Starting phenix.real_space_refine on Sat Sep 28 04:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/09_2024/3j5p_5778.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/09_2024/3j5p_5778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.275 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/09_2024/3j5p_5778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/09_2024/3j5p_5778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/09_2024/3j5p_5778.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/09_2024/3j5p_5778.cif" } resolution = 3.275 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 12108 2.51 5 N 3060 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 247 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18636 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4606 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 8, 'truncation_to_alanine': 13} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 562} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4606 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 8, 'truncation_to_alanine': 13} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 562} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4606 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 8, 'truncation_to_alanine': 13} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 562} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4606 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 8, 'truncation_to_alanine': 13} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 562} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 11.12, per 1000 atoms: 0.60 Number of scatterers: 18636 At special positions: 0 Unit cell: (149.519, 149.519, 119.129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3368 8.00 N 3060 7.00 C 12108 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=0, symmetry=0 Time building additional restraints: 5.54 Conformation dependent library (CDL) restraints added in 3.0 seconds 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 70.4% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'B' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 170 through 183 removed outlier: 4.314A pdb=" N ALA B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.844A pdb=" N ASP B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.545A pdb=" N TRP B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 455 removed outlier: 3.533A pdb=" N PHE B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 498 removed outlier: 3.519A pdb=" N TYR B 487 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 533 removed outlier: 3.967A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.938A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.812A pdb=" N ARG B 575 " --> pdb=" O LYS B 571 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 643 removed outlier: 4.193A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.900A pdb=" N PHE B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 711 removed outlier: 3.510A pdb=" N ALA B 690 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 170 through 183 removed outlier: 4.314A pdb=" N ALA A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 361 through 366 removed outlier: 4.244A pdb=" N LEU A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.844A pdb=" N ASP A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.545A pdb=" N TRP A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 455 removed outlier: 3.533A pdb=" N PHE A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 498 removed outlier: 3.519A pdb=" N TYR A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 533 removed outlier: 3.967A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.937A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.812A pdb=" N ARG A 575 " --> pdb=" O LYS A 571 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 643 removed outlier: 4.193A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.899A pdb=" N PHE A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 711 removed outlier: 3.510A pdb=" N ALA A 690 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.656A pdb=" N LEU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 170 through 183 removed outlier: 4.313A pdb=" N ALA C 174 " --> pdb=" O ASN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 361 through 366 removed outlier: 4.244A pdb=" N LEU C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.845A pdb=" N ASP C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.544A pdb=" N TRP C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 455 removed outlier: 3.533A pdb=" N PHE C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 498 removed outlier: 3.519A pdb=" N TYR C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 533 removed outlier: 3.968A pdb=" N ILE C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.938A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.812A pdb=" N ARG C 575 " --> pdb=" O LYS C 571 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 643 removed outlier: 4.194A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.900A pdb=" N PHE C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 711 removed outlier: 3.510A pdb=" N ALA C 690 " --> pdb=" O VAL C 686 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 170 through 183 removed outlier: 4.314A pdb=" N ALA D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 191 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 361 through 366 removed outlier: 4.244A pdb=" N LEU D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 removed outlier: 3.844A pdb=" N ASP D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.544A pdb=" N TRP D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 455 removed outlier: 3.533A pdb=" N PHE D 436 " --> pdb=" O ARG D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 498 removed outlier: 3.519A pdb=" N TYR D 487 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE D 488 " --> pdb=" O GLY D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 533 removed outlier: 3.968A pdb=" N ILE D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.937A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.812A pdb=" N ARG D 575 " --> pdb=" O LYS D 571 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 643 removed outlier: 4.193A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.900A pdb=" N PHE D 659 " --> pdb=" O PHE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 711 removed outlier: 3.510A pdb=" N ALA D 690 " --> pdb=" O VAL D 686 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'B' and resid 368 through 369 Processing sheet with id=B, first strand: chain 'A' and resid 368 through 369 Processing sheet with id=C, first strand: chain 'C' and resid 368 through 369 Processing sheet with id=D, first strand: chain 'D' and resid 368 through 369 1136 hydrogen bonds defined for protein. 3300 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: 6.72 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 5937 1.37 - 1.53: 10379 1.53 - 1.69: 2548 1.69 - 1.85: 144 1.85 - 2.01: 24 Bond restraints: 19032 Sorted by residual: bond pdb=" C LEU D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.331 1.406 -0.075 8.70e-03 1.32e+04 7.42e+01 bond pdb=" C LEU C 460 " pdb=" N PRO C 461 " ideal model delta sigma weight residual 1.331 1.406 -0.075 8.70e-03 1.32e+04 7.37e+01 bond pdb=" C LEU A 460 " pdb=" N PRO A 461 " ideal model delta sigma weight residual 1.331 1.406 -0.075 8.70e-03 1.32e+04 7.37e+01 bond pdb=" C LEU B 460 " pdb=" N PRO B 461 " ideal model delta sigma weight residual 1.331 1.406 -0.074 8.70e-03 1.32e+04 7.29e+01 bond pdb=" CG MET B 162 " pdb=" SD MET B 162 " ideal model delta sigma weight residual 1.803 2.008 -0.205 2.50e-02 1.60e+03 6.74e+01 ... (remaining 19027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 25051 3.85 - 7.70: 641 7.70 - 11.55: 36 11.55 - 15.40: 28 15.40 - 19.25: 4 Bond angle restraints: 25760 Sorted by residual: angle pdb=" N ASN B 408 " pdb=" CA ASN B 408 " pdb=" C ASN B 408 " ideal model delta sigma weight residual 112.41 126.27 -13.86 1.30e+00 5.92e-01 1.14e+02 angle pdb=" N ASN A 408 " pdb=" CA ASN A 408 " pdb=" C ASN A 408 " ideal model delta sigma weight residual 112.41 126.24 -13.83 1.30e+00 5.92e-01 1.13e+02 angle pdb=" N ASN C 408 " pdb=" CA ASN C 408 " pdb=" C ASN C 408 " ideal model delta sigma weight residual 112.41 126.24 -13.83 1.30e+00 5.92e-01 1.13e+02 angle pdb=" N ASN D 408 " pdb=" CA ASN D 408 " pdb=" C ASN D 408 " ideal model delta sigma weight residual 112.41 126.23 -13.82 1.30e+00 5.92e-01 1.13e+02 angle pdb=" N ASP C 383 " pdb=" CA ASP C 383 " pdb=" C ASP C 383 " ideal model delta sigma weight residual 111.07 121.77 -10.70 1.07e+00 8.73e-01 1.00e+02 ... (remaining 25755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 9732 24.93 - 49.85: 1244 49.85 - 74.78: 236 74.78 - 99.71: 24 99.71 - 124.63: 8 Dihedral angle restraints: 11244 sinusoidal: 4336 harmonic: 6908 Sorted by residual: dihedral pdb=" CA GLY C 244 " pdb=" C GLY C 244 " pdb=" N PHE C 245 " pdb=" CA PHE C 245 " ideal model delta harmonic sigma weight residual 180.00 55.37 124.63 0 5.00e+00 4.00e-02 6.21e+02 dihedral pdb=" CA GLY D 244 " pdb=" C GLY D 244 " pdb=" N PHE D 245 " pdb=" CA PHE D 245 " ideal model delta harmonic sigma weight residual 180.00 55.37 124.63 0 5.00e+00 4.00e-02 6.21e+02 dihedral pdb=" CA GLY A 244 " pdb=" C GLY A 244 " pdb=" N PHE A 245 " pdb=" CA PHE A 245 " ideal model delta harmonic sigma weight residual 180.00 55.40 124.60 0 5.00e+00 4.00e-02 6.21e+02 ... (remaining 11241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2383 0.105 - 0.211: 445 0.211 - 0.316: 96 0.316 - 0.421: 8 0.421 - 0.527: 8 Chirality restraints: 2940 Sorted by residual: chirality pdb=" CA GLU A 249 " pdb=" N GLU A 249 " pdb=" C GLU A 249 " pdb=" CB GLU A 249 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" CA GLU C 249 " pdb=" N GLU C 249 " pdb=" C GLU C 249 " pdb=" CB GLU C 249 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" CA GLU D 249 " pdb=" N GLU D 249 " pdb=" C GLU D 249 " pdb=" CB GLU D 249 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.86e+00 ... (remaining 2937 not shown) Planarity restraints: 3232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK B 753 " -0.023 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C UNK B 753 " 0.082 2.00e-02 2.50e+03 pdb=" O UNK B 753 " -0.032 2.00e-02 2.50e+03 pdb=" N UNK B 754 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK D 753 " 0.023 2.00e-02 2.50e+03 4.72e-02 2.22e+01 pdb=" C UNK D 753 " -0.081 2.00e-02 2.50e+03 pdb=" O UNK D 753 " 0.031 2.00e-02 2.50e+03 pdb=" N UNK D 754 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK A 753 " -0.023 2.00e-02 2.50e+03 4.71e-02 2.21e+01 pdb=" C UNK A 753 " 0.081 2.00e-02 2.50e+03 pdb=" O UNK A 753 " -0.031 2.00e-02 2.50e+03 pdb=" N UNK A 754 " -0.027 2.00e-02 2.50e+03 ... (remaining 3229 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.90: 63 1.90 - 2.65: 775 2.65 - 3.40: 28302 3.40 - 4.15: 45223 4.15 - 4.90: 81021 Nonbonded interactions: 155384 Sorted by model distance: nonbonded pdb=" OE2 GLU D 326 " pdb=" NH2 ARG D 355 " model vdw 1.156 3.120 nonbonded pdb=" OE2 GLU A 326 " pdb=" NH2 ARG A 355 " model vdw 1.156 3.120 nonbonded pdb=" OE2 GLU B 326 " pdb=" NH2 ARG B 355 " model vdw 1.156 3.120 nonbonded pdb=" OE2 GLU C 326 " pdb=" NH2 ARG C 355 " model vdw 1.157 3.120 nonbonded pdb=" CG1 VAL B 686 " pdb=" OE2 GLU A 684 " model vdw 1.355 3.460 ... (remaining 155379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 44.230 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:4.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.205 19032 Z= 0.714 Angle : 1.527 19.247 25760 Z= 1.045 Chirality : 0.091 0.527 2940 Planarity : 0.007 0.096 3232 Dihedral : 21.588 124.634 6812 Min Nonbonded Distance : 1.156 Molprobity Statistics. All-atom Clashscore : 79.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 27.79 % Allowed : 16.84 % Favored : 55.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 1.06 % 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 (0.16), residues: 2308 helix: 0.48 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -1.51 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 697 HIS 0.007 0.002 HIS B 289 PHE 0.024 0.001 PHE C 235 TYR 0.022 0.002 TYR A 309 ARG 0.004 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 548 poor density : 494 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 GLU cc_start: 0.1866 (OUTLIER) cc_final: 0.1429 (pt0) REVERT: B 187 LYS cc_start: -0.2051 (OUTLIER) cc_final: -0.2875 (mtpp) REVERT: B 669 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6642 (pp) REVERT: A 147 GLU cc_start: 0.1886 (OUTLIER) cc_final: 0.1420 (pt0) REVERT: A 187 LYS cc_start: -0.2484 (OUTLIER) cc_final: -0.3345 (mtpp) REVERT: A 597 THR cc_start: 0.7126 (p) cc_final: 0.6887 (p) REVERT: A 669 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6673 (pp) REVERT: C 147 GLU cc_start: 0.1888 (OUTLIER) cc_final: 0.1461 (pt0) REVERT: C 187 LYS cc_start: -0.2531 (OUTLIER) cc_final: -0.3312 (mtpp) REVERT: C 669 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6618 (pp) REVERT: D 147 GLU cc_start: 0.2002 (OUTLIER) cc_final: 0.1668 (pt0) REVERT: D 187 LYS cc_start: -0.2098 (OUTLIER) cc_final: -0.2855 (mtpp) REVERT: D 304 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5400 (p90) REVERT: D 597 THR cc_start: 0.7084 (p) cc_final: 0.6836 (p) REVERT: D 669 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6695 (pp) outliers start: 548 outliers final: 164 residues processed: 853 average time/residue: 0.3187 time to fit residues: 398.9422 Evaluate side-chains 522 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 345 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 631 TYR Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 LYS Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 717 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 631 TYR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 710 LYS Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 426 TRP Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 579 ARG Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 631 TYR Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 717 ARG Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 245 PHE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 362 CYS Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 369 PHE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 631 TYR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 717 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9990 chunk 178 optimal weight: 40.0000 chunk 99 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 214 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: B 164 ASN B 289 HIS B 410 HIS B 419 ASN B 498 GLN A 289 HIS A 419 ASN A 498 GLN C 289 HIS C 410 HIS C 419 ASN C 498 GLN D 289 HIS D 410 HIS D 419 ASN D 498 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19032 Z= 0.294 Angle : 0.962 13.781 25760 Z= 0.484 Chirality : 0.047 0.166 2940 Planarity : 0.006 0.076 3232 Dihedral : 13.617 71.776 2960 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.47 % Favored : 96.19 % Rotamer: Outliers : 10.04 % Allowed : 21.65 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.89 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2308 helix: 0.76 (0.12), residues: 1504 sheet: None (None), residues: 0 loop : -1.32 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 697 HIS 0.003 0.001 HIS C 289 PHE 0.026 0.002 PHE A 245 TYR 0.018 0.002 TYR B 584 ARG 0.009 0.001 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 368 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 187 LYS cc_start: -0.2038 (OUTLIER) cc_final: -0.2385 (mmtt) REVERT: B 664 LEU cc_start: 0.7634 (mp) cc_final: 0.7365 (mp) REVERT: A 664 LEU cc_start: 0.7625 (mp) cc_final: 0.7360 (mp) REVERT: C 187 LYS cc_start: -0.2122 (OUTLIER) cc_final: -0.2368 (mmtt) REVERT: C 664 LEU cc_start: 0.7648 (mp) cc_final: 0.7393 (mp) REVERT: D 187 LYS cc_start: -0.2238 (OUTLIER) cc_final: -0.2690 (mmtt) outliers start: 198 outliers final: 105 residues processed: 507 average time/residue: 0.3066 time to fit residues: 234.4131 Evaluate side-chains 374 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 266 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 426 TRP Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain D residue 706 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.2980 chunk 66 optimal weight: 8.9990 chunk 178 optimal weight: 50.0000 chunk 145 optimal weight: 7.9990 chunk 59 optimal weight: 50.0000 chunk 214 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 172 optimal weight: 0.3980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN A 498 GLN A 676 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN D 164 ASN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5731 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19032 Z= 0.239 Angle : 0.842 13.223 25760 Z= 0.424 Chirality : 0.044 0.220 2940 Planarity : 0.006 0.071 3232 Dihedral : 10.058 58.883 2719 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.03 % Favored : 95.80 % Rotamer: Outliers : 6.19 % Allowed : 23.48 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: 0.33 (0.17), residues: 2308 helix: 0.93 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -1.13 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 372 HIS 0.004 0.001 HIS A 289 PHE 0.028 0.001 PHE C 304 TYR 0.014 0.002 TYR C 584 ARG 0.011 0.001 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 333 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: -0.1694 (tpt) cc_final: -0.2636 (ttt) REVERT: B 664 LEU cc_start: 0.7631 (mp) cc_final: 0.7416 (mp) REVERT: A 162 MET cc_start: -0.1310 (tpt) cc_final: -0.2376 (ttt) REVERT: A 186 LEU cc_start: -0.1605 (OUTLIER) cc_final: -0.1808 (pt) REVERT: C 162 MET cc_start: -0.1271 (tpt) cc_final: -0.2340 (ttt) REVERT: C 630 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7246 (tt) REVERT: D 162 MET cc_start: -0.1691 (tpt) cc_final: -0.2574 (ttt) REVERT: D 630 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7255 (tt) outliers start: 122 outliers final: 84 residues processed: 420 average time/residue: 0.2857 time to fit residues: 184.8049 Evaluate side-chains 353 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 266 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 0.0030 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 0.0770 chunk 228 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 overall best weight: 0.6150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19032 Z= 0.205 Angle : 0.782 13.301 25760 Z= 0.393 Chirality : 0.043 0.203 2940 Planarity : 0.006 0.101 3232 Dihedral : 8.385 56.226 2664 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.48 % Allowed : 21.86 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2308 helix: 0.97 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.10 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 272 HIS 0.004 0.001 HIS A 289 PHE 0.021 0.001 PHE D 304 TYR 0.028 0.002 TYR C 401 ARG 0.011 0.001 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 319 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: -0.1557 (tpt) cc_final: -0.2615 (ttt) REVERT: A 186 LEU cc_start: -0.2082 (OUTLIER) cc_final: -0.2335 (pt) REVERT: D 162 MET cc_start: -0.1572 (tpt) cc_final: -0.2568 (ttt) outliers start: 108 outliers final: 75 residues processed: 392 average time/residue: 0.2687 time to fit residues: 167.9902 Evaluate side-chains 341 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 265 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 634 CYS Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 662 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 20.0000 chunk 129 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 116 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 498 GLN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 19032 Z= 0.241 Angle : 0.760 13.333 25760 Z= 0.380 Chirality : 0.040 0.143 2940 Planarity : 0.006 0.088 3232 Dihedral : 7.964 55.162 2650 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.27 % Allowed : 23.38 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.57 (0.17), residues: 2308 helix: 1.07 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.93 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 426 HIS 0.003 0.001 HIS C 289 PHE 0.025 0.001 PHE C 304 TYR 0.014 0.002 TYR D 444 ARG 0.004 0.001 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 280 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.0637 (OUTLIER) cc_final: -0.0915 (pt) REVERT: B 162 MET cc_start: -0.1564 (tpt) cc_final: -0.2725 (ttt) REVERT: A 162 MET cc_start: -0.1746 (tpt) cc_final: -0.2506 (ttt) REVERT: C 162 MET cc_start: -0.1667 (tpt) cc_final: -0.2550 (ttt) REVERT: D 136 LEU cc_start: -0.0511 (OUTLIER) cc_final: -0.0789 (pt) REVERT: D 162 MET cc_start: -0.1496 (tpt) cc_final: -0.2594 (ttt) outliers start: 104 outliers final: 85 residues processed: 350 average time/residue: 0.2609 time to fit residues: 145.1827 Evaluate side-chains 332 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 245 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 228 optimal weight: 0.0270 chunk 189 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN A 498 GLN C 498 GLN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5725 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19032 Z= 0.197 Angle : 0.771 14.120 25760 Z= 0.376 Chirality : 0.041 0.206 2940 Planarity : 0.005 0.075 3232 Dihedral : 7.689 53.849 2648 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.83 % Allowed : 23.33 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.63 (0.17), residues: 2308 helix: 1.09 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.83 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 372 HIS 0.002 0.000 HIS A 289 PHE 0.015 0.001 PHE D 304 TYR 0.027 0.002 TYR D 401 ARG 0.004 0.001 ARG D 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 285 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.0563 (OUTLIER) cc_final: -0.0808 (pt) REVERT: B 162 MET cc_start: -0.1540 (tpt) cc_final: -0.2611 (ttt) REVERT: A 136 LEU cc_start: -0.0683 (OUTLIER) cc_final: -0.0966 (pt) REVERT: A 162 MET cc_start: -0.1676 (tpt) cc_final: -0.2515 (ttt) REVERT: A 186 LEU cc_start: -0.2115 (OUTLIER) cc_final: -0.2341 (pt) REVERT: C 136 LEU cc_start: -0.0776 (OUTLIER) cc_final: -0.1021 (pt) REVERT: C 162 MET cc_start: -0.1668 (tpt) cc_final: -0.2506 (ttt) REVERT: D 136 LEU cc_start: -0.0644 (OUTLIER) cc_final: -0.0934 (pt) REVERT: D 162 MET cc_start: -0.1483 (tpt) cc_final: -0.2574 (ttt) REVERT: D 572 MET cc_start: 0.6527 (tpp) cc_final: 0.6264 (tpp) outliers start: 115 outliers final: 77 residues processed: 362 average time/residue: 0.2562 time to fit residues: 148.6725 Evaluate side-chains 332 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 250 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 5.9990 chunk 25 optimal weight: 0.0670 chunk 130 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19032 Z= 0.222 Angle : 0.764 12.861 25760 Z= 0.379 Chirality : 0.042 0.215 2940 Planarity : 0.005 0.071 3232 Dihedral : 7.551 51.950 2648 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.32 % Allowed : 23.58 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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 (0.17), residues: 2308 helix: 0.99 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.98 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 426 HIS 0.002 0.001 HIS A 320 PHE 0.041 0.001 PHE C 304 TYR 0.017 0.002 TYR C 401 ARG 0.005 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 258 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.0603 (OUTLIER) cc_final: -0.0837 (pt) REVERT: B 162 MET cc_start: -0.1469 (tpt) cc_final: -0.2556 (ttt) REVERT: A 136 LEU cc_start: -0.0791 (OUTLIER) cc_final: -0.1012 (pt) REVERT: A 162 MET cc_start: -0.1600 (tpt) cc_final: -0.2503 (ttt) REVERT: A 186 LEU cc_start: -0.2114 (OUTLIER) cc_final: -0.2334 (pt) REVERT: C 136 LEU cc_start: -0.0824 (OUTLIER) cc_final: -0.1061 (pt) REVERT: C 162 MET cc_start: -0.1604 (tpt) cc_final: -0.2440 (ttt) REVERT: C 308 MET cc_start: 0.4389 (OUTLIER) cc_final: 0.3899 (mtt) REVERT: D 136 LEU cc_start: -0.0671 (OUTLIER) cc_final: -0.0951 (pt) REVERT: D 162 MET cc_start: -0.1515 (tpt) cc_final: -0.2623 (ttt) outliers start: 105 outliers final: 83 residues processed: 326 average time/residue: 0.2783 time to fit residues: 146.2327 Evaluate side-chains 338 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 249 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 686 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 178 optimal weight: 0.0060 chunk 206 optimal weight: 0.0570 overall best weight: 0.9918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5742 moved from start: 0.6765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19032 Z= 0.207 Angle : 0.766 13.109 25760 Z= 0.376 Chirality : 0.041 0.200 2940 Planarity : 0.005 0.069 3232 Dihedral : 7.225 49.965 2644 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.92 % Allowed : 24.95 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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 (0.17), residues: 2308 helix: 0.97 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -1.02 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 372 HIS 0.002 0.000 HIS A 289 PHE 0.036 0.001 PHE C 304 TYR 0.027 0.002 TYR D 401 ARG 0.004 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 266 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.0630 (OUTLIER) cc_final: -0.0876 (pt) REVERT: B 162 MET cc_start: -0.1929 (tpt) cc_final: -0.3080 (ttt) REVERT: A 136 LEU cc_start: -0.0818 (OUTLIER) cc_final: -0.1046 (pt) REVERT: A 162 MET cc_start: -0.1656 (tpt) cc_final: -0.2451 (ttt) REVERT: A 186 LEU cc_start: -0.2131 (OUTLIER) cc_final: -0.2344 (pt) REVERT: C 136 LEU cc_start: -0.0848 (OUTLIER) cc_final: -0.1098 (pt) REVERT: C 162 MET cc_start: -0.1572 (tpt) cc_final: -0.2394 (ttt) REVERT: D 136 LEU cc_start: -0.0696 (OUTLIER) cc_final: -0.0995 (pt) REVERT: D 162 MET cc_start: -0.1433 (tpt) cc_final: -0.2490 (ttt) outliers start: 97 outliers final: 77 residues processed: 327 average time/residue: 0.2762 time to fit residues: 144.9174 Evaluate side-chains 330 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 248 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 655 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 706 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 5.9990 chunk 198 optimal weight: 0.0970 chunk 211 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 0.0370 chunk 65 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 200 optimal weight: 0.0570 chunk 139 optimal weight: 0.1980 chunk 224 optimal weight: 3.9990 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 498 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19032 Z= 0.201 Angle : 0.790 12.637 25760 Z= 0.386 Chirality : 0.041 0.206 2940 Planarity : 0.005 0.068 3232 Dihedral : 7.020 51.582 2640 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.41 % Allowed : 26.06 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.54 (0.17), residues: 2308 helix: 1.04 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -0.89 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 372 HIS 0.005 0.001 HIS C 410 PHE 0.035 0.001 PHE C 304 TYR 0.019 0.001 TYR A 584 ARG 0.006 0.000 ARG C 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 288 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.0669 (OUTLIER) cc_final: -0.0913 (pt) REVERT: B 162 MET cc_start: -0.1956 (tpt) cc_final: -0.3050 (ttt) REVERT: A 136 LEU cc_start: -0.0836 (OUTLIER) cc_final: -0.1066 (pt) REVERT: A 162 MET cc_start: -0.1675 (tpt) cc_final: -0.2419 (ttt) REVERT: A 308 MET cc_start: 0.4621 (ptp) cc_final: 0.4394 (mtt) REVERT: C 136 LEU cc_start: -0.0882 (OUTLIER) cc_final: -0.1122 (pt) REVERT: C 162 MET cc_start: -0.1607 (tpt) cc_final: -0.2386 (ttt) REVERT: D 136 LEU cc_start: -0.0716 (OUTLIER) cc_final: -0.1008 (pt) REVERT: D 162 MET cc_start: -0.1950 (tpt) cc_final: -0.2886 (ttt) outliers start: 87 outliers final: 69 residues processed: 345 average time/residue: 0.2600 time to fit residues: 142.5047 Evaluate side-chains 331 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 258 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 655 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 235 optimal weight: 20.0000 chunk 216 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 148 optimal weight: 0.0070 chunk 199 optimal weight: 0.9980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN A 551 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.7047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19032 Z= 0.218 Angle : 0.796 12.622 25760 Z= 0.393 Chirality : 0.042 0.208 2940 Planarity : 0.005 0.065 3232 Dihedral : 6.907 50.696 2640 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.60 % Allowed : 27.03 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.54 (0.17), residues: 2308 helix: 1.09 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -0.97 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 372 HIS 0.003 0.001 HIS B 410 PHE 0.037 0.001 PHE C 304 TYR 0.025 0.001 TYR C 401 ARG 0.004 0.000 ARG D 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 264 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.0681 (OUTLIER) cc_final: -0.0922 (pt) REVERT: B 162 MET cc_start: -0.1924 (tpt) cc_final: -0.3036 (ttt) REVERT: A 136 LEU cc_start: -0.0857 (OUTLIER) cc_final: -0.1079 (pt) REVERT: A 162 MET cc_start: -0.1647 (tpt) cc_final: -0.2406 (ttt) REVERT: C 136 LEU cc_start: -0.0886 (OUTLIER) cc_final: -0.1135 (pt) REVERT: C 162 MET cc_start: -0.1625 (tpt) cc_final: -0.2382 (ttt) REVERT: D 136 LEU cc_start: -0.0760 (OUTLIER) cc_final: -0.1051 (pt) REVERT: D 162 MET cc_start: -0.1427 (tpt) cc_final: -0.2454 (ttt) outliers start: 71 outliers final: 61 residues processed: 306 average time/residue: 0.2602 time to fit residues: 126.6758 Evaluate side-chains 326 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 261 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 187 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.125458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.072578 restraints weight = 47780.379| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 6.35 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19032 Z= 0.210 Angle : 0.803 15.008 25760 Z= 0.391 Chirality : 0.042 0.210 2940 Planarity : 0.005 0.065 3232 Dihedral : 6.795 51.091 2640 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.55 % Allowed : 27.64 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.31 (0.17), residues: 2308 helix: 0.97 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -1.27 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 372 HIS 0.002 0.000 HIS B 410 PHE 0.022 0.001 PHE D 304 TYR 0.020 0.001 TYR A 584 ARG 0.004 0.001 ARG B 499 =============================================================================== Job complete usr+sys time: 4186.67 seconds wall clock time: 76 minutes 15.61 seconds (4575.61 seconds total)