Starting phenix.real_space_refine on Mon Jun 16 04:16:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j5p_5778/06_2025/3j5p_5778.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j5p_5778/06_2025/3j5p_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/cci-nas-00/data/ceres_data/3j5p_5778/06_2025/3j5p_5778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j5p_5778/06_2025/3j5p_5778.map" model { file = "/net/cci-nas-00/data/ceres_data/3j5p_5778/06_2025/3j5p_5778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j5p_5778/06_2025/3j5p_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.68, per 1000 atoms: 0.57 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: 4.89 Conformation dependent library (CDL) restraints added in 2.4 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: 1.84 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: 5.40 Time building geometry restraints manager: 5.72 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 41.870 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.900 ------------------------------------------------------------------------------- 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= 0.674 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 Details of bonding type rmsd hydrogen bonds : bond 0.24935 ( 1136) hydrogen bonds : angle 8.75201 ( 3300) covalent geometry : bond 0.01089 (19032) covalent geometry : angle 1.52696 (25760) *********************** 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 to be fit. rotamer outliers: 548 poor density : 494 time to evaluate : 2.120 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: 0.3148 time to fit residues: 395.2878 Evaluate side-chains 522 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 345 time to evaluate : 2.197 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.126530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.073791 restraints weight = 47639.381| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 5.99 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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= 0.210 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 Details of bonding type rmsd hydrogen bonds : bond 0.06003 ( 1136) hydrogen bonds : angle 5.52851 ( 3300) covalent geometry : bond 0.00449 (19032) covalent geometry : angle 0.96184 (25760) *********************** 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 to be fit. rotamer outliers: 198 poor density : 368 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 187 LYS cc_start: -0.0859 (OUTLIER) cc_final: -0.1207 (mmtt) REVERT: B 408 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8222 (t0) REVERT: B 473 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9143 (m-10) REVERT: B 552 MET cc_start: 0.9159 (tpp) cc_final: 0.8915 (mtp) REVERT: B 598 LEU cc_start: 0.9539 (tp) cc_final: 0.9313 (tp) REVERT: B 636 GLU cc_start: 0.8921 (tp30) cc_final: 0.8641 (mm-30) REVERT: B 639 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8870 (mtmm) REVERT: A 187 LYS cc_start: -0.0556 (OUTLIER) cc_final: -0.0909 (mmtt) REVERT: A 310 ASN cc_start: 0.8937 (t0) cc_final: 0.8462 (t0) REVERT: A 408 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8195 (t0) REVERT: A 473 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.9160 (m-10) REVERT: A 541 MET cc_start: 0.8904 (ttm) cc_final: 0.8656 (ttp) REVERT: A 552 MET cc_start: 0.9141 (tpp) cc_final: 0.8903 (mtp) REVERT: A 636 GLU cc_start: 0.8921 (tp30) cc_final: 0.8637 (mm-30) REVERT: A 639 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8865 (mtmm) REVERT: A 676 ASN cc_start: 0.9188 (m-40) cc_final: 0.8959 (m110) REVERT: A 677 MET cc_start: 0.9272 (tpp) cc_final: 0.8896 (mmm) REVERT: C 187 LYS cc_start: -0.0784 (OUTLIER) cc_final: -0.1114 (mmtt) REVERT: C 310 ASN cc_start: 0.8959 (t0) cc_final: 0.8482 (t0) REVERT: C 408 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7607 (t0) REVERT: C 412 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8135 (mpp) REVERT: C 473 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.9168 (m-10) REVERT: C 579 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8654 (ttm-80) REVERT: C 598 LEU cc_start: 0.9555 (tp) cc_final: 0.9338 (tp) REVERT: C 636 GLU cc_start: 0.8918 (tp30) cc_final: 0.8664 (mm-30) REVERT: C 639 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8883 (mtmm) REVERT: C 676 ASN cc_start: 0.9176 (m-40) cc_final: 0.8959 (m110) REVERT: D 187 LYS cc_start: -0.0960 (OUTLIER) cc_final: -0.1287 (mmtt) REVERT: D 372 TRP cc_start: 0.7151 (m100) cc_final: 0.6598 (m100) REVERT: D 408 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7606 (t0) REVERT: D 473 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9197 (m-10) REVERT: D 541 MET cc_start: 0.8933 (ttm) cc_final: 0.8673 (ttp) REVERT: D 552 MET cc_start: 0.9158 (tpp) cc_final: 0.8929 (mtp) REVERT: D 578 CYS cc_start: 0.8951 (t) cc_final: 0.8749 (p) REVERT: D 636 GLU cc_start: 0.8931 (tp30) cc_final: 0.8672 (mm-30) REVERT: D 639 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8880 (mtmm) REVERT: D 676 ASN cc_start: 0.9176 (m-40) cc_final: 0.8952 (m110) outliers start: 198 outliers final: 105 residues processed: 507 average time/residue: 0.3001 time to fit residues: 230.4997 Evaluate side-chains 402 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 279 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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 408 ASN 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 473 PHE 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 639 LYS 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 187 LYS 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 408 ASN 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 473 PHE 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 639 LYS 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 408 ASN Chi-restraints excluded: chain C residue 412 MET 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 473 PHE 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 579 ARG 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 639 LYS 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 408 ASN 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 473 PHE 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 639 LYS 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 72 optimal weight: 0.0770 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- 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 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.125298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.070256 restraints weight = 52119.424| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 7.13 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19032 Z= 0.204 Angle : 0.836 13.590 25760 Z= 0.424 Chirality : 0.044 0.209 2940 Planarity : 0.006 0.069 3232 Dihedral : 10.421 59.409 2738 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 7.00 % Allowed : 23.43 % Favored : 69.57 % 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: 0.49 (0.17), residues: 2308 helix: 1.11 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.16 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 372 HIS 0.003 0.001 HIS C 320 PHE 0.025 0.002 PHE D 304 TYR 0.019 0.002 TYR D 198 ARG 0.011 0.001 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.05176 ( 1136) hydrogen bonds : angle 5.21471 ( 3300) covalent geometry : bond 0.00436 (19032) covalent geometry : angle 0.83648 (25760) *********************** 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 449 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 311 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.2512 (tpt) cc_final: 0.1617 (ttt) REVERT: B 293 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8486 (tm-30) REVERT: B 473 PHE cc_start: 0.9538 (OUTLIER) cc_final: 0.9335 (m-10) REVERT: B 523 MET cc_start: 0.9251 (tpp) cc_final: 0.8948 (mmm) REVERT: B 547 MET cc_start: 0.9093 (tpp) cc_final: 0.8872 (tpp) REVERT: B 552 MET cc_start: 0.9190 (tpp) cc_final: 0.8972 (mtp) REVERT: B 572 MET cc_start: 0.9011 (tpp) cc_final: 0.8540 (tpp) REVERT: B 577 LEU cc_start: 0.9314 (mt) cc_final: 0.9106 (mt) REVERT: B 584 TYR cc_start: 0.8722 (t80) cc_final: 0.8419 (t80) REVERT: B 639 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9009 (mtmm) REVERT: B 676 ASN cc_start: 0.9236 (m-40) cc_final: 0.8999 (m110) REVERT: B 677 MET cc_start: 0.8914 (mmm) cc_final: 0.8699 (mmm) REVERT: A 162 MET cc_start: 0.2762 (tpt) cc_final: 0.1803 (ttt) REVERT: A 293 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8482 (tm-30) REVERT: A 473 PHE cc_start: 0.9531 (OUTLIER) cc_final: 0.9330 (m-10) REVERT: A 523 MET cc_start: 0.9231 (tpp) cc_final: 0.8934 (mmm) REVERT: A 547 MET cc_start: 0.9099 (tpp) cc_final: 0.8889 (tpp) REVERT: A 552 MET cc_start: 0.9196 (tpp) cc_final: 0.8979 (mtp) REVERT: A 639 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.9001 (mtmm) REVERT: A 701 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8257 (ttm-80) REVERT: C 162 MET cc_start: 0.2742 (tpt) cc_final: 0.1767 (ttt) REVERT: C 523 MET cc_start: 0.9251 (tpp) cc_final: 0.8970 (mmm) REVERT: C 579 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8618 (mtp-110) REVERT: C 630 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8616 (tt) REVERT: C 639 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9026 (mtmm) REVERT: C 677 MET cc_start: 0.8985 (mmm) cc_final: 0.8748 (mmm) REVERT: D 162 MET cc_start: 0.2550 (tpt) cc_final: 0.1669 (ttt) REVERT: D 408 ASN cc_start: 0.8373 (t0) cc_final: 0.7958 (t0) REVERT: D 412 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7784 (mpp) REVERT: D 473 PHE cc_start: 0.9537 (OUTLIER) cc_final: 0.9331 (m-10) REVERT: D 523 MET cc_start: 0.9256 (tpp) cc_final: 0.8965 (mmm) REVERT: D 547 MET cc_start: 0.9094 (tpp) cc_final: 0.8885 (tpp) REVERT: D 552 MET cc_start: 0.9184 (tpp) cc_final: 0.8877 (ttm) REVERT: D 571 LYS cc_start: 0.9415 (mmtp) cc_final: 0.9098 (mmmt) REVERT: D 577 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9124 (mt) REVERT: D 630 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8667 (tt) REVERT: D 639 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9025 (mtmm) REVERT: D 701 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8259 (ttm-80) outliers start: 138 outliers final: 98 residues processed: 410 average time/residue: 0.3013 time to fit residues: 189.9592 Evaluate side-chains 360 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 248 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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 323 LEU 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 412 MET 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 473 PHE 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 639 LYS 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 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 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 396 LEU 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 442 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 473 PHE 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 639 LYS Chi-restraints excluded: chain A residue 647 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 685 THR Chi-restraints excluded: chain A residue 701 ARG 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 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 481 SER Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 579 ARG 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 639 LYS Chi-restraints excluded: chain C residue 647 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 685 THR Chi-restraints excluded: chain C residue 701 ARG 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 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 473 PHE 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 577 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 639 LYS Chi-restraints excluded: chain D residue 647 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 701 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 27 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 153 optimal weight: 0.0040 chunk 171 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 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 = 0.3973 r_free = 0.3973 target = 0.123761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070848 restraints weight = 52656.860| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 7.26 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19032 Z= 0.157 Angle : 0.766 13.739 25760 Z= 0.387 Chirality : 0.042 0.204 2940 Planarity : 0.005 0.104 3232 Dihedral : 9.003 56.711 2682 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 6.64 % Allowed : 22.16 % Favored : 71.20 % 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: 0.52 (0.17), residues: 2308 helix: 1.09 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -1.06 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 372 HIS 0.004 0.001 HIS D 289 PHE 0.019 0.001 PHE D 304 TYR 0.022 0.002 TYR B 401 ARG 0.005 0.001 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 1136) hydrogen bonds : angle 5.04271 ( 3300) covalent geometry : bond 0.00342 (19032) covalent geometry : angle 0.76560 (25760) *********************** 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 422 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 291 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.2641 (tpt) cc_final: 0.1779 (ttt) REVERT: B 293 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8435 (tm-30) REVERT: B 473 PHE cc_start: 0.9497 (OUTLIER) cc_final: 0.9282 (m-10) REVERT: B 571 LYS cc_start: 0.9470 (mmmt) cc_final: 0.8960 (mmmm) REVERT: B 639 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8927 (mtmm) REVERT: B 677 MET cc_start: 0.9099 (mmm) cc_final: 0.8874 (mmm) REVERT: A 162 MET cc_start: 0.2716 (tpt) cc_final: 0.1704 (ttm) REVERT: A 293 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 473 PHE cc_start: 0.9511 (OUTLIER) cc_final: 0.9297 (m-10) REVERT: A 676 ASN cc_start: 0.9289 (m-40) cc_final: 0.9081 (m110) REVERT: C 162 MET cc_start: 0.2856 (tpt) cc_final: 0.1827 (ttm) REVERT: C 523 MET cc_start: 0.9167 (tpp) cc_final: 0.8787 (tpt) REVERT: C 541 MET cc_start: 0.9150 (ttm) cc_final: 0.8881 (ttp) REVERT: C 571 LYS cc_start: 0.9505 (mmtp) cc_final: 0.9101 (mmmm) REVERT: C 579 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8624 (mtp-110) REVERT: C 630 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8509 (tt) REVERT: C 676 ASN cc_start: 0.9176 (m-40) cc_final: 0.8942 (m110) REVERT: C 677 MET cc_start: 0.9140 (mmm) cc_final: 0.8742 (mmm) REVERT: D 162 MET cc_start: 0.2569 (tpt) cc_final: 0.1681 (ttt) REVERT: D 412 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7771 (mpp) REVERT: D 473 PHE cc_start: 0.9500 (OUTLIER) cc_final: 0.9266 (m-10) REVERT: D 571 LYS cc_start: 0.9550 (mmtp) cc_final: 0.9253 (mmmt) REVERT: D 682 MET cc_start: 0.8604 (mtp) cc_final: 0.8376 (mtp) outliers start: 131 outliers final: 85 residues processed: 381 average time/residue: 0.2870 time to fit residues: 169.6606 Evaluate side-chains 342 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 250 time to evaluate : 2.000 ------------------------------------------------------------------------------- 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 323 LEU 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 412 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 481 SER 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 639 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 673 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 287 VAL 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 396 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 473 PHE 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 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 706 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 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 521 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 579 ARG 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 662 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 701 ARG 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 384 LEU Chi-restraints excluded: chain D residue 387 ILE 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 473 PHE 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 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 635 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 701 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 175 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 178 optimal weight: 0.0570 chunk 198 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.122713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068737 restraints weight = 48242.464| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 6.29 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 19032 Z= 0.161 Angle : 0.738 13.530 25760 Z= 0.373 Chirality : 0.041 0.206 2940 Planarity : 0.005 0.087 3232 Dihedral : 8.483 55.629 2669 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 6.14 % Allowed : 22.16 % Favored : 71.70 % 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: 0.60 (0.17), residues: 2308 helix: 1.16 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.04 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 372 HIS 0.003 0.001 HIS A 320 PHE 0.027 0.001 PHE C 304 TYR 0.025 0.002 TYR D 401 ARG 0.005 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 1136) hydrogen bonds : angle 4.96318 ( 3300) covalent geometry : bond 0.00361 (19032) covalent geometry : angle 0.73819 (25760) *********************** 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 405 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 284 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.2027 (tpt) cc_final: 0.1160 (ttt) REVERT: B 293 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8314 (tm-30) REVERT: B 473 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.9162 (m-10) REVERT: B 523 MET cc_start: 0.8942 (tpp) cc_final: 0.8613 (tpt) REVERT: A 162 MET cc_start: 0.2079 (tpt) cc_final: 0.1066 (ttm) REVERT: A 293 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8324 (tm-30) REVERT: A 473 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.9155 (m-10) REVERT: A 523 MET cc_start: 0.8916 (tpp) cc_final: 0.8594 (tpt) REVERT: A 571 LYS cc_start: 0.9498 (mmtp) cc_final: 0.8921 (mmmm) REVERT: A 682 MET cc_start: 0.8810 (mtp) cc_final: 0.8551 (mtp) REVERT: C 162 MET cc_start: 0.2054 (tpt) cc_final: 0.1044 (ttm) REVERT: C 523 MET cc_start: 0.8874 (tpp) cc_final: 0.8552 (tpt) REVERT: C 579 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8696 (mtp-110) REVERT: C 630 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8525 (tt) REVERT: D 162 MET cc_start: 0.1939 (tpt) cc_final: 0.1057 (ttt) REVERT: D 473 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9216 (m-10) REVERT: D 523 MET cc_start: 0.8954 (tpp) cc_final: 0.8633 (tpt) REVERT: D 571 LYS cc_start: 0.9471 (mmtp) cc_final: 0.8951 (mmmm) REVERT: D 582 PHE cc_start: 0.8952 (t80) cc_final: 0.8627 (t80) REVERT: D 630 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8475 (tt) REVERT: D 682 MET cc_start: 0.8784 (mtp) cc_final: 0.8465 (mtp) outliers start: 121 outliers final: 88 residues processed: 361 average time/residue: 0.2741 time to fit residues: 155.8457 Evaluate side-chains 348 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 254 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 287 VAL Chi-restraints excluded: chain B residue 346 ILE 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 473 PHE Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 GLU 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 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 358 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 396 LEU 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 473 PHE 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 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 138 ARG Chi-restraints excluded: chain C residue 157 CYS 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 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 481 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 579 ARG 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 674 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 310 ASN 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 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 473 PHE 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 630 LEU 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 674 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 88 optimal weight: 0.0670 chunk 204 optimal weight: 0.0870 chunk 123 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 overall best weight: 0.9900 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.123567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071202 restraints weight = 47067.278| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 6.34 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19032 Z= 0.147 Angle : 0.757 13.673 25760 Z= 0.374 Chirality : 0.041 0.205 2940 Planarity : 0.005 0.076 3232 Dihedral : 8.058 56.551 2660 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.88 % Allowed : 23.68 % Favored : 70.44 % 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: 0.67 (0.17), residues: 2308 helix: 1.19 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -0.95 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 372 HIS 0.002 0.000 HIS D 289 PHE 0.023 0.001 PHE C 304 TYR 0.023 0.002 TYR B 401 ARG 0.006 0.000 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 1136) hydrogen bonds : angle 4.88150 ( 3300) covalent geometry : bond 0.00325 (19032) covalent geometry : angle 0.75686 (25760) *********************** 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 412 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 296 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.1808 (tpt) cc_final: 0.0971 (ttt) REVERT: B 293 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 473 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.9150 (m-10) REVERT: B 523 MET cc_start: 0.8889 (tpp) cc_final: 0.8620 (tpt) REVERT: B 571 LYS cc_start: 0.9405 (mmmt) cc_final: 0.8952 (mmmm) REVERT: B 644 MET cc_start: 0.8937 (mmp) cc_final: 0.8705 (mmt) REVERT: A 162 MET cc_start: 0.1968 (tpt) cc_final: 0.0973 (ttm) REVERT: A 293 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 413 LEU cc_start: 0.9286 (mt) cc_final: 0.9041 (mt) REVERT: A 473 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.9169 (m-10) REVERT: A 523 MET cc_start: 0.8874 (tpp) cc_final: 0.8606 (tpt) REVERT: C 162 MET cc_start: 0.1942 (tpt) cc_final: 0.0954 (ttm) REVERT: C 311 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8819 (mm-30) REVERT: C 523 MET cc_start: 0.8911 (tpp) cc_final: 0.8652 (tpt) REVERT: C 579 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8671 (mtp-110) REVERT: C 630 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8514 (tt) REVERT: D 162 MET cc_start: 0.1790 (tpt) cc_final: 0.0920 (ttt) REVERT: D 473 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.9126 (m-10) REVERT: D 523 MET cc_start: 0.8909 (tpp) cc_final: 0.8636 (tpt) REVERT: D 571 LYS cc_start: 0.9474 (mmtp) cc_final: 0.8954 (mmmm) REVERT: D 630 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8553 (tt) outliers start: 116 outliers final: 75 residues processed: 378 average time/residue: 0.2756 time to fit residues: 165.0777 Evaluate side-chains 341 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 260 time to evaluate : 2.093 ------------------------------------------------------------------------------- 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 287 VAL Chi-restraints excluded: chain B residue 346 ILE 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 473 PHE Chi-restraints excluded: chain B residue 481 SER 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 662 LEU Chi-restraints excluded: chain B residue 685 THR 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 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE 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 396 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 473 PHE 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 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 C residue 131 SER 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 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 579 ARG 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 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 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 473 PHE 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 570 GLU 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 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 662 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 59 optimal weight: 50.0000 chunk 76 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 164 optimal weight: 0.5980 chunk 184 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 227 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.122435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069649 restraints weight = 47716.167| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 6.23 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19032 Z= 0.165 Angle : 0.753 13.497 25760 Z= 0.375 Chirality : 0.042 0.195 2940 Planarity : 0.005 0.068 3232 Dihedral : 7.918 58.120 2658 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 6.03 % Allowed : 24.59 % 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: 0.63 (0.17), residues: 2308 helix: 1.13 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.89 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 372 HIS 0.004 0.001 HIS C 410 PHE 0.025 0.001 PHE C 304 TYR 0.023 0.002 TYR D 401 ARG 0.004 0.000 ARG C 420 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 1136) hydrogen bonds : angle 4.90530 ( 3300) covalent geometry : bond 0.00371 (19032) covalent geometry : angle 0.75287 (25760) *********************** 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 390 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 271 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: 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: 0.1389 (tpt) cc_final: 0.0554 (ttt) REVERT: B 293 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8479 (tm-30) REVERT: B 473 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.9139 (m-10) REVERT: B 523 MET cc_start: 0.9063 (tpp) cc_final: 0.8766 (tpt) REVERT: B 571 LYS cc_start: 0.9363 (mmmt) cc_final: 0.8952 (mmmm) REVERT: A 162 MET cc_start: 0.0224 (tpt) cc_final: -0.0635 (ttt) REVERT: A 293 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8469 (tm-30) REVERT: A 413 LEU cc_start: 0.9222 (mt) cc_final: 0.8968 (mt) REVERT: A 523 MET cc_start: 0.9042 (tpp) cc_final: 0.8752 (tpt) REVERT: C 162 MET cc_start: 0.0397 (tpt) cc_final: -0.0462 (ttt) REVERT: C 311 GLU cc_start: 0.9232 (mm-30) cc_final: 0.9006 (mm-30) REVERT: C 523 MET cc_start: 0.9044 (tpp) cc_final: 0.8779 (tpt) REVERT: C 579 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8718 (mtp-110) REVERT: C 630 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8513 (tt) REVERT: C 701 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8877 (ptm160) REVERT: D 162 MET cc_start: 0.1445 (tpt) cc_final: 0.0561 (ttt) REVERT: D 523 MET cc_start: 0.9089 (tpp) cc_final: 0.8799 (tpt) REVERT: D 582 PHE cc_start: 0.8846 (t80) cc_final: 0.8522 (t80) REVERT: D 630 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8522 (tt) outliers start: 119 outliers final: 94 residues processed: 353 average time/residue: 0.2770 time to fit residues: 152.9795 Evaluate side-chains 354 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 255 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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 287 VAL Chi-restraints excluded: chain B residue 346 ILE 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 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 GLU 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 706 LEU Chi-restraints excluded: chain A residue 131 SER 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 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 418 LEU Chi-restraints excluded: chain A residue 442 CYS 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 570 GLU Chi-restraints excluded: chain A residue 585 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 639 LYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 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 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 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 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 579 ARG 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 701 ARG 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 351 TYR 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 413 LEU Chi-restraints excluded: chain D residue 418 LEU 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 570 GLU 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 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 655 PHE Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain D residue 706 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 67 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.125401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070854 restraints weight = 51750.600| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 6.75 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19032 Z= 0.163 Angle : 0.759 13.361 25760 Z= 0.380 Chirality : 0.042 0.229 2940 Planarity : 0.005 0.068 3232 Dihedral : 7.684 54.358 2654 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.38 % Allowed : 25.30 % Favored : 69.32 % 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: 0.72 (0.17), residues: 2308 helix: 1.19 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.86 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 372 HIS 0.002 0.001 HIS B 320 PHE 0.034 0.001 PHE C 304 TYR 0.018 0.002 TYR A 401 ARG 0.004 0.000 ARG C 455 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 1136) hydrogen bonds : angle 4.88467 ( 3300) covalent geometry : bond 0.00365 (19032) covalent geometry : angle 0.75935 (25760) *********************** 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 371 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 265 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.1572 (tpt) cc_final: 0.0722 (ttt) REVERT: B 293 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8520 (tm-30) REVERT: B 523 MET cc_start: 0.9117 (tpp) cc_final: 0.8850 (tpt) REVERT: B 541 MET cc_start: 0.9222 (ttm) cc_final: 0.9018 (ttp) REVERT: B 571 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8957 (mmmm) REVERT: A 162 MET cc_start: 0.0818 (tpt) cc_final: -0.0108 (ttm) REVERT: A 293 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 413 LEU cc_start: 0.9219 (mt) cc_final: 0.8969 (mt) REVERT: A 523 MET cc_start: 0.9130 (tpp) cc_final: 0.8825 (tpt) REVERT: A 571 LYS cc_start: 0.9212 (mmtp) cc_final: 0.8882 (mmmm) REVERT: C 311 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9121 (mm-30) REVERT: C 523 MET cc_start: 0.9112 (tpp) cc_final: 0.8850 (tpt) REVERT: C 579 ARG cc_start: 0.8921 (mtp85) cc_final: 0.8665 (mtp-110) REVERT: C 630 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8541 (tt) REVERT: D 162 MET cc_start: 0.1714 (tpt) cc_final: 0.0762 (ttm) REVERT: D 523 MET cc_start: 0.9162 (tpp) cc_final: 0.8889 (tpt) REVERT: D 582 PHE cc_start: 0.8747 (t80) cc_final: 0.8441 (t80) REVERT: D 630 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8537 (tt) REVERT: D 677 MET cc_start: 0.8983 (tpp) cc_final: 0.8326 (mmm) outliers start: 106 outliers final: 91 residues processed: 334 average time/residue: 0.2790 time to fit residues: 147.2775 Evaluate side-chains 350 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 257 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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 287 VAL Chi-restraints excluded: chain B residue 346 ILE 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 418 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 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 131 SER 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 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 418 LEU Chi-restraints excluded: chain A residue 442 CYS 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 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 639 LYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 131 SER 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 359 GLU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE 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 481 SER 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 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 706 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 351 TYR 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 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 570 GLU 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 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 655 PHE Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 33 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 63 optimal weight: 30.0000 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3966 r_free = 0.3966 target = 0.125983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.070126 restraints weight = 51333.701| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 7.00 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.6821 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= 0.152 Angle : 0.752 13.416 25760 Z= 0.376 Chirality : 0.042 0.209 2940 Planarity : 0.005 0.064 3232 Dihedral : 7.341 49.201 2646 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.02 % Allowed : 26.01 % Favored : 68.97 % 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: 0.72 (0.17), residues: 2308 helix: 1.23 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -0.91 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 549 HIS 0.003 0.000 HIS B 410 PHE 0.031 0.001 PHE C 304 TYR 0.023 0.002 TYR D 401 ARG 0.004 0.000 ARG C 420 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 1136) hydrogen bonds : angle 4.82962 ( 3300) covalent geometry : bond 0.00345 (19032) covalent geometry : angle 0.75201 (25760) *********************** 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 365 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 266 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.1227 (tpt) cc_final: 0.0344 (ttt) REVERT: B 293 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8503 (tm-30) REVERT: B 408 ASN cc_start: 0.8272 (t0) cc_final: 0.7884 (t0) REVERT: B 523 MET cc_start: 0.9031 (tpp) cc_final: 0.8795 (tpt) REVERT: B 541 MET cc_start: 0.9225 (ttm) cc_final: 0.9022 (ttp) REVERT: B 571 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8861 (mmmm) REVERT: A 293 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 311 GLU cc_start: 0.9317 (mm-30) cc_final: 0.9103 (mm-30) REVERT: A 413 LEU cc_start: 0.9249 (mt) cc_final: 0.9006 (mt) REVERT: A 523 MET cc_start: 0.9039 (tpp) cc_final: 0.8802 (tpt) REVERT: A 582 PHE cc_start: 0.8720 (t80) cc_final: 0.8444 (t80) REVERT: C 162 MET cc_start: 0.2564 (tpt) cc_final: 0.1863 (ttt) REVERT: C 311 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9070 (mm-30) REVERT: C 579 ARG cc_start: 0.8955 (mtp85) cc_final: 0.8704 (mtp-110) REVERT: C 582 PHE cc_start: 0.8695 (t80) cc_final: 0.8442 (t80) REVERT: C 630 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8543 (tt) REVERT: D 162 MET cc_start: 0.2551 (tpt) cc_final: 0.1595 (ttm) REVERT: D 523 MET cc_start: 0.9049 (tpp) cc_final: 0.8836 (tpt) REVERT: D 571 LYS cc_start: 0.9311 (mmtp) cc_final: 0.8936 (mmmt) REVERT: D 572 MET cc_start: 0.8315 (tpp) cc_final: 0.8112 (tpp) REVERT: D 582 PHE cc_start: 0.8720 (t80) cc_final: 0.8398 (t80) REVERT: D 630 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8533 (tt) outliers start: 99 outliers final: 89 residues processed: 331 average time/residue: 0.2987 time to fit residues: 157.6273 Evaluate side-chains 354 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 263 time to evaluate : 1.964 ------------------------------------------------------------------------------- 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 287 VAL Chi-restraints excluded: chain B residue 346 ILE 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 457 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 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 131 SER 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 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 481 SER 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 639 LYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain C residue 131 SER 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 359 GLU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE 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 481 SER 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 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 701 ARG 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 351 TYR 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 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 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 655 PHE 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 221 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 122 optimal weight: 40.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 164 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.126895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.070148 restraints weight = 51193.041| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 7.17 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 19032 Z= 0.147 Angle : 0.781 14.318 25760 Z= 0.385 Chirality : 0.042 0.206 2940 Planarity : 0.005 0.065 3232 Dihedral : 7.189 47.199 2646 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.61 % Allowed : 26.42 % Favored : 68.97 % 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: 0.50 (0.17), residues: 2308 helix: 1.09 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -1.17 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 272 HIS 0.004 0.001 HIS B 410 PHE 0.022 0.001 PHE D 304 TYR 0.019 0.001 TYR A 401 ARG 0.004 0.000 ARG C 420 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 1136) hydrogen bonds : angle 4.76809 ( 3300) covalent geometry : bond 0.00335 (19032) covalent geometry : angle 0.78069 (25760) ********************** 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 363 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 272 time to evaluate : 2.012 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 162 MET cc_start: 0.1392 (tpt) cc_final: 0.0513 (ttt) REVERT: B 541 MET cc_start: 0.9230 (ttm) cc_final: 0.9030 (ttp) REVERT: B 568 MET cc_start: 0.8984 (mtm) cc_final: 0.8756 (mtp) REVERT: B 635 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9159 (tm) REVERT: B 684 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8706 (mm-30) REVERT: A 162 MET cc_start: 0.2714 (tpt) cc_final: 0.2010 (ttt) REVERT: A 311 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9037 (mm-30) REVERT: A 523 MET cc_start: 0.9011 (tpp) cc_final: 0.8778 (tpt) REVERT: A 582 PHE cc_start: 0.8687 (t80) cc_final: 0.8437 (t80) REVERT: C 162 MET cc_start: 0.2853 (tpt) cc_final: 0.2138 (ttt) REVERT: C 311 GLU cc_start: 0.9267 (mm-30) cc_final: 0.9065 (mm-30) REVERT: C 582 PHE cc_start: 0.8709 (t80) cc_final: 0.8452 (t80) REVERT: C 630 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8554 (tt) REVERT: C 677 MET cc_start: 0.8950 (tpp) cc_final: 0.8367 (mmm) REVERT: C 701 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8638 (ttp80) REVERT: D 162 MET cc_start: 0.1669 (tpt) cc_final: 0.0726 (ttm) REVERT: D 309 TYR cc_start: 0.9164 (t80) cc_final: 0.8750 (t80) REVERT: D 523 MET cc_start: 0.9009 (tpp) cc_final: 0.8798 (tpt) REVERT: D 571 LYS cc_start: 0.9289 (mmtp) cc_final: 0.9030 (mmmm) REVERT: D 582 PHE cc_start: 0.8698 (t80) cc_final: 0.8416 (t80) REVERT: D 630 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8559 (tt) REVERT: D 677 MET cc_start: 0.9058 (tpp) cc_final: 0.8689 (mmm) outliers start: 91 outliers final: 77 residues processed: 331 average time/residue: 0.2739 time to fit residues: 142.8345 Evaluate side-chains 341 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 260 time to evaluate : 1.986 ------------------------------------------------------------------------------- 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 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 418 LEU Chi-restraints excluded: chain B residue 481 SER 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 131 SER 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 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 481 SER 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 639 LYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain C residue 131 SER 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 359 GLU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 570 GLU 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 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 701 ARG 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 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 598 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 655 PHE Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 672 ILE 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 50 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 115 optimal weight: 0.0470 chunk 195 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.126976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072588 restraints weight = 51221.832| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 7.35 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.7090 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= 0.152 Angle : 0.794 13.093 25760 Z= 0.392 Chirality : 0.042 0.200 2940 Planarity : 0.005 0.062 3232 Dihedral : 6.979 47.840 2642 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.01 % Allowed : 27.08 % Favored : 68.91 % 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: 0.70 (0.17), residues: 2308 helix: 1.21 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -0.93 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 549 HIS 0.001 0.000 HIS A 320 PHE 0.016 0.001 PHE D 304 TYR 0.019 0.002 TYR A 401 ARG 0.008 0.001 ARG C 579 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 1136) hydrogen bonds : angle 4.76651 ( 3300) covalent geometry : bond 0.00348 (19032) covalent geometry : angle 0.79400 (25760) =============================================================================== Job complete usr+sys time: 9667.20 seconds wall clock time: 166 minutes 22.64 seconds (9982.64 seconds total)