Starting phenix.real_space_refine on Mon Feb 19 13:43:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/02_2024/6d03_7783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/02_2024/6d03_7783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/02_2024/6d03_7783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/02_2024/6d03_7783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/02_2024/6d03_7783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/02_2024/6d03_7783_updated.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 S 132 5.16 5 C 15757 2.51 5 N 4200 2.21 5 O 4749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C ARG 568": "NH1" <-> "NH2" Residue "C ARG 581": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D ARG 522": "NH1" <-> "NH2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 581": "NH1" <-> "NH2" Residue "D ARG 632": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 242": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 468": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24844 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 614} Chain: "B" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "D" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 455} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.15, per 1000 atoms: 0.53 Number of scatterers: 24844 At special positions: 0 Unit cell: (144.45, 149.85, 163.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 132 16.00 O 4749 8.00 N 4200 7.00 C 15757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 363 " distance=2.02 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 363 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 596 " distance=2.02 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 674 " distance=2.02 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 637 " distance=2.02 Simple disulfide: pdb=" SG CYS C 450 " - pdb=" SG CYS C 523 " distance=2.02 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 665 " distance=2.03 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 506 " distance=2.02 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 48 " distance=2.02 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 174 " distance=2.02 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 171 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 241 " distance=2.01 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 596 " distance=2.03 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 377 " distance=2.01 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 368 " distance=2.03 Simple disulfide: pdb=" SG CYS D 402 " - pdb=" SG CYS D 674 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 637 " distance=2.03 Simple disulfide: pdb=" SG CYS D 450 " - pdb=" SG CYS D 523 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 665 " distance=2.02 Simple disulfide: pdb=" SG CYS D 484 " - pdb=" SG CYS D 498 " distance=2.02 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 506 " distance=2.02 Simple disulfide: pdb=" SG CYS D 563 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 620 " distance=2.02 Simple disulfide: pdb=" SG CYS E 240 " - pdb=" SG CYS E 284 " distance=2.05 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " BETA2-4 " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 802 " - " ASN A 251 " " NAG B 802 " - " ASN B 251 " " NAG C 707 " - " ASN C 611 " " NAG D 707 " - " ASN D 611 " " NAG F 1 " - " ASN A 317 " " NAG G 1 " - " ASN A 727 " " NAG H 1 " - " ASN B 317 " " NAG I 1 " - " ASN B 727 " " NAG J 1 " - " ASN C 413 " " NAG K 1 " - " ASN D 413 " Time building additional restraints: 9.92 Conformation dependent library (CDL) restraints added in 4.5 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 22 sheets defined 39.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.885A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.883A pdb=" N LEU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 438 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 500 through 511 removed outlier: 4.815A pdb=" N THR A 504 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 583 through 601 Processing helix chain 'A' and resid 611 through 635 removed outlier: 3.680A pdb=" N TYR A 614 " --> pdb=" O TYR A 611 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 616 " --> pdb=" O ARG A 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 619 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 622 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 623 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 626 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A 629 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 630 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A 633 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 661 Processing helix chain 'A' and resid 669 through 678 removed outlier: 3.656A pdb=" N LYS A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 709 through 717 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 728 through 749 Processing helix chain 'B' and resid 124 through 135 removed outlier: 3.741A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 removed outlier: 3.539A pdb=" N ASN B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.808A pdb=" N ARG B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.576A pdb=" N LYS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 438 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.942A pdb=" N TRP B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 511 removed outlier: 5.028A pdb=" N THR B 504 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 545 No H-bonds generated for 'chain 'B' and resid 542 through 545' Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 583 through 602 Processing helix chain 'B' and resid 613 through 635 removed outlier: 3.563A pdb=" N LEU B 619 " --> pdb=" O SER B 616 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 622 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 623 " --> pdb=" O SER B 620 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 626 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN B 627 " --> pdb=" O ASP B 624 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA B 630 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 632 " --> pdb=" O ARG B 629 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 633 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 661 Processing helix chain 'B' and resid 669 through 681 removed outlier: 3.912A pdb=" N LYS B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 674 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 681 " --> pdb=" O ARG B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 709 through 721 removed outlier: 4.396A pdb=" N LEU B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN B 721 " --> pdb=" O LYS B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 749 Processing helix chain 'C' and resid 13 through 29 removed outlier: 4.778A pdb=" N LYS C 18 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL C 29 " --> pdb=" O HIS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 64 through 67 No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 125 through 134 removed outlier: 5.323A pdb=" N ILE C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Proline residue: C 131 - end of helix Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 146 through 151 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 260 through 274 removed outlier: 3.583A pdb=" N GLN C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU C 272 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 374 through 383 removed outlier: 3.680A pdb=" N ALA C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 461 through 471 removed outlier: 4.047A pdb=" N ASN C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 496 No H-bonds generated for 'chain 'C' and resid 493 through 496' Processing helix chain 'C' and resid 516 through 526 Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 549 through 552 No H-bonds generated for 'chain 'C' and resid 549 through 552' Processing helix chain 'C' and resid 594 through 608 removed outlier: 3.804A pdb=" N HIS C 606 " --> pdb=" O ARG C 602 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 608 " --> pdb=" O GLN C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 651 Processing helix chain 'C' and resid 653 through 660 Processing helix chain 'C' and resid 669 through 675 Processing helix chain 'D' and resid 13 through 28 Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 64 through 67 No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.777A pdb=" N LEU D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 131 through 135' Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'D' and resid 188 through 196 removed outlier: 3.599A pdb=" N PHE D 192 " --> pdb=" O TYR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 213 Processing helix chain 'D' and resid 217 through 222 removed outlier: 3.715A pdb=" N GLN D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.746A pdb=" N ARG D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 361 Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'D' and resid 393 through 401 removed outlier: 3.793A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 removed outlier: 3.625A pdb=" N LEU D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 470 " --> pdb=" O LEU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 526 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 594 through 607 removed outlier: 3.513A pdb=" N GLN D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 Processing helix chain 'D' and resid 653 through 665 removed outlier: 4.220A pdb=" N LEU D 662 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 663 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LYS D 664 " --> pdb=" O GLY D 660 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N CYS D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 676 removed outlier: 3.571A pdb=" N THR D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 209 removed outlier: 3.923A pdb=" N ARG E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 239 removed outlier: 4.942A pdb=" N HIS E 222 " --> pdb=" O GLU E 219 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS E 223 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 225 " --> pdb=" O HIS E 222 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL E 226 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN E 227 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 230 " --> pdb=" O ASN E 227 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN E 231 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER E 234 " --> pdb=" O ASN E 231 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 237 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 255 removed outlier: 3.506A pdb=" N THR E 246 " --> pdb=" O ARG E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 267 through 309 removed outlier: 3.840A pdb=" N ARG E 272 " --> pdb=" O ASP E 268 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS E 291 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ASN E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS E 309 " --> pdb=" O ASP E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 334 removed outlier: 3.643A pdb=" N LYS E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 363 removed outlier: 3.719A pdb=" N ARG E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS E 363 " --> pdb=" O ARG E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 406 Processing helix chain 'E' and resid 416 through 460 removed outlier: 4.519A pdb=" N ASP E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER E 439 " --> pdb=" O PHE E 435 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 476 removed outlier: 4.057A pdb=" N GLU E 466 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLU E 467 " --> pdb=" O HIS E 464 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 470 " --> pdb=" O GLU E 467 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE E 473 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP E 474 " --> pdb=" O LYS E 471 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER E 475 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 509 removed outlier: 3.964A pdb=" N ASN E 484 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 565 removed outlier: 4.298A pdb=" N ASN E 527 " --> pdb=" O LYS E 523 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU E 556 " --> pdb=" O TYR E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 588 Processing helix chain 'E' and resid 592 through 631 removed outlier: 4.027A pdb=" N LEU E 616 " --> pdb=" O LYS E 612 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 180 through 193 removed outlier: 3.871A pdb=" N LYS A 180 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N GLU A 398 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 10.619A pdb=" N ILE A 449 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 13.326A pdb=" N ASP A 400 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 15.064A pdb=" N ALA A 451 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 15.397A pdb=" N TYR A 402 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 16.469A pdb=" N TRP A 453 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 15.244A pdb=" N VAL A 404 " --> pdb=" O TRP A 453 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 227 through 230 removed outlier: 3.870A pdb=" N VAL A 200 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 214 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 202 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU A 212 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.806A pdb=" N ILE A 254 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 282 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE A 281 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN A 335 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 495 through 498 Processing sheet with id= E, first strand: chain 'B' and resid 180 through 193 removed outlier: 3.641A pdb=" N LYS B 180 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP B 453 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL B 404 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR B 481 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY B 406 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN B 483 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N GLN B 408 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 226 through 230 removed outlier: 5.865A pdb=" N ILE B 202 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU B 212 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.680A pdb=" N ILE B 254 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 495 through 498 Processing sheet with id= I, first strand: chain 'C' and resid 5 through 10 removed outlier: 6.494A pdb=" N SER C 36 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TRP C 8 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 38 " --> pdb=" O TRP C 8 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA C 10 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL C 40 " --> pdb=" O ALA C 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 60 through 62 removed outlier: 3.677A pdb=" N VAL C 60 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 81 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 253 " --> pdb=" O PRO C 79 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY C 301 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 244 through 246 removed outlier: 3.827A pdb=" N ALA C 244 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 224 through 226 removed outlier: 3.565A pdb=" N LYS C 233 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 342 through 347 Processing sheet with id= N, first strand: chain 'C' and resid 389 through 391 removed outlier: 3.712A pdb=" N LEU C 408 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 589 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 580 through 582 removed outlier: 3.907A pdb=" N ALA C 580 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.745A pdb=" N SER D 36 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TRP D 8 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA D 38 " --> pdb=" O TRP D 8 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA D 10 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 40 " --> pdb=" O ALA D 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.692A pdb=" N VAL D 60 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL D 81 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA D 253 " --> pdb=" O PRO D 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 244 through 247 removed outlier: 3.856A pdb=" N ALA D 244 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 100 through 102 Processing sheet with id= T, first strand: chain 'D' and resid 342 through 345 Processing sheet with id= U, first strand: chain 'D' and resid 388 through 391 removed outlier: 3.604A pdb=" N LEU D 408 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR D 589 " --> pdb=" O PRO D 406 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS D 637 " --> pdb=" O ASN D 411 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 580 through 582 removed outlier: 3.903A pdb=" N ALA D 580 " --> pdb=" O ALA D 428 " (cutoff:3.500A) 882 hydrogen bonds defined for protein. 2424 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: 8.45 Time building geometry restraints manager: 10.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8008 1.34 - 1.47: 6440 1.47 - 1.60: 10762 1.60 - 1.73: 1 1.73 - 1.87: 176 Bond restraints: 25387 Sorted by residual: bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C1 NAG D 707 " pdb=" O5 NAG D 707 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CA GLU B 582 " pdb=" CB GLU B 582 " ideal model delta sigma weight residual 1.527 1.607 -0.080 2.48e-02 1.63e+03 1.04e+01 bond pdb=" CG1 ILE E 175 " pdb=" CD1 ILE E 175 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.25e+00 bond pdb=" N GLU A 759 " pdb=" CA GLU A 759 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.23e-02 6.61e+03 6.14e+00 ... (remaining 25382 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.71: 400 104.71 - 112.70: 13160 112.70 - 120.70: 12814 120.70 - 128.69: 7742 128.69 - 136.69: 211 Bond angle restraints: 34327 Sorted by residual: angle pdb=" C ALA E 569 " pdb=" N ASN E 570 " pdb=" CA ASN E 570 " ideal model delta sigma weight residual 122.07 135.44 -13.37 1.43e+00 4.89e-01 8.74e+01 angle pdb=" C GLN E 317 " pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta sigma weight residual 121.70 136.69 -14.99 1.80e+00 3.09e-01 6.93e+01 angle pdb=" C ILE A 756 " pdb=" N ASP A 757 " pdb=" CA ASP A 757 " ideal model delta sigma weight residual 121.70 136.04 -14.34 1.80e+00 3.09e-01 6.35e+01 angle pdb=" C ASN A 758 " pdb=" N GLU A 759 " pdb=" CA GLU A 759 " ideal model delta sigma weight residual 120.82 130.15 -9.33 1.50e+00 4.44e-01 3.87e+01 angle pdb=" C ASP E 407 " pdb=" N GLY E 408 " pdb=" CA GLY E 408 " ideal model delta sigma weight residual 121.70 132.65 -10.95 1.80e+00 3.09e-01 3.70e+01 ... (remaining 34322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.95: 14981 26.95 - 53.89: 529 53.89 - 80.84: 40 80.84 - 107.79: 27 107.79 - 134.73: 4 Dihedral angle restraints: 15581 sinusoidal: 6519 harmonic: 9062 Sorted by residual: dihedral pdb=" CA ALA E 569 " pdb=" C ALA E 569 " pdb=" N ASN E 570 " pdb=" CA ASN E 570 " ideal model delta harmonic sigma weight residual 180.00 45.27 134.73 0 5.00e+00 4.00e-02 7.26e+02 dihedral pdb=" CB CYS C 161 " pdb=" SG CYS C 161 " pdb=" SG CYS C 179 " pdb=" CB CYS C 179 " ideal model delta sinusoidal sigma weight residual -86.00 -175.56 89.56 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS C 345 " pdb=" SG CYS C 345 " pdb=" SG CYS C 377 " pdb=" CB CYS C 377 " ideal model delta sinusoidal sigma weight residual 93.00 -177.62 -89.38 1 1.00e+01 1.00e-02 9.50e+01 ... (remaining 15578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.480: 3770 0.480 - 0.960: 1 0.960 - 1.440: 0 1.440 - 1.920: 0 1.920 - 2.400: 1 Chirality restraints: 3772 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C1 NAG J 2 " pdb=" C1 NAG J 2 " both_signs ideal model delta sigma weight residual False 2.40 0.00 2.40 2.00e-02 2.50e+03 1.44e+04 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 317 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CG LEU E 447 " pdb=" CB LEU E 447 " pdb=" CD1 LEU E 447 " pdb=" CD2 LEU E 447 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 3769 not shown) Planarity restraints: 4436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 691 " -0.058 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO B 692 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 692 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 692 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 521 " -0.021 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE E 521 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE E 521 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE E 521 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE E 521 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 521 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE E 521 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 334 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO C 335 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " 0.041 5.00e-02 4.00e+02 ... (remaining 4433 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 159 2.55 - 3.14: 18509 3.14 - 3.72: 37361 3.72 - 4.31: 51572 4.31 - 4.90: 85260 Nonbonded interactions: 192861 Sorted by model distance: nonbonded pdb="FE FE C 703 " pdb=" O1 CO3 C 704 " model vdw 1.960 2.260 nonbonded pdb=" OD1 ASP D 63 " pdb="FE FE D 703 " model vdw 2.005 2.260 nonbonded pdb="FE FE D 703 " pdb=" O3 CO3 D 704 " model vdw 2.012 2.260 nonbonded pdb=" OH TYR C 95 " pdb="FE FE C 703 " model vdw 2.015 2.260 nonbonded pdb=" OH TYR D 188 " pdb="FE FE D 703 " model vdw 2.040 2.260 ... (remaining 192856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.000 Extract box with map and model: 2.440 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 65.710 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.009 0.104 25387 Z= 0.608 Angle : 1.192 14.988 34327 Z= 0.662 Chirality : 0.074 2.400 3772 Planarity : 0.008 0.089 4426 Dihedral : 13.129 134.734 9621 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 1.12 % Allowed : 7.30 % Favored : 91.59 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.23 % Twisted Proline : 0.83 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.12), residues: 3096 helix: -2.78 (0.10), residues: 1242 sheet: -1.75 (0.26), residues: 346 loop : -2.17 (0.13), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP C 358 HIS 0.023 0.003 HIS A 515 PHE 0.055 0.004 PHE E 521 TYR 0.037 0.004 TYR B 643 ARG 0.023 0.001 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 343 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9006 (mt) REVERT: A 671 MET cc_start: 0.8625 (mmm) cc_final: 0.8193 (mmt) REVERT: B 365 MET cc_start: 0.9059 (mmm) cc_final: 0.8613 (mmm) REVERT: B 384 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9138 (pp) REVERT: C 367 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 389 MET cc_start: 0.8760 (ttt) cc_final: 0.8452 (ttt) REVERT: D 26 MET cc_start: 0.8538 (mmm) cc_final: 0.7986 (mpp) REVERT: D 267 LEU cc_start: 0.8731 (tm) cc_final: 0.8204 (tp) REVERT: D 323 ILE cc_start: 0.9427 (tt) cc_final: 0.9030 (tt) REVERT: E 185 ASN cc_start: 0.7972 (m-40) cc_final: 0.7741 (t0) REVERT: E 220 ASP cc_start: 0.7914 (t0) cc_final: 0.7292 (p0) REVERT: E 244 LYS cc_start: 0.8203 (tmmm) cc_final: 0.7876 (ttmt) REVERT: E 261 LYS cc_start: 0.8297 (tmtp) cc_final: 0.8071 (mmtp) REVERT: E 321 TYR cc_start: 0.7008 (t80) cc_final: 0.6566 (t80) REVERT: E 525 TYR cc_start: 0.7577 (t80) cc_final: 0.7147 (t80) REVERT: E 601 MET cc_start: 0.7740 (mtt) cc_final: 0.7486 (mtm) REVERT: E 626 GLN cc_start: 0.7571 (tt0) cc_final: 0.7363 (tm-30) outliers start: 30 outliers final: 6 residues processed: 367 average time/residue: 0.4018 time to fit residues: 224.5222 Evaluate side-chains 175 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 279 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 171 ASN A 206 ASN A 348 ASN A 379 ASN A 515 HIS A 603 HIS A 626 ASN A 715 ASN B 171 ASN B 302 HIS B 483 ASN B 608 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 715 ASN C 25 HIS C 55 ASN C 213 ASN C 536 GLN C 540 GLN C 546 ASN C 603 GLN C 618 ASN D 25 HIS D 55 ASN D 172 GLN D 268 ASN D 383 ASN D 411 ASN D 417 ASN D 469 ASN D 618 ASN E 174 ASN E 245 ASN E 252 ASN E 289 ASN E 314 GLN ** E 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 ASN E 483 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25387 Z= 0.187 Angle : 0.641 11.361 34327 Z= 0.332 Chirality : 0.058 2.400 3772 Planarity : 0.005 0.055 4426 Dihedral : 9.903 111.921 3707 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 2.27 % Allowed : 10.24 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.14), residues: 3096 helix: -0.93 (0.13), residues: 1256 sheet: -1.20 (0.27), residues: 348 loop : -1.68 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 740 HIS 0.009 0.001 HIS D 473 PHE 0.023 0.002 PHE B 726 TYR 0.029 0.002 TYR C 514 ARG 0.007 0.001 ARG E 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 202 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8695 (t) REVERT: B 384 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9052 (pt) REVERT: C 389 MET cc_start: 0.8655 (ttt) cc_final: 0.8425 (ttt) REVERT: C 421 THR cc_start: 0.8502 (m) cc_final: 0.8148 (p) REVERT: D 26 MET cc_start: 0.8684 (mmm) cc_final: 0.8015 (mpp) REVERT: D 323 ILE cc_start: 0.9326 (tt) cc_final: 0.8932 (tt) REVERT: D 382 MET cc_start: 0.8300 (mtp) cc_final: 0.8020 (mtp) REVERT: D 411 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8259 (m110) REVERT: D 497 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8769 (tt) REVERT: E 220 ASP cc_start: 0.7749 (t0) cc_final: 0.7455 (m-30) REVERT: E 244 LYS cc_start: 0.8197 (tmmm) cc_final: 0.7753 (ttmt) REVERT: E 261 LYS cc_start: 0.8239 (tmtp) cc_final: 0.7941 (mmtp) REVERT: E 264 ARG cc_start: 0.8792 (mpp80) cc_final: 0.7985 (mmm160) REVERT: E 321 TYR cc_start: 0.6934 (t80) cc_final: 0.6545 (t80) REVERT: E 601 MET cc_start: 0.7797 (mtt) cc_final: 0.7532 (mtm) REVERT: E 612 LYS cc_start: 0.8580 (tptp) cc_final: 0.8328 (tptt) REVERT: E 626 GLN cc_start: 0.7713 (tt0) cc_final: 0.7283 (tm-30) outliers start: 61 outliers final: 30 residues processed: 255 average time/residue: 0.3763 time to fit residues: 153.0599 Evaluate side-chains 182 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 385 ILE Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 232 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 280 optimal weight: 0.8980 chunk 302 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 475 HIS A 493 ASN B 401 HIS ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 604 GLN D 110 ASN D 383 ASN D 541 ASN D 584 ASN E 185 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25387 Z= 0.354 Angle : 0.675 10.840 34327 Z= 0.348 Chirality : 0.060 2.400 3772 Planarity : 0.005 0.050 4426 Dihedral : 8.833 111.601 3704 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 3.05 % Allowed : 11.73 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3096 helix: -0.19 (0.14), residues: 1249 sheet: -1.22 (0.27), residues: 360 loop : -1.46 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 740 HIS 0.008 0.001 HIS C 349 PHE 0.022 0.002 PHE A 442 TYR 0.025 0.002 TYR C 514 ARG 0.007 0.001 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 151 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7889 (mm-40) REVERT: A 375 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7680 (pt) REVERT: B 384 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9137 (pt) REVERT: B 565 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7302 (p90) REVERT: B 679 MET cc_start: 0.8908 (mtt) cc_final: 0.8597 (mtt) REVERT: B 720 LYS cc_start: 0.8538 (ptmt) cc_final: 0.8325 (ptpp) REVERT: C 225 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7657 (pp) REVERT: C 367 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8025 (mm-30) REVERT: C 421 THR cc_start: 0.8502 (m) cc_final: 0.8090 (p) REVERT: C 534 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7799 (ptmt) REVERT: C 542 THR cc_start: 0.7442 (m) cc_final: 0.6906 (p) REVERT: C 604 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8590 (mm-40) REVERT: D 46 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8474 (mm) REVERT: D 382 MET cc_start: 0.8435 (mtp) cc_final: 0.8043 (mtp) REVERT: D 497 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8677 (tt) REVERT: E 211 TYR cc_start: 0.6518 (m-10) cc_final: 0.6308 (m-10) REVERT: E 220 ASP cc_start: 0.7765 (t0) cc_final: 0.7495 (m-30) REVERT: E 244 LYS cc_start: 0.8144 (tmmm) cc_final: 0.7806 (ttmt) REVERT: E 321 TYR cc_start: 0.6922 (t80) cc_final: 0.6611 (t80) REVERT: E 335 MET cc_start: 0.6904 (tpp) cc_final: 0.5370 (ttt) REVERT: E 352 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8926 (mt) REVERT: E 612 LYS cc_start: 0.8555 (tptp) cc_final: 0.8334 (tptt) outliers start: 82 outliers final: 45 residues processed: 224 average time/residue: 0.3567 time to fit residues: 129.8196 Evaluate side-chains 191 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 138 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 603 GLN Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 675 THR Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 chunk 145 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 281 optimal weight: 0.9990 chunk 297 optimal weight: 20.0000 chunk 146 optimal weight: 0.6980 chunk 266 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN D 383 ASN D 411 ASN E 185 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 25387 Z= 0.151 Angle : 0.573 10.632 34327 Z= 0.292 Chirality : 0.057 2.400 3772 Planarity : 0.004 0.046 4426 Dihedral : 8.108 109.424 3704 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 2.83 % Allowed : 12.47 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3096 helix: 0.50 (0.15), residues: 1247 sheet: -1.04 (0.27), residues: 360 loop : -1.32 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 740 HIS 0.010 0.001 HIS D 585 PHE 0.027 0.001 PHE E 462 TYR 0.034 0.001 TYR C 514 ARG 0.006 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 158 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7853 (mm-40) REVERT: A 375 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7789 (pt) REVERT: B 198 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8149 (p0) REVERT: B 384 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9081 (pt) REVERT: B 565 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.6978 (p90) REVERT: C 225 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7569 (pp) REVERT: C 271 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: C 421 THR cc_start: 0.8421 (m) cc_final: 0.8061 (p) REVERT: C 542 THR cc_start: 0.7494 (m) cc_final: 0.6996 (p) REVERT: D 85 TYR cc_start: 0.8270 (m-10) cc_final: 0.8036 (m-10) REVERT: D 382 MET cc_start: 0.8284 (mtp) cc_final: 0.7933 (mtp) REVERT: D 497 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8666 (tt) REVERT: E 244 LYS cc_start: 0.8085 (tmmm) cc_final: 0.7802 (ttmt) REVERT: E 292 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7928 (m-40) REVERT: E 321 TYR cc_start: 0.6742 (t80) cc_final: 0.6450 (t80) REVERT: E 525 TYR cc_start: 0.7890 (t80) cc_final: 0.7445 (t80) outliers start: 76 outliers final: 40 residues processed: 225 average time/residue: 0.3472 time to fit residues: 129.1053 Evaluate side-chains 182 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 134 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 221 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 254 optimal weight: 0.4980 chunk 205 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 0.1980 chunk 267 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN D 383 ASN E 185 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 628 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25387 Z= 0.161 Angle : 0.552 10.724 34327 Z= 0.280 Chirality : 0.057 2.400 3772 Planarity : 0.003 0.041 4426 Dihedral : 7.720 108.791 3704 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 2.76 % Allowed : 12.81 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3096 helix: 0.89 (0.15), residues: 1250 sheet: -0.91 (0.27), residues: 360 loop : -1.21 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 740 HIS 0.006 0.001 HIS D 585 PHE 0.020 0.001 PHE A 120 TYR 0.020 0.001 TYR B 683 ARG 0.004 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 157 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7962 (pt) REVERT: A 714 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6733 (tm-30) REVERT: B 198 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8151 (p0) REVERT: B 384 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9078 (pt) REVERT: B 510 MET cc_start: 0.8283 (mmm) cc_final: 0.7964 (mtt) REVERT: B 565 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.6898 (p90) REVERT: C 225 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7607 (pp) REVERT: C 271 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: C 421 THR cc_start: 0.8414 (m) cc_final: 0.8056 (p) REVERT: C 466 LEU cc_start: 0.7593 (tp) cc_final: 0.7368 (tt) REVERT: C 534 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7442 (ptpp) REVERT: C 542 THR cc_start: 0.7534 (m) cc_final: 0.7045 (p) REVERT: C 630 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9097 (tp) REVERT: D 382 MET cc_start: 0.8283 (mtp) cc_final: 0.7915 (mtp) REVERT: D 497 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8690 (tt) REVERT: D 564 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7103 (mt) REVERT: E 244 LYS cc_start: 0.7956 (tmmm) cc_final: 0.7738 (ttmt) REVERT: E 321 TYR cc_start: 0.6760 (t80) cc_final: 0.6437 (t80) REVERT: E 555 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8687 (mm) outliers start: 74 outliers final: 47 residues processed: 225 average time/residue: 0.3362 time to fit residues: 125.1518 Evaluate side-chains 201 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 144 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 58 optimal weight: 0.1980 chunk 174 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 0.0040 chunk 156 optimal weight: 0.0980 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN E 185 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 464 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25387 Z= 0.156 Angle : 0.545 15.538 34327 Z= 0.277 Chirality : 0.056 2.400 3772 Planarity : 0.003 0.037 4426 Dihedral : 7.434 108.020 3702 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 2.94 % Allowed : 13.55 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3096 helix: 1.16 (0.15), residues: 1250 sheet: -0.83 (0.27), residues: 374 loop : -1.10 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 740 HIS 0.006 0.001 HIS D 585 PHE 0.030 0.001 PHE E 462 TYR 0.021 0.001 TYR B 683 ARG 0.005 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 155 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6931 (tm-30) REVERT: B 198 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8182 (p0) REVERT: B 384 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9077 (pt) REVERT: B 510 MET cc_start: 0.8338 (mmm) cc_final: 0.8134 (mtt) REVERT: B 565 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.6924 (p90) REVERT: C 225 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7585 (pp) REVERT: C 271 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: C 421 THR cc_start: 0.8404 (m) cc_final: 0.8054 (p) REVERT: C 542 THR cc_start: 0.7587 (m) cc_final: 0.7074 (p) REVERT: D 205 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8837 (m) REVERT: D 382 MET cc_start: 0.8288 (mtp) cc_final: 0.7921 (mtp) REVERT: D 497 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8702 (tt) REVERT: D 564 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7082 (mt) REVERT: E 244 LYS cc_start: 0.7955 (tmmm) cc_final: 0.7700 (ttmt) REVERT: E 321 TYR cc_start: 0.6669 (t80) cc_final: 0.6398 (t80) REVERT: E 525 TYR cc_start: 0.7995 (t80) cc_final: 0.7529 (t80) outliers start: 79 outliers final: 54 residues processed: 224 average time/residue: 0.3387 time to fit residues: 124.4697 Evaluate side-chains 199 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 137 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 614 TYR Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 217 optimal weight: 0.1980 chunk 168 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 296 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 640 GLN C 213 ASN ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN D 383 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25387 Z= 0.281 Angle : 0.603 15.198 34327 Z= 0.307 Chirality : 0.058 2.400 3772 Planarity : 0.004 0.039 4426 Dihedral : 7.449 108.644 3702 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.57 % Rotamer: Outliers : 3.35 % Allowed : 13.70 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3096 helix: 1.11 (0.15), residues: 1250 sheet: -0.86 (0.27), residues: 360 loop : -1.13 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 740 HIS 0.006 0.001 HIS D 585 PHE 0.019 0.002 PHE A 120 TYR 0.017 0.002 TYR B 683 ARG 0.004 0.001 ARG B 698 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 143 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7075 (tm-30) REVERT: B 198 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8243 (p0) REVERT: B 365 MET cc_start: 0.8915 (mmm) cc_final: 0.8652 (mmm) REVERT: B 384 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9130 (pt) REVERT: B 565 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7293 (p90) REVERT: C 225 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7752 (pp) REVERT: C 271 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: C 421 THR cc_start: 0.8401 (m) cc_final: 0.7983 (p) REVERT: C 542 THR cc_start: 0.7599 (m) cc_final: 0.7038 (p) REVERT: C 629 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8485 (pp) REVERT: D 205 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8894 (m) REVERT: D 497 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8735 (tt) REVERT: D 564 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7032 (mt) REVERT: E 244 LYS cc_start: 0.8035 (tmmm) cc_final: 0.7803 (ttmt) REVERT: E 321 TYR cc_start: 0.6646 (t80) cc_final: 0.6367 (t80) REVERT: E 352 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8922 (mt) REVERT: E 522 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7218 (mtpt) outliers start: 90 outliers final: 63 residues processed: 225 average time/residue: 0.3310 time to fit residues: 123.1230 Evaluate side-chains 211 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 137 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 614 TYR Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 723 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 385 ILE Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 522 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 574 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 202 optimal weight: 0.4980 chunk 146 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 233 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN C 536 GLN D 383 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 25387 Z= 0.161 Angle : 0.549 14.534 34327 Z= 0.279 Chirality : 0.056 2.400 3772 Planarity : 0.003 0.043 4426 Dihedral : 7.266 107.513 3702 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 2.94 % Allowed : 14.41 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3096 helix: 1.38 (0.15), residues: 1248 sheet: -0.77 (0.27), residues: 374 loop : -1.01 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 740 HIS 0.007 0.001 HIS D 585 PHE 0.018 0.001 PHE D 22 TYR 0.023 0.001 TYR B 683 ARG 0.004 0.000 ARG C 475 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 145 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8180 (p0) REVERT: B 384 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9086 (pt) REVERT: B 565 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7178 (p90) REVERT: C 225 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7683 (pp) REVERT: C 271 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: C 382 MET cc_start: 0.7568 (mtt) cc_final: 0.7281 (mtt) REVERT: C 421 THR cc_start: 0.8371 (m) cc_final: 0.7975 (p) REVERT: C 542 THR cc_start: 0.7595 (m) cc_final: 0.7040 (p) REVERT: D 497 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8710 (tt) REVERT: E 244 LYS cc_start: 0.7965 (tmmm) cc_final: 0.7742 (ttmt) REVERT: E 352 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8853 (mt) REVERT: E 525 TYR cc_start: 0.8042 (t80) cc_final: 0.7585 (t80) outliers start: 79 outliers final: 57 residues processed: 218 average time/residue: 0.3522 time to fit residues: 126.9311 Evaluate side-chains 202 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 138 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 614 TYR Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 723 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.5980 chunk 284 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 166 optimal weight: 0.0010 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 451 HIS D 383 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25387 Z= 0.163 Angle : 0.547 14.098 34327 Z= 0.275 Chirality : 0.056 2.400 3772 Planarity : 0.003 0.045 4426 Dihedral : 7.099 107.115 3702 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 2.72 % Allowed : 14.48 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3096 helix: 1.49 (0.15), residues: 1246 sheet: -0.72 (0.26), residues: 392 loop : -0.96 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 264 HIS 0.007 0.001 HIS D 585 PHE 0.040 0.001 PHE A 298 TYR 0.020 0.001 TYR E 218 ARG 0.004 0.000 ARG C 475 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 147 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8180 (p0) REVERT: B 384 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9090 (pt) REVERT: B 565 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7286 (p90) REVERT: C 225 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7683 (pp) REVERT: C 271 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7137 (pt0) REVERT: C 421 THR cc_start: 0.8369 (m) cc_final: 0.7977 (p) REVERT: C 542 THR cc_start: 0.7679 (m) cc_final: 0.7108 (p) REVERT: C 550 TRP cc_start: 0.7307 (p-90) cc_final: 0.7091 (p-90) REVERT: D 205 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8860 (m) REVERT: D 564 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7084 (mt) REVERT: E 352 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8843 (mt) REVERT: E 525 TYR cc_start: 0.8060 (t80) cc_final: 0.7571 (t80) outliers start: 73 outliers final: 59 residues processed: 215 average time/residue: 0.3798 time to fit residues: 135.3300 Evaluate side-chains 202 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 135 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 614 TYR Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 723 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 574 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 chunk 282 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 149 optimal weight: 0.3980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN D 383 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25387 Z= 0.242 Angle : 0.586 14.223 34327 Z= 0.296 Chirality : 0.058 2.400 3772 Planarity : 0.003 0.042 4426 Dihedral : 7.150 107.214 3702 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 2.68 % Allowed : 14.78 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3096 helix: 1.43 (0.15), residues: 1246 sheet: -0.77 (0.27), residues: 378 loop : -0.97 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 740 HIS 0.009 0.001 HIS D 585 PHE 0.029 0.001 PHE A 298 TYR 0.021 0.001 TYR C 514 ARG 0.005 0.000 ARG B 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 136 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8215 (p0) REVERT: B 384 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9119 (pt) REVERT: B 510 MET cc_start: 0.8475 (mmm) cc_final: 0.8133 (mtt) REVERT: B 565 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7472 (p90) REVERT: C 225 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7760 (pp) REVERT: C 271 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7271 (pt0) REVERT: C 421 THR cc_start: 0.8356 (m) cc_final: 0.7919 (p) REVERT: C 550 TRP cc_start: 0.7509 (p-90) cc_final: 0.7297 (p-90) REVERT: D 205 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8910 (m) REVERT: D 382 MET cc_start: 0.8302 (mtp) cc_final: 0.8049 (mtp) REVERT: D 564 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7096 (mt) REVERT: E 352 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8902 (mt) REVERT: E 517 GLU cc_start: 0.2695 (OUTLIER) cc_final: 0.2429 (pt0) REVERT: E 525 TYR cc_start: 0.8049 (t80) cc_final: 0.7519 (t80) outliers start: 72 outliers final: 58 residues processed: 203 average time/residue: 0.3223 time to fit residues: 110.4710 Evaluate side-chains 199 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 132 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 614 TYR Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 723 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 517 GLU Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.7980 chunk 260 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN D 383 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.109441 restraints weight = 38851.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.109859 restraints weight = 38506.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110825 restraints weight = 32486.794| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25387 Z= 0.152 Angle : 0.552 13.832 34327 Z= 0.278 Chirality : 0.056 2.400 3772 Planarity : 0.003 0.042 4426 Dihedral : 6.946 106.036 3702 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.46 % Allowed : 15.04 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3096 helix: 1.54 (0.15), residues: 1254 sheet: -0.62 (0.27), residues: 378 loop : -0.91 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 264 HIS 0.010 0.001 HIS E 628 PHE 0.027 0.001 PHE A 298 TYR 0.021 0.001 TYR C 514 ARG 0.005 0.000 ARG B 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4080.61 seconds wall clock time: 76 minutes 27.94 seconds (4587.94 seconds total)