vdw 2.067 2.250 ... (remaining 244592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 272 or (resid 273 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 274 through 591 or resid 593 thro \ ugh 600 or resid 701 through 703)) selection = (chain 'B' and (resid 2 through 192 or resid 200 through 591 or resid 593 throug \ h 600 or resid 701 through 703)) selection = (chain 'C' and (resid 2 through 272 or (resid 273 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 274 through 591 or resid 593 thro \ ugh 600 or resid 701 through 703)) selection = (chain 'D' and (resid 2 through 192 or resid 200 through 600 or resid 701 throug \ h 703)) selection = (chain 'E' and (resid 2 through 272 or (resid 273 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 274 through 591 or resid 593 thro \ ugh 600 or resid 701 through 703)) selection = (chain 'F' and (resid 2 through 192 or resid 200 through 591 or resid 593 throug \ h 600 or resid 701 through 703)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 147.510 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: 0.030 Extract box with map and model: 1.370 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 76.200 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 230.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 : 0.010 0.464 29478 Z= 0.786 Angle : 0.838 17.680 40057 Z= 0.577 Chirality : 0.044 0.333 4433 Planarity : 0.003 0.058 5082 Dihedral : 19.231 122.377 11159 Min Nonbonded Distance : 1.487 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.29 % Favored : 94.51 % Rotamer: Outliers : 0.36 % Allowed : 28.47 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 3555 helix: 1.46 (0.13), residues: 1700 sheet: -0.27 (0.26), residues: 460 loop : -1.04 (0.18), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP E 157 HIS 0.009 0.001 HIS E 21 PHE 0.026 0.001 PHE A 27 TYR 0.024 0.001 TYR A 430 ARG 0.014 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.15209 ( 1284) hydrogen bonds : angle 6.02123 ( 3699) covalent geometry : bond 0.00903 (29466) covalent geometry : angle 0.83798 (40057) Misc. bond : bond 0.16148 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 LYS cc_start: 0.8619 (tmtt) cc_final: 0.8416 (tmtt) REVERT: D 271 ARG cc_start: 0.8617 (mmp80) cc_final: 0.8338 (mmp80) REVERT: E 138 PHE cc_start: 0.7810 (m-10) cc_final: 0.7603 (m-80) outliers start: 11 outliers final: 7 residues processed: 201 average time/residue: 0.4127 time to fit residues: 133.5275 Evaluate side-chains 187 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain F residue 448 HIS Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 597 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 144 optimal weight: 0.0000 chunk 279 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 323 optimal weight: 6.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 406 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN C 353 GLN C 406 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN D 356 ASN D 377 ASN D 406 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 356 ASN F 406 GLN F 452 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.100090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.064229 restraints weight = 75877.475| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.70 r_work: 0.2885 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29478 Z= 0.166 Angle : 0.581 10.686 40057 Z= 0.299 Chirality : 0.042 0.182 4433 Planarity : 0.004 0.049 5082 Dihedral : 14.152 123.224 4380 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 2.66 % Allowed : 25.15 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3555 helix: 1.48 (0.13), residues: 1717 sheet: -0.32 (0.26), residues: 454 loop : -1.10 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 157 HIS 0.005 0.001 HIS D 50 PHE 0.029 0.001 PHE D 74 TYR 0.012 0.001 TYR D 431 ARG 0.008 0.001 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 1284) hydrogen bonds : angle 4.84544 ( 3699) covalent geometry : bond 0.00385 (29466) covalent geometry : angle 0.58086 (40057) Misc. bond : bond 0.00247 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 185 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 495 MET cc_start: 0.8269 (ptt) cc_final: 0.7873 (ptt) REVERT: D 151 MET cc_start: 0.7229 (pmm) cc_final: 0.6660 (pmm) REVERT: D 153 TYR cc_start: 0.7846 (t80) cc_final: 0.7368 (t80) REVERT: D 173 CYS cc_start: 0.3970 (OUTLIER) cc_final: 0.3457 (m) REVERT: E 56 ARG cc_start: 0.8603 (tpt-90) cc_final: 0.8352 (tpt-90) REVERT: E 314 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8686 (tp40) REVERT: E 337 ASN cc_start: 0.9394 (OUTLIER) cc_final: 0.9033 (m110) REVERT: F 89 MET cc_start: 0.8332 (mpp) cc_final: 0.8074 (mpp) outliers start: 82 outliers final: 29 residues processed: 258 average time/residue: 0.4172 time to fit residues: 175.9817 Evaluate side-chains 211 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 339 TYR Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 448 HIS Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 574 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 257 optimal weight: 0.4980 chunk 292 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 350 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 231 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 341 optimal weight: 0.8980 chunk 238 optimal weight: 7.9990 chunk 41 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 HIS D 83 GLN D 120 GLN D 353 GLN D 356 ASN D 406 GLN E 46 ASN E 337 ASN ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.101298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065617 restraints weight = 75563.225| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.70 r_work: 0.2925 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29478 Z= 0.111 Angle : 0.542 10.500 40057 Z= 0.277 Chirality : 0.041 0.175 4433 Planarity : 0.004 0.050 5082 Dihedral : 13.695 122.291 4368 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.15 % Favored : 94.66 % Rotamer: Outliers : 2.24 % Allowed : 25.48 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.36 (0.15), residues: 3555 helix: 1.50 (0.13), residues: 1711 sheet: -0.36 (0.26), residues: 454 loop : -1.15 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 157 HIS 0.008 0.001 HIS D 50 PHE 0.030 0.001 PHE D 74 TYR 0.012 0.001 TYR A 430 ARG 0.008 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1284) hydrogen bonds : angle 4.53470 ( 3699) covalent geometry : bond 0.00249 (29466) covalent geometry : angle 0.54231 (40057) Misc. bond : bond 0.00137 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 194 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7526 (tmm160) cc_final: 0.6882 (tmm160) REVERT: A 404 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8879 (mtp) REVERT: A 523 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9011 (mt-10) REVERT: B 265 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8677 (pm20) REVERT: C 495 MET cc_start: 0.8050 (ptt) cc_final: 0.7704 (ptt) REVERT: D 151 MET cc_start: 0.7505 (pmm) cc_final: 0.7100 (pmm) REVERT: D 153 TYR cc_start: 0.7812 (t80) cc_final: 0.7456 (t80) REVERT: D 161 ARG cc_start: 0.7999 (ptp90) cc_final: 0.7568 (ptp90) REVERT: E 80 MET cc_start: 0.8824 (mmm) cc_final: 0.8493 (mmt) REVERT: E 91 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8404 (p0) REVERT: E 296 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9051 (mm) REVERT: E 314 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8596 (tp40) REVERT: E 337 ASN cc_start: 0.9392 (OUTLIER) cc_final: 0.9121 (m110) REVERT: F 89 MET cc_start: 0.8455 (mpp) cc_final: 0.8189 (mpp) REVERT: F 154 GLU cc_start: 0.8273 (pt0) cc_final: 0.8041 (pt0) outliers start: 69 outliers final: 35 residues processed: 252 average time/residue: 0.3905 time to fit residues: 160.7336 Evaluate side-chains 221 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 448 HIS Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 574 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 80 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.100744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.065050 restraints weight = 76175.113| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.72 r_work: 0.2910 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29478 Z= 0.125 Angle : 0.538 10.680 40057 Z= 0.273 Chirality : 0.041 0.175 4433 Planarity : 0.004 0.047 5082 Dihedral : 13.557 121.102 4368 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.29 % Favored : 94.51 % Rotamer: Outliers : 2.73 % Allowed : 25.41 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 3555 helix: 1.57 (0.13), residues: 1702 sheet: -0.41 (0.26), residues: 440 loop : -1.16 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 157 HIS 0.007 0.001 HIS D 50 PHE 0.032 0.001 PHE D 74 TYR 0.013 0.001 TYR F 77 ARG 0.009 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 1284) hydrogen bonds : angle 4.41755 ( 3699) covalent geometry : bond 0.00289 (29466) covalent geometry : angle 0.53789 (40057) Misc. bond : bond 0.00144 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 191 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7987 (m-30) cc_final: 0.7460 (t0) REVERT: A 72 ARG cc_start: 0.7569 (tmm160) cc_final: 0.6887 (tmm160) REVERT: A 188 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: A 404 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8898 (mtp) REVERT: A 509 MET cc_start: 0.6326 (tpt) cc_final: 0.6073 (mmm) REVERT: B 138 PHE cc_start: 0.9242 (m-80) cc_final: 0.8849 (m-80) REVERT: C 495 MET cc_start: 0.8171 (ptt) cc_final: 0.7865 (ptt) REVERT: D 147 HIS cc_start: 0.7269 (m90) cc_final: 0.6915 (m-70) REVERT: D 151 MET cc_start: 0.7577 (pmm) cc_final: 0.7223 (pmm) REVERT: D 161 ARG cc_start: 0.8013 (ptp90) cc_final: 0.7569 (ptp90) REVERT: D 173 CYS cc_start: 0.4144 (OUTLIER) cc_final: 0.3749 (m) REVERT: E 91 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8434 (p0) REVERT: E 296 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9046 (mm) REVERT: E 314 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8669 (tp40) REVERT: E 598 ILE cc_start: -0.1694 (OUTLIER) cc_final: -0.2075 (tt) REVERT: F 5 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5635 (mm) REVERT: F 80 MET cc_start: 0.8736 (mmm) cc_final: 0.8460 (mmm) REVERT: F 154 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: F 188 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6168 (tt0) REVERT: F 384 ARG cc_start: 0.3493 (OUTLIER) cc_final: 0.2977 (mtm180) outliers start: 84 outliers final: 49 residues processed: 261 average time/residue: 0.3804 time to fit residues: 165.0236 Evaluate side-chains 243 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 183 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 594 CYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 448 HIS Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 485 THR Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 574 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 40 optimal weight: 2.9990 chunk 352 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 212 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 302 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 254 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 HIS ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.101226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.064914 restraints weight = 75506.352| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.87 r_work: 0.2882 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29478 Z= 0.114 Angle : 0.531 10.638 40057 Z= 0.270 Chirality : 0.041 0.175 4433 Planarity : 0.004 0.050 5082 Dihedral : 13.344 110.219 4368 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.20 % Favored : 94.60 % Rotamer: Outliers : 3.09 % Allowed : 25.22 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.40 (0.15), residues: 3555 helix: 1.57 (0.13), residues: 1708 sheet: -0.31 (0.26), residues: 436 loop : -1.18 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 157 HIS 0.006 0.001 HIS D 50 PHE 0.037 0.001 PHE D 74 TYR 0.012 0.001 TYR F 77 ARG 0.010 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 1284) hydrogen bonds : angle 4.30824 ( 3699) covalent geometry : bond 0.00261 (29466) covalent geometry : angle 0.53061 (40057) Misc. bond : bond 0.00129 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 193 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8111 (m-30) cc_final: 0.7569 (t0) REVERT: A 188 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7414 (tp30) REVERT: A 404 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8808 (mtp) REVERT: A 448 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.6509 (m-70) REVERT: A 509 MET cc_start: 0.6276 (tpt) cc_final: 0.6064 (mmm) REVERT: A 523 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9008 (mt-10) REVERT: B 138 PHE cc_start: 0.9239 (m-80) cc_final: 0.8862 (m-80) REVERT: B 188 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.4769 (tm-30) REVERT: B 214 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8232 (mp) REVERT: C 92 ASN cc_start: 0.8559 (p0) cc_final: 0.8335 (p0) REVERT: C 495 MET cc_start: 0.7982 (ptt) cc_final: 0.7696 (ptt) REVERT: D 147 HIS cc_start: 0.7236 (m90) cc_final: 0.6910 (m-70) REVERT: D 153 TYR cc_start: 0.7698 (t80) cc_final: 0.7235 (t80) REVERT: D 161 ARG cc_start: 0.7966 (ptp90) cc_final: 0.7624 (ptp90) REVERT: D 173 CYS cc_start: 0.4202 (OUTLIER) cc_final: 0.3788 (m) REVERT: E 80 MET cc_start: 0.8843 (mmm) cc_final: 0.8504 (mmt) REVERT: E 91 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8512 (p0) REVERT: E 296 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8980 (mm) REVERT: E 314 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8502 (tp40) REVERT: E 598 ILE cc_start: -0.1883 (OUTLIER) cc_final: -0.2239 (tt) REVERT: F 5 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5657 (mm) REVERT: F 80 MET cc_start: 0.8719 (mmm) cc_final: 0.8421 (mmm) REVERT: F 154 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: F 384 ARG cc_start: 0.3421 (OUTLIER) cc_final: 0.2910 (mtm180) outliers start: 95 outliers final: 47 residues processed: 276 average time/residue: 0.3708 time to fit residues: 168.8543 Evaluate side-chains 237 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 177 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 448 HIS Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 598 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 0 optimal weight: 10.0000 chunk 297 optimal weight: 0.0770 chunk 275 optimal weight: 1.9990 chunk 243 optimal weight: 0.0470 chunk 160 optimal weight: 8.9990 chunk 227 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 352 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.101366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066629 restraints weight = 76351.297| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.59 r_work: 0.2976 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29478 Z= 0.103 Angle : 0.535 10.531 40057 Z= 0.270 Chirality : 0.041 0.174 4433 Planarity : 0.004 0.051 5082 Dihedral : 13.169 108.520 4368 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.95 % Favored : 94.85 % Rotamer: Outliers : 2.50 % Allowed : 25.67 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.41 (0.15), residues: 3555 helix: 1.62 (0.13), residues: 1693 sheet: -0.49 (0.26), residues: 461 loop : -1.14 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 157 HIS 0.009 0.001 HIS E 11 PHE 0.035 0.001 PHE D 74 TYR 0.021 0.001 TYR A 430 ARG 0.011 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 1284) hydrogen bonds : angle 4.22772 ( 3699) covalent geometry : bond 0.00233 (29466) covalent geometry : angle 0.53495 (40057) Misc. bond : bond 0.00121 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 191 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7940 (m-30) cc_final: 0.7377 (t0) REVERT: A 72 ARG cc_start: 0.7578 (ttp80) cc_final: 0.6892 (tmm160) REVERT: A 188 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: A 509 MET cc_start: 0.6541 (tpt) cc_final: 0.6337 (mmm) REVERT: A 523 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9029 (mt-10) REVERT: B 138 PHE cc_start: 0.9221 (m-80) cc_final: 0.8808 (m-80) REVERT: B 162 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8187 (tpp80) REVERT: B 188 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.4959 (tm-30) REVERT: B 204 ASN cc_start: 0.7187 (m-40) cc_final: 0.6724 (m-40) REVERT: C 78 GLN cc_start: 0.8044 (tp40) cc_final: 0.7622 (tp-100) REVERT: C 92 ASN cc_start: 0.8503 (p0) cc_final: 0.8232 (p0) REVERT: C 495 MET cc_start: 0.8087 (ptt) cc_final: 0.7811 (ptt) REVERT: D 147 HIS cc_start: 0.7327 (m90) cc_final: 0.6939 (m-70) REVERT: D 151 MET cc_start: 0.7931 (ppp) cc_final: 0.7617 (ppp) REVERT: D 153 TYR cc_start: 0.7801 (t80) cc_final: 0.7443 (t80) REVERT: D 161 ARG cc_start: 0.8057 (ptp90) cc_final: 0.7701 (ptp90) REVERT: D 173 CYS cc_start: 0.4251 (OUTLIER) cc_final: 0.3863 (m) REVERT: D 196 MET cc_start: 0.8686 (tpp) cc_final: 0.8359 (tpt) REVERT: E 91 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8369 (p0) REVERT: E 296 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9083 (mm) REVERT: E 314 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8670 (tp40) REVERT: E 598 ILE cc_start: -0.1564 (OUTLIER) cc_final: -0.1961 (tt) REVERT: F 5 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5883 (mm) REVERT: F 80 MET cc_start: 0.8857 (mmm) cc_final: 0.8554 (mmm) REVERT: F 154 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: F 204 ASN cc_start: 0.5848 (p0) cc_final: 0.5485 (p0) REVERT: F 384 ARG cc_start: 0.3565 (OUTLIER) cc_final: 0.3067 (mtm180) REVERT: F 397 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9066 (mp) outliers start: 77 outliers final: 46 residues processed: 257 average time/residue: 0.3948 time to fit residues: 166.8330 Evaluate side-chains 241 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain E residue 11 HIS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 157 TRP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 448 HIS Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 574 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 292 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 305 optimal weight: 0.8980 chunk 344 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 260 optimal weight: 0.7980 chunk 214 optimal weight: 0.6980 chunk 268 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 HIS ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** 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 = 0.3881 r_free = 0.3881 target = 0.100932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.065474 restraints weight = 77400.858| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.68 r_work: 0.2958 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29478 Z= 0.118 Angle : 0.534 10.690 40057 Z= 0.269 Chirality : 0.041 0.176 4433 Planarity : 0.004 0.050 5082 Dihedral : 13.114 107.859 4368 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.01 % Favored : 94.80 % Rotamer: Outliers : 2.60 % Allowed : 25.45 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.44 (0.15), residues: 3555 helix: 1.65 (0.13), residues: 1696 sheet: -0.50 (0.26), residues: 461 loop : -1.11 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 157 HIS 0.008 0.001 HIS C 433 PHE 0.036 0.001 PHE D 74 TYR 0.013 0.001 TYR F 77 ARG 0.010 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 1284) hydrogen bonds : angle 4.23546 ( 3699) covalent geometry : bond 0.00274 (29466) covalent geometry : angle 0.53363 (40057) Misc. bond : bond 0.00121 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 183 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7933 (m-30) cc_final: 0.7372 (t0) REVERT: A 72 ARG cc_start: 0.7553 (ttp80) cc_final: 0.6855 (tmm160) REVERT: A 188 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7441 (tp30) REVERT: A 404 MET cc_start: 0.9122 (mtp) cc_final: 0.8917 (mtp) REVERT: A 523 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9029 (mt-10) REVERT: B 138 PHE cc_start: 0.9216 (m-80) cc_final: 0.8892 (m-80) REVERT: B 162 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.8208 (tpp80) REVERT: B 188 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.4904 (tm-30) REVERT: B 204 ASN cc_start: 0.7211 (m-40) cc_final: 0.6748 (m-40) REVERT: B 509 MET cc_start: 0.8814 (ttm) cc_final: 0.8550 (ttm) REVERT: C 78 GLN cc_start: 0.8059 (tp40) cc_final: 0.7755 (tp-100) REVERT: C 80 MET cc_start: 0.7920 (tpp) cc_final: 0.7301 (mpp) REVERT: C 92 ASN cc_start: 0.8490 (p0) cc_final: 0.8193 (p0) REVERT: C 495 MET cc_start: 0.8158 (ptt) cc_final: 0.7884 (ptt) REVERT: D 147 HIS cc_start: 0.7330 (m90) cc_final: 0.6930 (m-70) REVERT: D 151 MET cc_start: 0.7987 (ppp) cc_final: 0.7628 (ppp) REVERT: D 161 ARG cc_start: 0.8073 (ptp90) cc_final: 0.7616 (ptp90) REVERT: D 173 CYS cc_start: 0.4169 (OUTLIER) cc_final: 0.3767 (m) REVERT: E 14 MET cc_start: 0.5778 (ptt) cc_final: 0.5022 (ptm) REVERT: E 80 MET cc_start: 0.8786 (mmm) cc_final: 0.8471 (mmt) REVERT: E 91 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8376 (p0) REVERT: E 296 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9080 (mm) REVERT: E 314 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8716 (tp40) REVERT: E 458 ILE cc_start: 0.9526 (OUTLIER) cc_final: 0.9290 (mp) REVERT: E 598 ILE cc_start: -0.1607 (OUTLIER) cc_final: -0.2089 (tt) REVERT: F 5 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5971 (mm) REVERT: F 80 MET cc_start: 0.8912 (mmm) cc_final: 0.8611 (mmm) REVERT: F 154 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: F 384 ARG cc_start: 0.3609 (OUTLIER) cc_final: 0.3088 (mtm180) REVERT: F 397 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9071 (mp) outliers start: 80 outliers final: 52 residues processed: 254 average time/residue: 0.3939 time to fit residues: 165.6982 Evaluate side-chains 241 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 594 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain E residue 11 HIS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 157 TRP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 458 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 448 HIS Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 598 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 53 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 262 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 208 optimal weight: 0.2980 chunk 345 optimal weight: 4.9990 chunk 350 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 HIS C 500 ASN D 236 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.097913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.062229 restraints weight = 76640.209| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.70 r_work: 0.2841 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29478 Z= 0.219 Angle : 0.599 11.403 40057 Z= 0.304 Chirality : 0.043 0.179 4433 Planarity : 0.004 0.049 5082 Dihedral : 13.312 108.594 4368 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.71 % Favored : 94.09 % Rotamer: Outliers : 2.92 % Allowed : 25.12 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3555 helix: 1.56 (0.13), residues: 1711 sheet: -0.57 (0.25), residues: 479 loop : -1.12 (0.18), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 157 HIS 0.042 0.001 HIS E 11 PHE 0.035 0.001 PHE D 74 TYR 0.015 0.001 TYR E 431 ARG 0.015 0.001 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 1284) hydrogen bonds : angle 4.45124 ( 3699) covalent geometry : bond 0.00512 (29466) covalent geometry : angle 0.59923 (40057) Misc. bond : bond 0.00143 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 183 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8051 (m-30) cc_final: 0.7426 (t0) REVERT: A 72 ARG cc_start: 0.7549 (ttp80) cc_final: 0.6880 (tmm160) REVERT: A 188 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: A 509 MET cc_start: 0.6504 (mmm) cc_final: 0.6280 (mmm) REVERT: B 138 PHE cc_start: 0.9293 (m-80) cc_final: 0.9007 (m-80) REVERT: B 188 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.4929 (tm-30) REVERT: B 196 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8674 (tpp) REVERT: B 204 ASN cc_start: 0.7409 (m-40) cc_final: 0.6934 (m-40) REVERT: B 214 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8368 (mp) REVERT: B 509 MET cc_start: 0.8914 (ttm) cc_final: 0.8592 (ttm) REVERT: C 78 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7658 (tp-100) REVERT: C 92 ASN cc_start: 0.8616 (p0) cc_final: 0.8353 (p0) REVERT: C 290 LEU cc_start: 0.8436 (tp) cc_final: 0.8219 (tt) REVERT: D 161 ARG cc_start: 0.8079 (ptp90) cc_final: 0.7730 (ptp90) REVERT: D 173 CYS cc_start: 0.4266 (OUTLIER) cc_final: 0.3874 (m) REVERT: E 56 ARG cc_start: 0.8747 (tpt-90) cc_final: 0.8385 (tpt-90) REVERT: E 91 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8510 (p0) REVERT: E 138 PHE cc_start: 0.7655 (m-10) cc_final: 0.7411 (m-10) REVERT: E 296 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9055 (mm) REVERT: E 314 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8639 (tp40) REVERT: E 458 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9209 (mp) REVERT: E 598 ILE cc_start: -0.1921 (OUTLIER) cc_final: -0.2501 (tt) REVERT: F 5 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6057 (mm) REVERT: F 29 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6620 (pp20) REVERT: F 80 MET cc_start: 0.8947 (mmm) cc_final: 0.8689 (mmm) REVERT: F 188 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6124 (tt0) outliers start: 90 outliers final: 59 residues processed: 260 average time/residue: 0.4056 time to fit residues: 174.1817 Evaluate side-chains 246 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 174 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 594 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 157 TRP Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 448 HIS Chi-restraints excluded: chain E residue 458 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 448 HIS Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 574 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 123 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 64 optimal weight: 0.0470 chunk 298 optimal weight: 9.9990 chunk 253 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 221 optimal weight: 0.0980 chunk 4 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 ASN D 531 ASN E 177 ASN ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.100050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.064665 restraints weight = 75852.598| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.71 r_work: 0.2902 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 29478 Z= 0.108 Angle : 0.571 12.620 40057 Z= 0.283 Chirality : 0.041 0.179 4433 Planarity : 0.004 0.056 5082 Dihedral : 13.039 109.039 4368 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.98 % Favored : 94.82 % Rotamer: Outliers : 2.34 % Allowed : 25.87 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.42 (0.15), residues: 3555 helix: 1.60 (0.13), residues: 1702 sheet: -0.46 (0.25), residues: 475 loop : -1.12 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 157 HIS 0.012 0.001 HIS C 433 PHE 0.033 0.001 PHE D 74 TYR 0.014 0.001 TYR F 77 ARG 0.013 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 1284) hydrogen bonds : angle 4.26862 ( 3699) covalent geometry : bond 0.00245 (29466) covalent geometry : angle 0.57115 (40057) Misc. bond : bond 0.00121 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 179 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8044 (m-30) cc_final: 0.7434 (t0) REVERT: A 72 ARG cc_start: 0.7502 (ttp80) cc_final: 0.6842 (tmm160) REVERT: A 188 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7408 (tp30) REVERT: A 436 LYS cc_start: 0.8676 (tmtt) cc_final: 0.8466 (tptt) REVERT: A 509 MET cc_start: 0.6547 (mmm) cc_final: 0.6292 (mmm) REVERT: B 138 PHE cc_start: 0.9272 (m-80) cc_final: 0.8980 (m-80) REVERT: B 188 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.4867 (tm-30) REVERT: B 204 ASN cc_start: 0.7192 (m-40) cc_final: 0.6787 (m-40) REVERT: B 214 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8181 (mp) REVERT: B 509 MET cc_start: 0.8796 (ttm) cc_final: 0.8528 (ttm) REVERT: C 78 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7683 (tp-100) REVERT: C 92 ASN cc_start: 0.8633 (p0) cc_final: 0.8374 (p0) REVERT: C 290 LEU cc_start: 0.8375 (tp) cc_final: 0.8153 (tt) REVERT: D 161 ARG cc_start: 0.8012 (ptp90) cc_final: 0.7661 (ptp90) REVERT: D 173 CYS cc_start: 0.4309 (OUTLIER) cc_final: 0.3918 (m) REVERT: D 432 GLU cc_start: 0.6955 (pm20) cc_final: 0.6359 (pp20) REVERT: D 459 TRP cc_start: 0.8809 (t60) cc_final: 0.8576 (t-100) REVERT: E 80 MET cc_start: 0.8782 (mmm) cc_final: 0.8496 (mmt) REVERT: E 138 PHE cc_start: 0.7629 (m-10) cc_final: 0.7359 (m-10) REVERT: E 296 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9025 (mm) REVERT: E 314 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8615 (tp40) REVERT: E 458 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9179 (mp) REVERT: E 598 ILE cc_start: -0.1888 (OUTLIER) cc_final: -0.2459 (tt) REVERT: F 80 MET cc_start: 0.8951 (mmm) cc_final: 0.8697 (mmm) REVERT: F 154 GLU cc_start: 0.8695 (pm20) cc_final: 0.8387 (pm20) REVERT: F 188 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6513 (tt0) REVERT: F 384 ARG cc_start: 0.3419 (OUTLIER) cc_final: 0.2944 (mtm180) outliers start: 72 outliers final: 51 residues processed: 242 average time/residue: 0.4178 time to fit residues: 169.6804 Evaluate side-chains 237 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 594 CYS Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain E residue 157 TRP Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 458 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 448 HIS Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 574 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 316 optimal weight: 0.1980 chunk 350 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 23 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 chunk 171 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** 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 = 0.3895 r_free = 0.3895 target = 0.101874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.066446 restraints weight = 79628.907| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.73 r_work: 0.2985 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29478 Z= 0.106 Angle : 0.563 13.047 40057 Z= 0.279 Chirality : 0.041 0.180 4433 Planarity : 0.004 0.061 5082 Dihedral : 12.867 109.221 4368 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.09 % Favored : 94.71 % Rotamer: Outliers : 2.08 % Allowed : 26.06 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3555 helix: 1.65 (0.13), residues: 1690 sheet: -0.49 (0.25), residues: 479 loop : -1.08 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 157 HIS 0.012 0.001 HIS C 433 PHE 0.028 0.001 PHE D 74 TYR 0.014 0.001 TYR F 77 ARG 0.015 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 1284) hydrogen bonds : angle 4.18505 ( 3699) covalent geometry : bond 0.00242 (29466) covalent geometry : angle 0.56294 (40057) Misc. bond : bond 0.00116 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 3.244 Fit side-chains revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7970 (m-30) cc_final: 0.7401 (t0) REVERT: A 72 ARG cc_start: 0.7502 (ttp80) cc_final: 0.6818 (tmm160) REVERT: A 188 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: A 509 MET cc_start: 0.6674 (mmm) cc_final: 0.6407 (mmm) REVERT: A 523 GLU cc_start: 0.9257 (mm-30) cc_final: 0.9028 (mt-10) REVERT: B 138 PHE cc_start: 0.9265 (m-80) cc_final: 0.8961 (m-80) REVERT: B 188 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.4927 (tm-30) REVERT: B 204 ASN cc_start: 0.7159 (m-40) cc_final: 0.6687 (m-40) REVERT: B 214 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8173 (mp) REVERT: C 78 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7677 (tp-100) REVERT: C 92 ASN cc_start: 0.8577 (p0) cc_final: 0.8317 (p0) REVERT: D 154 GLU cc_start: 0.7388 (tp30) cc_final: 0.7076 (tt0) REVERT: D 161 ARG cc_start: 0.8145 (ptp90) cc_final: 0.7816 (ptp90) REVERT: D 432 GLU cc_start: 0.6802 (pm20) cc_final: 0.6270 (pp20) REVERT: D 459 TRP cc_start: 0.8954 (t60) cc_final: 0.8740 (t-100) REVERT: E 80 MET cc_start: 0.8779 (mmm) cc_final: 0.8480 (mmt) REVERT: E 138 PHE cc_start: 0.7629 (m-10) cc_final: 0.7354 (m-10) REVERT: E 296 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9091 (mm) REVERT: E 314 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8673 (tp40) REVERT: E 458 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9308 (mp) REVERT: E 598 ILE cc_start: -0.1444 (OUTLIER) cc_final: -0.2037 (tt) REVERT: F 29 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6763 (pp20) REVERT: F 80 MET cc_start: 0.9067 (mmm) cc_final: 0.8778 (mmm) REVERT: F 154 GLU cc_start: 0.8667 (pm20) cc_final: 0.8412 (pm20) REVERT: F 384 ARG cc_start: 0.3713 (OUTLIER) cc_final: 0.3181 (mtm180) REVERT: F 483 MET cc_start: 0.9326 (ttp) cc_final: 0.9058 (ttm) outliers start: 64 outliers final: 49 residues processed: 239 average time/residue: 0.3956 time to fit residues: 156.1948 Evaluate side-chains 234 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 594 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain E residue 157 TRP Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 458 ILE Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 448 HIS Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 574 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 326 optimal weight: 5.9990 chunk 144 optimal weight: 0.3980 chunk 243 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 111 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 216 optimal weight: 4.9990 chunk 184 optimal weight: 0.0970 chunk 354 optimal weight: 0.9980 chunk 352 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN E 177 ASN ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** 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 = 0.3897 r_free = 0.3897 target = 0.101999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066650 restraints weight = 79514.643| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.68 r_work: 0.2991 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29478 Z= 0.106 Angle : 0.560 12.830 40057 Z= 0.277 Chirality : 0.041 0.179 4433 Planarity : 0.004 0.061 5082 Dihedral : 12.755 109.506 4368 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.01 % Favored : 94.80 % Rotamer: Outliers : 2.08 % Allowed : 26.19 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.49 (0.15), residues: 3555 helix: 1.67 (0.13), residues: 1690 sheet: -0.47 (0.25), residues: 479 loop : -1.07 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 157 HIS 0.009 0.001 HIS A 243 PHE 0.026 0.001 PHE D 74 TYR 0.014 0.001 TYR F 77 ARG 0.014 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 1284) hydrogen bonds : angle 4.14333 ( 3699) covalent geometry : bond 0.00242 (29466) covalent geometry : angle 0.55976 (40057) Misc. bond : bond 0.00114 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15237.47 seconds wall clock time: 265 minutes 17.86 seconds (15917.86 seconds total)