Starting phenix.real_space_refine on Thu Sep 18 16:10:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j5p_5778/09_2025/3j5p_5778.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j5p_5778/09_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_5778/09_2025/3j5p_5778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j5p_5778/09_2025/3j5p_5778.map" model { file = "/net/cci-nas-00/data/ceres_data/3j5p_5778/09_2025/3j5p_5778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j5p_5778/09_2025/3j5p_5778.cif" } resolution = 3.275 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} 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: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} 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: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} 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: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} 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: 4.01, per 1000 atoms: 0.22 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: 1.72 Conformation dependent library (CDL) restraints added in 827.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.51 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: 2.38 Time building geometry restraints manager: 2.08 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: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.850 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- 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 : 79.09 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 181 TYR 0.022 0.002 TYR A 309 PHE 0.024 0.001 PHE C 235 TRP 0.012 0.002 TRP A 697 HIS 0.007 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01089 (19032) covalent geometry : angle 1.52696 (25760) hydrogen bonds : bond 0.24935 ( 1136) hydrogen bonds : angle 8.75201 ( 3300) *********************** 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 : 0.727 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: 0.1435 time to fit residues: 182.6683 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 : 0.585 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.0970 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 20.0000 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.125857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.070766 restraints weight = 49347.283| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 6.62 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19032 Z= 0.214 Angle : 0.950 13.549 25760 Z= 0.481 Chirality : 0.046 0.167 2940 Planarity : 0.006 0.074 3232 Dihedral : 13.588 71.852 2960 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.47 % Favored : 96.19 % Rotamer: Outliers : 9.94 % Allowed : 22.11 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 2308 helix: 0.81 (0.12), residues: 1504 sheet: None (None), residues: 0 loop : -1.28 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 499 TYR 0.018 0.002 TYR B 584 PHE 0.026 0.002 PHE A 245 TRP 0.014 0.003 TRP B 372 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00455 (19032) covalent geometry : angle 0.95040 (25760) hydrogen bonds : bond 0.06073 ( 1136) hydrogen bonds : angle 5.51966 ( 3300) *********************** 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 560 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 364 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 187 LYS cc_start: -0.0771 (OUTLIER) cc_final: -0.1099 (mmtt) REVERT: B 408 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8214 (t0) REVERT: B 473 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.9182 (m-10) REVERT: B 552 MET cc_start: 0.9185 (tpp) cc_final: 0.8922 (mtp) REVERT: B 598 LEU cc_start: 0.9576 (tp) cc_final: 0.9347 (tp) REVERT: B 636 GLU cc_start: 0.8866 (tp30) cc_final: 0.8609 (mm-30) REVERT: B 639 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8924 (mtmm) REVERT: B 664 LEU cc_start: 0.9652 (mp) cc_final: 0.9447 (mp) REVERT: A 187 LYS cc_start: -0.0666 (OUTLIER) cc_final: -0.1008 (mmtt) REVERT: A 283 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8657 (p) REVERT: A 408 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8191 (t0) REVERT: A 473 PHE cc_start: 0.9451 (OUTLIER) cc_final: 0.9186 (m-10) REVERT: A 541 MET cc_start: 0.9035 (ttm) cc_final: 0.8775 (ttp) REVERT: A 552 MET cc_start: 0.9163 (tpp) cc_final: 0.8897 (mtp) REVERT: A 636 GLU cc_start: 0.8874 (tp30) cc_final: 0.8617 (mm-30) REVERT: A 639 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.8905 (mtmm) REVERT: A 664 LEU cc_start: 0.9658 (mp) cc_final: 0.9446 (mp) REVERT: A 676 ASN cc_start: 0.9161 (m-40) cc_final: 0.8927 (m110) REVERT: A 677 MET cc_start: 0.9141 (tpp) cc_final: 0.8816 (mmm) REVERT: C 187 LYS cc_start: -0.0766 (OUTLIER) cc_final: -0.1080 (mmtt) REVERT: C 310 ASN cc_start: 0.9136 (t0) cc_final: 0.8652 (t0) REVERT: C 408 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7616 (t0) REVERT: C 412 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8217 (mpp) REVERT: C 473 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.9197 (m-10) REVERT: C 552 MET cc_start: 0.9167 (tpp) cc_final: 0.8962 (mtp) REVERT: C 579 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8658 (ttm-80) REVERT: C 598 LEU cc_start: 0.9580 (tp) cc_final: 0.9363 (tp) REVERT: C 636 GLU cc_start: 0.8879 (tp30) cc_final: 0.8654 (mm-30) REVERT: C 639 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8939 (mtmm) REVERT: C 664 LEU cc_start: 0.9652 (mp) cc_final: 0.9449 (mp) REVERT: C 676 ASN cc_start: 0.9139 (m-40) cc_final: 0.8910 (m110) REVERT: D 187 LYS cc_start: -0.0864 (OUTLIER) cc_final: -0.1178 (mmtt) REVERT: D 408 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7617 (t0) REVERT: D 412 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8204 (mpp) REVERT: D 473 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.9231 (m-10) REVERT: D 541 MET cc_start: 0.9067 (ttm) cc_final: 0.8793 (ttp) REVERT: D 636 GLU cc_start: 0.8892 (tp30) cc_final: 0.8653 (mm-30) REVERT: D 639 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8925 (mtmm) REVERT: D 676 ASN cc_start: 0.9147 (m-40) cc_final: 0.8908 (m110) outliers start: 196 outliers final: 104 residues processed: 503 average time/residue: 0.1337 time to fit residues: 103.1307 Evaluate side-chains 401 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 277 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 413 LEU 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 283 VAL 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 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 412 MET 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 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 217 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 112 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN B 498 GLN A 498 GLN C 164 ASN C 498 GLN D 164 ASN D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.127127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078145 restraints weight = 58199.210| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 7.28 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19032 Z= 0.165 Angle : 0.834 13.383 25760 Z= 0.421 Chirality : 0.044 0.203 2940 Planarity : 0.005 0.084 3232 Dihedral : 10.278 59.622 2744 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.33 % Favored : 95.49 % Rotamer: Outliers : 6.80 % Allowed : 22.52 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2308 helix: 1.06 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.99 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 499 TYR 0.022 0.002 TYR D 198 PHE 0.026 0.002 PHE D 304 TRP 0.014 0.002 TRP C 372 HIS 0.005 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00349 (19032) covalent geometry : angle 0.83415 (25760) hydrogen bonds : bond 0.05031 ( 1136) hydrogen bonds : angle 5.04751 ( 3300) *********************** 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 499 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 365 time to evaluate : 0.735 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: B 162 MET cc_start: 0.1992 (tpt) cc_final: 0.1122 (ttt) REVERT: B 309 TYR cc_start: 0.9279 (t80) cc_final: 0.8952 (t80) REVERT: B 310 ASN cc_start: 0.9360 (t0) cc_final: 0.9080 (t0) REVERT: B 378 HIS cc_start: 0.8578 (m-70) cc_final: 0.8357 (m-70) REVERT: B 473 PHE cc_start: 0.9504 (OUTLIER) cc_final: 0.9298 (m-10) REVERT: B 541 MET cc_start: 0.9231 (ttm) cc_final: 0.8914 (ttp) REVERT: B 552 MET cc_start: 0.9150 (tpp) cc_final: 0.8881 (ttm) REVERT: B 572 MET cc_start: 0.8874 (tpp) cc_final: 0.8607 (tpp) REVERT: B 630 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8677 (tt) REVERT: B 639 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8911 (mtmm) REVERT: A 162 MET cc_start: 0.2282 (tpt) cc_final: 0.1406 (ttt) REVERT: A 309 TYR cc_start: 0.9308 (t80) cc_final: 0.9009 (t80) REVERT: A 310 ASN cc_start: 0.9343 (t0) cc_final: 0.9040 (t0) REVERT: A 426 TRP cc_start: 0.8569 (OUTLIER) cc_final: 0.8308 (t-100) REVERT: A 473 PHE cc_start: 0.9502 (OUTLIER) cc_final: 0.9300 (m-10) REVERT: A 552 MET cc_start: 0.9192 (tpp) cc_final: 0.8934 (ttm) REVERT: A 636 GLU cc_start: 0.8860 (tp30) cc_final: 0.8518 (mm-30) REVERT: A 639 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8820 (mtmm) REVERT: A 668 ILE cc_start: 0.9615 (mp) cc_final: 0.9409 (mp) REVERT: A 701 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8202 (ttm-80) REVERT: C 162 MET cc_start: 0.2393 (tpt) cc_final: 0.1490 (ttt) REVERT: C 309 TYR cc_start: 0.9298 (t80) cc_final: 0.9056 (t80) REVERT: C 378 HIS cc_start: 0.8577 (m-70) cc_final: 0.8364 (m-70) REVERT: C 426 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.8306 (t-100) REVERT: C 473 PHE cc_start: 0.9499 (OUTLIER) cc_final: 0.9297 (m-10) REVERT: C 552 MET cc_start: 0.9218 (tpp) cc_final: 0.8959 (ttm) REVERT: C 579 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8703 (ttm-80) REVERT: C 630 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8563 (tt) REVERT: C 639 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8909 (mtmm) REVERT: C 677 MET cc_start: 0.8945 (mmm) cc_final: 0.8666 (mmm) REVERT: C 701 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8194 (ttm-80) REVERT: D 162 MET cc_start: 0.1970 (tpt) cc_final: 0.1108 (ttt) REVERT: D 310 ASN cc_start: 0.9389 (t0) cc_final: 0.9049 (t0) REVERT: D 311 GLU cc_start: 0.9459 (tp30) cc_final: 0.9242 (mm-30) REVERT: D 473 PHE cc_start: 0.9509 (OUTLIER) cc_final: 0.9279 (m-10) REVERT: D 630 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8596 (tt) REVERT: D 639 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8933 (mtmm) REVERT: D 701 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8218 (ttm-80) outliers start: 134 outliers final: 89 residues processed: 455 average time/residue: 0.1268 time to fit residues: 90.0524 Evaluate side-chains 393 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 287 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 323 LEU 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 396 LEU Chi-restraints excluded: chain B residue 402 SER 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 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 630 LEU 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 662 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 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 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 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 426 TRP 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 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 662 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 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 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 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 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 662 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 685 THR 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 79 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 202 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 A 498 GLN C 498 GLN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.123697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071159 restraints weight = 49375.394| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 6.17 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 19032 Z= 0.151 Angle : 0.777 13.363 25760 Z= 0.389 Chirality : 0.041 0.159 2940 Planarity : 0.005 0.064 3232 Dihedral : 9.127 58.957 2692 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.14 % Allowed : 22.92 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.17), residues: 2308 helix: 1.05 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -1.06 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 420 TYR 0.025 0.002 TYR D 401 PHE 0.021 0.001 PHE A 304 TRP 0.009 0.002 TRP C 372 HIS 0.004 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00333 (19032) covalent geometry : angle 0.77715 (25760) hydrogen bonds : bond 0.04536 ( 1136) hydrogen bonds : angle 4.95214 ( 3300) *********************** 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 432 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 311 time to evaluate : 0.745 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: 0.1669 (tpt) cc_final: 0.0796 (ttt) REVERT: B 293 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8359 (tm-30) REVERT: B 378 HIS cc_start: 0.8549 (m-70) cc_final: 0.8295 (m-70) REVERT: B 473 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.9186 (m-10) REVERT: B 523 MET cc_start: 0.9062 (tpp) cc_final: 0.8654 (tpt) REVERT: B 541 MET cc_start: 0.9058 (ttm) cc_final: 0.8789 (ttp) REVERT: B 547 MET cc_start: 0.9074 (tpp) cc_final: 0.8868 (tpp) REVERT: B 639 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8920 (mtmm) REVERT: A 162 MET cc_start: 0.1770 (tpt) cc_final: 0.0827 (ttt) REVERT: A 293 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 473 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.9189 (m-10) REVERT: A 571 LYS cc_start: 0.9506 (mmtp) cc_final: 0.9072 (mmmm) REVERT: A 636 GLU cc_start: 0.8815 (tp30) cc_final: 0.8569 (mm-30) REVERT: A 639 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8948 (mtmm) REVERT: A 676 ASN cc_start: 0.9304 (m-40) cc_final: 0.9097 (m110) REVERT: A 677 MET cc_start: 0.9261 (tpp) cc_final: 0.8672 (mmm) REVERT: A 701 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8225 (ttm-80) REVERT: C 162 MET cc_start: 0.1862 (tpt) cc_final: 0.0918 (ttt) REVERT: C 309 TYR cc_start: 0.8953 (t80) cc_final: 0.8678 (t80) REVERT: C 378 HIS cc_start: 0.8523 (m-70) cc_final: 0.8272 (m-70) REVERT: C 473 PHE cc_start: 0.9461 (OUTLIER) cc_final: 0.9197 (m-10) REVERT: C 523 MET cc_start: 0.9088 (tpp) cc_final: 0.8674 (tpt) REVERT: C 541 MET cc_start: 0.9027 (ttm) cc_final: 0.8759 (ttp) REVERT: C 630 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8553 (tt) REVERT: C 677 MET cc_start: 0.9145 (mmm) cc_final: 0.8719 (tmm) REVERT: C 701 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8218 (ttm-80) REVERT: D 162 MET cc_start: 0.1618 (tpt) cc_final: 0.0760 (ttt) REVERT: D 473 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.9181 (m-10) REVERT: D 523 MET cc_start: 0.9104 (tpp) cc_final: 0.8682 (tpt) REVERT: D 571 LYS cc_start: 0.9487 (mmtp) cc_final: 0.9045 (mmmm) REVERT: D 639 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8911 (mtmm) REVERT: D 701 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8745 (ttm170) outliers start: 121 outliers final: 75 residues processed: 393 average time/residue: 0.1238 time to fit residues: 77.1101 Evaluate side-chains 356 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 270 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 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 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 323 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 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 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 701 ARG 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 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 473 PHE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 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 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 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 639 LYS 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 193 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 153 optimal weight: 0.0670 chunk 199 optimal weight: 0.9990 chunk 72 optimal weight: 0.0040 overall best weight: 0.5934 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.125201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.073683 restraints weight = 47232.128| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 6.43 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 19032 Z= 0.141 Angle : 0.748 12.996 25760 Z= 0.372 Chirality : 0.040 0.155 2940 Planarity : 0.005 0.058 3232 Dihedral : 8.282 54.509 2666 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.48 % Allowed : 23.63 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.17), residues: 2308 helix: 1.10 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -1.00 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 579 TYR 0.019 0.002 TYR D 401 PHE 0.020 0.001 PHE A 304 TRP 0.012 0.002 TRP A 272 HIS 0.003 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00312 (19032) covalent geometry : angle 0.74813 (25760) hydrogen bonds : bond 0.04321 ( 1136) hydrogen bonds : angle 4.79242 ( 3300) *********************** 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 424 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 316 time to evaluate : 0.726 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: 0.1412 (tpt) cc_final: 0.0574 (ttt) REVERT: B 293 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8576 (tm-30) REVERT: B 311 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9128 (mm-30) REVERT: B 378 HIS cc_start: 0.8427 (m-70) cc_final: 0.8136 (m-70) REVERT: B 408 ASN cc_start: 0.8535 (t0) cc_final: 0.8329 (t0) REVERT: B 473 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.9125 (m-10) REVERT: B 523 MET cc_start: 0.9204 (tpp) cc_final: 0.8763 (tpt) REVERT: B 630 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8486 (tt) REVERT: B 639 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9041 (mtmm) REVERT: A 162 MET cc_start: 0.1400 (tpt) cc_final: 0.0492 (ttt) REVERT: A 293 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8445 (tm-30) REVERT: A 473 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.9122 (m-10) REVERT: A 523 MET cc_start: 0.9079 (tpp) cc_final: 0.8775 (tpt) REVERT: A 571 LYS cc_start: 0.9376 (mmtp) cc_final: 0.8976 (mmmm) REVERT: A 636 GLU cc_start: 0.8632 (tp30) cc_final: 0.8242 (mm-30) REVERT: A 639 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8819 (mtmm) REVERT: A 661 ILE cc_start: 0.9455 (mm) cc_final: 0.9248 (mm) REVERT: A 677 MET cc_start: 0.8998 (tpp) cc_final: 0.8379 (tpp) REVERT: A 701 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8691 (ttm170) REVERT: C 162 MET cc_start: 0.1441 (tpt) cc_final: 0.0535 (ttt) REVERT: C 291 LEU cc_start: 0.9473 (mt) cc_final: 0.9124 (tp) REVERT: C 473 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.9117 (m-10) REVERT: C 523 MET cc_start: 0.9237 (tpp) cc_final: 0.8841 (tpt) REVERT: C 701 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8727 (ttm170) REVERT: D 162 MET cc_start: 0.1417 (tpt) cc_final: 0.0585 (ttt) REVERT: D 473 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.9103 (m-10) REVERT: D 523 MET cc_start: 0.9221 (tpp) cc_final: 0.8800 (tpt) REVERT: D 630 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8563 (tt) REVERT: D 639 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9062 (mtmm) REVERT: D 677 MET cc_start: 0.9020 (mmm) cc_final: 0.8728 (mmm) REVERT: D 701 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8770 (ttm170) outliers start: 108 outliers final: 74 residues processed: 382 average time/residue: 0.1290 time to fit residues: 77.0054 Evaluate side-chains 367 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 281 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 323 LEU 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 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 553 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 630 LEU 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 662 LEU Chi-restraints excluded: chain B residue 672 ILE 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 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 473 PHE 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 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 674 LEU 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 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 473 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU 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 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 473 PHE 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 639 LYS Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 701 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 135 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.124245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070187 restraints weight = 47467.278| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 6.55 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19032 Z= 0.155 Angle : 0.753 13.321 25760 Z= 0.373 Chirality : 0.040 0.164 2940 Planarity : 0.005 0.061 3232 Dihedral : 8.028 53.366 2666 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 6.44 % Allowed : 24.34 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.17), residues: 2308 helix: 1.19 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.87 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.027 0.002 TYR C 401 PHE 0.019 0.001 PHE C 304 TRP 0.008 0.001 TRP D 372 HIS 0.003 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00343 (19032) covalent geometry : angle 0.75282 (25760) hydrogen bonds : bond 0.04193 ( 1136) hydrogen bonds : angle 4.80167 ( 3300) *********************** 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 407 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 280 time to evaluate : 0.715 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: 0.1842 (tpt) cc_final: 0.0962 (ttt) REVERT: B 293 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8249 (tm-30) REVERT: B 378 HIS cc_start: 0.8480 (m-70) cc_final: 0.8191 (m-70) REVERT: B 413 LEU cc_start: 0.9266 (mt) cc_final: 0.9054 (mt) REVERT: B 473 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.9155 (m-10) REVERT: B 523 MET cc_start: 0.8883 (tpp) cc_final: 0.8621 (tpt) REVERT: B 572 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8451 (ttm) REVERT: B 630 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 639 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9032 (mtmm) REVERT: B 677 MET cc_start: 0.9198 (tpp) cc_final: 0.8835 (mmm) REVERT: A 162 MET cc_start: 0.1923 (tpt) cc_final: 0.0984 (ttt) REVERT: A 293 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8262 (tm-30) REVERT: A 661 ILE cc_start: 0.9539 (mm) cc_final: 0.9300 (mm) REVERT: A 677 MET cc_start: 0.8921 (tpp) cc_final: 0.8473 (tpp) REVERT: A 701 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8532 (ttm170) REVERT: C 162 MET cc_start: 0.2135 (tpt) cc_final: 0.1203 (ttt) REVERT: C 473 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.9148 (m-10) REVERT: C 523 MET cc_start: 0.8883 (tpp) cc_final: 0.8616 (tpt) REVERT: C 630 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8356 (tt) REVERT: C 701 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8687 (ttm170) REVERT: D 162 MET cc_start: 0.1857 (tpt) cc_final: 0.0993 (ttt) REVERT: D 523 MET cc_start: 0.8891 (tpp) cc_final: 0.8603 (tpt) REVERT: D 630 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8475 (tt) REVERT: D 639 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9037 (mtmm) REVERT: D 701 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8572 (ttm170) outliers start: 127 outliers final: 87 residues processed: 365 average time/residue: 0.1229 time to fit residues: 71.2852 Evaluate side-chains 355 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 257 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 348 VAL 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 402 SER Chi-restraints excluded: chain B residue 418 LEU 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 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 630 LEU 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 672 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 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 442 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 516 PHE 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 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 672 ILE 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 348 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 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 672 ILE Chi-restraints excluded: chain C residue 679 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 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 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 639 LYS Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 701 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 185 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 202 GLN ** 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 = 0.3947 r_free = 0.3947 target = 0.121482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.067989 restraints weight = 49426.488| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 6.64 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19032 Z= 0.199 Angle : 0.763 13.174 25760 Z= 0.384 Chirality : 0.041 0.204 2940 Planarity : 0.005 0.061 3232 Dihedral : 7.824 51.982 2658 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.98 % Allowed : 23.63 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.17), residues: 2308 helix: 1.16 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -1.02 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 455 TYR 0.017 0.002 TYR C 653 PHE 0.022 0.001 PHE B 712 TRP 0.023 0.002 TRP D 372 HIS 0.005 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00434 (19032) covalent geometry : angle 0.76323 (25760) hydrogen bonds : bond 0.04283 ( 1136) hydrogen bonds : angle 4.92004 ( 3300) *********************** 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 377 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 259 time to evaluate : 0.684 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: B 162 MET cc_start: 0.1996 (tpt) cc_final: 0.1116 (ttt) REVERT: B 293 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8433 (tm-30) REVERT: B 378 HIS cc_start: 0.8450 (m-70) cc_final: 0.8193 (m-70) REVERT: B 413 LEU cc_start: 0.9264 (mt) cc_final: 0.9019 (mt) REVERT: B 523 MET cc_start: 0.8970 (tpp) cc_final: 0.8711 (tpt) REVERT: B 630 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8526 (tt) REVERT: B 639 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9060 (mtmm) REVERT: A 162 MET cc_start: 0.2024 (tpt) cc_final: 0.1042 (ttm) REVERT: A 293 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8360 (tm-30) REVERT: A 661 ILE cc_start: 0.9646 (mm) cc_final: 0.9407 (mm) REVERT: C 162 MET cc_start: 0.2140 (tpt) cc_final: 0.1151 (ttm) REVERT: C 523 MET cc_start: 0.8943 (tpp) cc_final: 0.8675 (tpt) REVERT: C 582 PHE cc_start: 0.8887 (t80) cc_final: 0.8539 (t80) REVERT: C 630 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8456 (tt) REVERT: D 162 MET cc_start: 0.1994 (tpt) cc_final: 0.1111 (ttt) REVERT: D 523 MET cc_start: 0.8963 (tpp) cc_final: 0.8687 (tpt) REVERT: D 582 PHE cc_start: 0.8883 (t80) cc_final: 0.8566 (t80) REVERT: D 630 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8568 (tt) REVERT: D 639 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9052 (mtmm) REVERT: D 677 MET cc_start: 0.9086 (tpp) cc_final: 0.8441 (mmm) REVERT: D 701 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8635 (ttm170) outliers start: 118 outliers final: 91 residues processed: 338 average time/residue: 0.1164 time to fit residues: 63.0995 Evaluate side-chains 345 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 248 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 396 LEU Chi-restraints excluded: chain B residue 402 SER 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 516 PHE 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 598 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 630 LEU 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 706 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 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 442 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 516 PHE 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 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 598 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 672 ILE 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 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 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 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 701 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 73 optimal weight: 6.9990 chunk 4 optimal weight: 40.0000 chunk 127 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.125181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068675 restraints weight = 51760.091| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 7.13 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19032 Z= 0.165 Angle : 0.749 13.786 25760 Z= 0.371 Chirality : 0.041 0.227 2940 Planarity : 0.005 0.061 3232 Dihedral : 7.527 51.463 2652 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.43 % Allowed : 24.39 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2308 helix: 1.15 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -1.06 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 455 TYR 0.015 0.002 TYR B 444 PHE 0.019 0.001 PHE C 304 TRP 0.010 0.001 TRP D 372 HIS 0.002 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00369 (19032) covalent geometry : angle 0.74853 (25760) hydrogen bonds : bond 0.04166 ( 1136) hydrogen bonds : angle 4.86575 ( 3300) *********************** 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 374 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 267 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.2886 (tpt) cc_final: 0.1980 (ttt) REVERT: B 293 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8427 (tm-30) REVERT: B 378 HIS cc_start: 0.8433 (m-70) cc_final: 0.8162 (m-70) REVERT: B 413 LEU cc_start: 0.9221 (mt) cc_final: 0.8987 (mt) REVERT: B 523 MET cc_start: 0.9009 (tpp) cc_final: 0.8803 (tpt) REVERT: B 571 LYS cc_start: 0.9472 (mmtp) cc_final: 0.9018 (mmmm) REVERT: B 630 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8611 (tt) REVERT: B 639 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9125 (mtmm) REVERT: B 677 MET cc_start: 0.8938 (tpp) cc_final: 0.8557 (mmm) REVERT: A 293 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8484 (tm-30) REVERT: A 636 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8460 (mm-30) REVERT: A 661 ILE cc_start: 0.9670 (mm) cc_final: 0.9403 (mm) REVERT: A 701 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7821 (ttm170) REVERT: C 523 MET cc_start: 0.9025 (tpp) cc_final: 0.8804 (tpt) REVERT: C 571 LYS cc_start: 0.9384 (mmtp) cc_final: 0.9042 (mmmt) REVERT: C 582 PHE cc_start: 0.8818 (t80) cc_final: 0.8465 (t80) REVERT: C 630 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8413 (tt) REVERT: C 676 ASN cc_start: 0.9315 (m-40) cc_final: 0.9050 (m110) REVERT: C 677 MET cc_start: 0.9235 (tpp) cc_final: 0.8488 (mmm) REVERT: D 162 MET cc_start: 0.2969 (tpt) cc_final: 0.2004 (ttm) REVERT: D 523 MET cc_start: 0.9007 (tpp) cc_final: 0.8778 (tpt) REVERT: D 541 MET cc_start: 0.9241 (ttp) cc_final: 0.8522 (ptm) REVERT: D 571 LYS cc_start: 0.9372 (mmtp) cc_final: 0.8990 (mmmt) REVERT: D 582 PHE cc_start: 0.8771 (t80) cc_final: 0.8452 (t80) REVERT: D 630 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8528 (tt) REVERT: D 639 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9105 (mtmm) outliers start: 107 outliers final: 90 residues processed: 331 average time/residue: 0.1255 time to fit residues: 65.5424 Evaluate side-chains 349 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 253 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 396 LEU Chi-restraints excluded: chain B residue 402 SER 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 598 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 630 LEU 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 662 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 679 ILE 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 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 457 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 ILE 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 674 LEU 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 348 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 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 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 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 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 662 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 701 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 12 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 193 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.124107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.069556 restraints weight = 51981.186| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 7.38 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19032 Z= 0.199 Angle : 0.769 13.918 25760 Z= 0.386 Chirality : 0.042 0.235 2940 Planarity : 0.005 0.058 3232 Dihedral : 7.438 50.441 2652 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.58 % Allowed : 25.15 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.17), residues: 2308 helix: 1.12 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -1.05 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 420 TYR 0.019 0.002 TYR A 584 PHE 0.018 0.001 PHE A 591 TRP 0.012 0.002 TRP D 372 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00445 (19032) covalent geometry : angle 0.76891 (25760) hydrogen bonds : bond 0.04271 ( 1136) hydrogen bonds : angle 4.95116 ( 3300) *********************** 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 372 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 262 time to evaluate : 0.593 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: B 413 LEU cc_start: 0.9259 (mt) cc_final: 0.9025 (mt) REVERT: B 630 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8613 (tt) REVERT: B 639 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9157 (mtmm) REVERT: B 676 ASN cc_start: 0.9170 (m110) cc_final: 0.8967 (m110) REVERT: B 677 MET cc_start: 0.8960 (tpp) cc_final: 0.8737 (mmm) REVERT: A 162 MET cc_start: 0.2602 (tpt) cc_final: 0.1894 (ttt) REVERT: A 523 MET cc_start: 0.9371 (mmm) cc_final: 0.8948 (tpt) REVERT: A 541 MET cc_start: 0.9325 (ttp) cc_final: 0.8626 (ptm) REVERT: A 636 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8483 (mm-30) REVERT: A 661 ILE cc_start: 0.9695 (mm) cc_final: 0.9440 (mm) REVERT: A 676 ASN cc_start: 0.9109 (m110) cc_final: 0.8873 (m110) REVERT: A 677 MET cc_start: 0.8889 (tpp) cc_final: 0.8386 (tpp) REVERT: C 162 MET cc_start: 0.2523 (tpt) cc_final: 0.1800 (ttt) REVERT: C 582 PHE cc_start: 0.8809 (t80) cc_final: 0.8443 (t80) REVERT: C 630 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8480 (tt) REVERT: D 308 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8429 (mtt) REVERT: D 571 LYS cc_start: 0.9328 (mmtp) cc_final: 0.9018 (mmmm) REVERT: D 582 PHE cc_start: 0.8833 (t80) cc_final: 0.8509 (t80) REVERT: D 630 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8529 (tt) REVERT: D 639 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9126 (mtmm) outliers start: 110 outliers final: 95 residues processed: 327 average time/residue: 0.1185 time to fit residues: 61.8580 Evaluate side-chains 349 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 248 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 348 VAL 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 402 SER 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 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 630 LEU 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 679 ILE Chi-restraints excluded: chain B residue 686 VAL 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 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 521 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 ILE 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 672 ILE Chi-restraints excluded: chain A residue 674 LEU 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 348 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 598 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 639 LYS Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 679 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 308 MET Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 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 655 PHE Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 701 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 50 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** D 676 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.129029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.073191 restraints weight = 51946.441| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 7.30 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.7034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19032 Z= 0.151 Angle : 0.822 13.577 25760 Z= 0.401 Chirality : 0.042 0.239 2940 Planarity : 0.005 0.064 3232 Dihedral : 7.124 51.779 2646 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.17), residues: 2308 helix: 1.14 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.84 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 211 TYR 0.018 0.001 TYR A 584 PHE 0.018 0.001 PHE B 304 TRP 0.009 0.001 TRP C 272 HIS 0.001 0.000 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00342 (19032) covalent geometry : angle 0.82198 (25760) hydrogen bonds : bond 0.04191 ( 1136) hydrogen bonds : angle 4.85795 ( 3300) ********************** 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 358 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 267 time to evaluate : 0.741 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 413 LEU cc_start: 0.9169 (mt) cc_final: 0.8925 (mt) REVERT: B 523 MET cc_start: 0.9149 (mmm) cc_final: 0.8648 (mmm) REVERT: B 630 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8623 (tt) REVERT: B 677 MET cc_start: 0.8946 (tpp) cc_final: 0.8692 (mmm) REVERT: B 684 GLU cc_start: 0.8871 (pp20) cc_final: 0.8625 (pp20) REVERT: A 162 MET cc_start: 0.2586 (tpt) cc_final: 0.1902 (ttt) REVERT: A 418 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9366 (pp) REVERT: A 523 MET cc_start: 0.9253 (mmm) cc_final: 0.8863 (tpt) REVERT: A 571 LYS cc_start: 0.9206 (mmtp) cc_final: 0.8859 (mmmm) REVERT: A 582 PHE cc_start: 0.8679 (t80) cc_final: 0.8404 (t80) REVERT: A 636 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8438 (mm-30) REVERT: A 661 ILE cc_start: 0.9663 (mm) cc_final: 0.9393 (mm) REVERT: A 701 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8023 (ttm170) REVERT: C 162 MET cc_start: 0.2580 (tpt) cc_final: 0.1894 (ttt) REVERT: C 523 MET cc_start: 0.9134 (mmm) cc_final: 0.8612 (mmm) REVERT: C 571 LYS cc_start: 0.9216 (mmtp) cc_final: 0.8945 (mmmm) REVERT: C 677 MET cc_start: 0.8932 (tpp) cc_final: 0.8577 (mmm) REVERT: C 682 MET cc_start: 0.9072 (ptm) cc_final: 0.8802 (ptp) REVERT: D 523 MET cc_start: 0.9177 (mmm) cc_final: 0.8686 (mmm) REVERT: D 541 MET cc_start: 0.9179 (ttp) cc_final: 0.8508 (ptm) REVERT: D 571 LYS cc_start: 0.9192 (mmtp) cc_final: 0.8960 (mmmm) REVERT: D 582 PHE cc_start: 0.8729 (t80) cc_final: 0.8443 (t80) REVERT: D 630 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8552 (tt) REVERT: D 644 MET cc_start: 0.8796 (mmp) cc_final: 0.8408 (mmm) REVERT: D 677 MET cc_start: 0.8862 (tpp) cc_final: 0.8510 (mmm) REVERT: D 701 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7880 (ttm170) outliers start: 91 outliers final: 77 residues processed: 321 average time/residue: 0.1286 time to fit residues: 65.6443 Evaluate side-chains 333 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 251 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 396 LEU 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 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain 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 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 ILE 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 672 ILE 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 348 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 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 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 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 664 LEU Chi-restraints excluded: chain D residue 701 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 74 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 40.0000 chunk 15 optimal weight: 8.9990 chunk 130 optimal weight: 30.0000 chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.123029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.068029 restraints weight = 53864.847| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 7.21 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.7115 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= 0.178 Angle : 0.826 13.642 25760 Z= 0.405 Chirality : 0.043 0.228 2940 Planarity : 0.005 0.059 3232 Dihedral : 7.046 50.805 2646 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 4.36 % Allowed : 27.54 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.17), residues: 2308 helix: 1.11 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.83 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 211 TYR 0.019 0.002 TYR B 584 PHE 0.019 0.001 PHE D 304 TRP 0.009 0.001 TRP D 372 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00410 (19032) covalent geometry : angle 0.82596 (25760) hydrogen bonds : bond 0.04204 ( 1136) hydrogen bonds : angle 4.88361 ( 3300) =============================================================================== Job complete usr+sys time: 4657.49 seconds wall clock time: 80 minutes 42.58 seconds (4842.58 seconds total)