Starting phenix.real_space_refine on Wed Mar 20 02:00:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr2_0487/03_2024/6nr2_0487_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr2_0487/03_2024/6nr2_0487.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr2_0487/03_2024/6nr2_0487_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr2_0487/03_2024/6nr2_0487_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr2_0487/03_2024/6nr2_0487_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr2_0487/03_2024/6nr2_0487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr2_0487/03_2024/6nr2_0487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr2_0487/03_2024/6nr2_0487_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr2_0487/03_2024/6nr2_0487_neut_trim_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 124 5.16 5 C 16944 2.51 5 N 4264 2.21 5 O 4444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A PHE 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1025": "NH1" <-> "NH2" Residue "B PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B ARG 884": "NH1" <-> "NH2" Residue "B PHE 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1025": "NH1" <-> "NH2" Residue "C PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 841": "NH1" <-> "NH2" Residue "C ARG 884": "NH1" <-> "NH2" Residue "C PHE 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1025": "NH1" <-> "NH2" Residue "D PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ARG 884": "NH1" <-> "NH2" Residue "D PHE 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1025": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25788 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6393 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 21, 'TRANS': 837} Chain breaks: 14 Unresolved non-hydrogen bonds: 638 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 487 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 5, 'ASN:plan1': 8, 'TYR:plan': 1, 'UNK:plan-1': 45, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 372 Chain: "B" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6393 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 21, 'TRANS': 837} Chain breaks: 14 Unresolved non-hydrogen bonds: 638 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 487 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 5, 'ASN:plan1': 8, 'TYR:plan': 1, 'UNK:plan-1': 45, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 372 Chain: "C" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6393 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 21, 'TRANS': 837} Chain breaks: 14 Unresolved non-hydrogen bonds: 638 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 487 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 5, 'ASN:plan1': 8, 'TYR:plan': 1, 'UNK:plan-1': 45, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 372 Chain: "D" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6393 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 21, 'TRANS': 837} Chain breaks: 14 Unresolved non-hydrogen bonds: 638 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 487 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 5, 'ASN:plan1': 8, 'TYR:plan': 1, 'UNK:plan-1': 45, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 372 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'KXP': 1, 'KXS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'KXP:plan-3': 1, 'KXP:plan-2': 1, 'KXP:plan-6': 1, 'KXP:plan-5': 1, 'KXP:plan-4': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'KXP': 1, 'KXS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'KXP:plan-3': 1, 'KXP:plan-2': 1, 'KXP:plan-6': 1, 'KXP:plan-5': 1, 'KXP:plan-4': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'KXP': 1, 'KXS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'KXP:plan-3': 1, 'KXP:plan-2': 1, 'KXP:plan-6': 1, 'KXP:plan-5': 1, 'KXP:plan-4': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'KXP': 1, 'KXS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'KXP:plan-3': 1, 'KXP:plan-2': 1, 'KXP:plan-6': 1, 'KXP:plan-5': 1, 'KXP:plan-4': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 13.50, per 1000 atoms: 0.52 Number of scatterers: 25788 At special positions: 0 Unit cell: (152.28, 152.28, 144.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 12 15.00 O 4444 8.00 N 4264 7.00 C 16944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A1042 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B1042 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C1042 " distance=2.03 Simple disulfide: pdb=" SG CYS D 648 " - pdb=" SG CYS D1042 " 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 Time building additional restraints: 9.66 Conformation dependent library (CDL) restraints added in 4.6 seconds 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 4 sheets defined 68.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.11 Creating SS restraints... Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.892A pdb=" N LEU A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.959A pdb=" N ARG A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 455 through 467 removed outlier: 5.067A pdb=" N ASP A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 removed outlier: 4.381A pdb=" N PHE A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 490 through 497 Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.623A pdb=" N ASN A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.548A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 602 removed outlier: 3.698A pdb=" N SER A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 635 removed outlier: 3.890A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 656 through 663 removed outlier: 3.777A pdb=" N VAL A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 703 through 706 No H-bonds generated for 'chain 'A' and resid 703 through 706' Processing helix chain 'A' and resid 722 through 731 Processing helix chain 'A' and resid 734 through 757 Processing helix chain 'A' and resid 766 through 789 Processing helix chain 'A' and resid 791 through 794 No H-bonds generated for 'chain 'A' and resid 791 through 794' Processing helix chain 'A' and resid 797 through 817 removed outlier: 3.618A pdb=" N VAL A 814 " --> pdb=" O ILE A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 849 Processing helix chain 'A' and resid 856 through 888 removed outlier: 4.218A pdb=" N ARG A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 911 removed outlier: 3.560A pdb=" N PHE A 899 " --> pdb=" O TRP A 895 " (cutoff:3.500A) Proline residue: A 906 - end of helix Processing helix chain 'A' and resid 955 through 977 removed outlier: 3.600A pdb=" N MET A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN A 972 " --> pdb=" O ILE A 968 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1006 removed outlier: 3.680A pdb=" N SER A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1025 removed outlier: 5.278A pdb=" N ILE A1016 " --> pdb=" O PRO A1013 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL A1023 " --> pdb=" O ILE A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1067 removed outlier: 3.646A pdb=" N ALA A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A1065 " --> pdb=" O ASN A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1099 Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.892A pdb=" N LEU B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.960A pdb=" N ARG B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 384 Processing helix chain 'B' and resid 403 through 419 Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 455 through 467 removed outlier: 5.067A pdb=" N ASP B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 removed outlier: 4.381A pdb=" N PHE B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 490 through 497 Processing helix chain 'B' and resid 503 through 515 removed outlier: 3.622A pdb=" N ASN B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 532 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.547A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 602 removed outlier: 3.697A pdb=" N SER B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 635 removed outlier: 3.889A pdb=" N GLU B 613 " --> pdb=" O ASN B 609 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 656 through 663 removed outlier: 3.777A pdb=" N VAL B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 703 through 706 No H-bonds generated for 'chain 'B' and resid 703 through 706' Processing helix chain 'B' and resid 722 through 731 Processing helix chain 'B' and resid 734 through 757 Processing helix chain 'B' and resid 766 through 789 Processing helix chain 'B' and resid 791 through 794 No H-bonds generated for 'chain 'B' and resid 791 through 794' Processing helix chain 'B' and resid 797 through 817 removed outlier: 3.619A pdb=" N VAL B 814 " --> pdb=" O ILE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 849 Processing helix chain 'B' and resid 856 through 888 removed outlier: 4.217A pdb=" N ARG B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 911 removed outlier: 3.559A pdb=" N PHE B 899 " --> pdb=" O TRP B 895 " (cutoff:3.500A) Proline residue: B 906 - end of helix Processing helix chain 'B' and resid 955 through 977 removed outlier: 3.601A pdb=" N MET B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN B 972 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1006 removed outlier: 3.680A pdb=" N SER B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1025 removed outlier: 5.278A pdb=" N ILE B1016 " --> pdb=" O PRO B1013 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL B1023 " --> pdb=" O ILE B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1067 removed outlier: 3.646A pdb=" N ALA B1053 " --> pdb=" O ASN B1049 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP B1054 " --> pdb=" O GLU B1050 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B1065 " --> pdb=" O ASN B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1099 Processing helix chain 'C' and resid 126 through 135 Processing helix chain 'C' and resid 161 through 175 Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 278 through 287 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 354 through 361 removed outlier: 3.891A pdb=" N LEU C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.959A pdb=" N ARG C 368 " --> pdb=" O ARG C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 384 Processing helix chain 'C' and resid 403 through 419 Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 455 through 467 removed outlier: 5.066A pdb=" N ASP C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 removed outlier: 4.381A pdb=" N PHE C 477 " --> pdb=" O PHE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 490 through 497 Processing helix chain 'C' and resid 503 through 515 removed outlier: 3.622A pdb=" N ASN C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 532 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.548A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 602 removed outlier: 3.698A pdb=" N SER C 600 " --> pdb=" O LYS C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 635 removed outlier: 3.890A pdb=" N GLU C 613 " --> pdb=" O ASN C 609 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 Processing helix chain 'C' and resid 656 through 663 removed outlier: 3.777A pdb=" N VAL C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 683 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 703 through 706 No H-bonds generated for 'chain 'C' and resid 703 through 706' Processing helix chain 'C' and resid 722 through 731 Processing helix chain 'C' and resid 734 through 757 Processing helix chain 'C' and resid 766 through 789 Processing helix chain 'C' and resid 791 through 794 No H-bonds generated for 'chain 'C' and resid 791 through 794' Processing helix chain 'C' and resid 797 through 817 removed outlier: 3.618A pdb=" N VAL C 814 " --> pdb=" O ILE C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 849 Processing helix chain 'C' and resid 856 through 888 removed outlier: 4.217A pdb=" N ARG C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 911 removed outlier: 3.559A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) Proline residue: C 906 - end of helix Processing helix chain 'C' and resid 955 through 977 removed outlier: 3.600A pdb=" N MET C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN C 972 " --> pdb=" O ILE C 968 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1006 removed outlier: 3.679A pdb=" N SER C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1025 removed outlier: 5.277A pdb=" N ILE C1016 " --> pdb=" O PRO C1013 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL C1023 " --> pdb=" O ILE C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1067 removed outlier: 3.645A pdb=" N ALA C1053 " --> pdb=" O ASN C1049 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP C1054 " --> pdb=" O GLU C1050 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C1065 " --> pdb=" O ASN C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1099 Processing helix chain 'D' and resid 126 through 135 Processing helix chain 'D' and resid 161 through 175 Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 278 through 287 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 354 through 361 removed outlier: 3.892A pdb=" N LEU D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 368 removed outlier: 3.960A pdb=" N ARG D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 384 Processing helix chain 'D' and resid 403 through 419 Processing helix chain 'D' and resid 426 through 435 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 455 through 467 removed outlier: 5.066A pdb=" N ASP D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 removed outlier: 4.382A pdb=" N PHE D 477 " --> pdb=" O PHE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 487 No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 490 through 497 Processing helix chain 'D' and resid 503 through 515 removed outlier: 3.623A pdb=" N ASN D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 532 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.547A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 602 removed outlier: 3.698A pdb=" N SER D 600 " --> pdb=" O LYS D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 635 removed outlier: 3.889A pdb=" N GLU D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 Processing helix chain 'D' and resid 656 through 663 removed outlier: 3.778A pdb=" N VAL D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 683 Processing helix chain 'D' and resid 692 through 700 Processing helix chain 'D' and resid 703 through 706 No H-bonds generated for 'chain 'D' and resid 703 through 706' Processing helix chain 'D' and resid 722 through 731 Processing helix chain 'D' and resid 734 through 757 Processing helix chain 'D' and resid 766 through 789 Processing helix chain 'D' and resid 791 through 794 No H-bonds generated for 'chain 'D' and resid 791 through 794' Processing helix chain 'D' and resid 797 through 817 removed outlier: 3.619A pdb=" N VAL D 814 " --> pdb=" O ILE D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 849 Processing helix chain 'D' and resid 856 through 888 removed outlier: 4.218A pdb=" N ARG D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 911 removed outlier: 3.560A pdb=" N PHE D 899 " --> pdb=" O TRP D 895 " (cutoff:3.500A) Proline residue: D 906 - end of helix Processing helix chain 'D' and resid 955 through 977 removed outlier: 3.601A pdb=" N MET D 963 " --> pdb=" O VAL D 959 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN D 972 " --> pdb=" O ILE D 968 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1006 removed outlier: 3.680A pdb=" N SER D1006 " --> pdb=" O GLN D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1025 removed outlier: 5.277A pdb=" N ILE D1016 " --> pdb=" O PRO D1013 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL D1023 " --> pdb=" O ILE D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1067 removed outlier: 3.646A pdb=" N ALA D1053 " --> pdb=" O ASN D1049 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP D1054 " --> pdb=" O GLU D1050 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS D1065 " --> pdb=" O ASN D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1078 through 1099 Processing sheet with id= A, first strand: chain 'A' and resid 391 through 394 removed outlier: 6.219A pdb=" N CYS A 326 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE A 394 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL A 328 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA A 305 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 144 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASN A 208 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR A 181 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL A 210 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.219A pdb=" N CYS B 326 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE B 394 " --> pdb=" O CYS B 326 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B 328 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA B 305 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 144 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN B 208 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N THR B 181 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL B 210 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.217A pdb=" N CYS C 326 " --> pdb=" O THR C 392 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE C 394 " --> pdb=" O CYS C 326 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL C 328 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA C 305 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 144 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASN C 208 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N THR C 181 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C 210 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.218A pdb=" N CYS D 326 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE D 394 " --> pdb=" O CYS D 326 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL D 328 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 144 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASN D 208 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR D 181 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL D 210 " --> pdb=" O THR D 181 " (cutoff:3.500A) 1500 hydrogen bonds defined for protein. 4392 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: 8.35 Time building geometry restraints manager: 10.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3956 1.31 - 1.44: 7544 1.44 - 1.56: 14664 1.56 - 1.69: 16 1.69 - 1.81: 184 Bond restraints: 26364 Sorted by residual: bond pdb=" C08 KXS C1302 " pdb=" N10 KXS C1302 " ideal model delta sigma weight residual 1.355 1.446 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C08 KXS B1302 " pdb=" N10 KXS B1302 " ideal model delta sigma weight residual 1.355 1.446 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C08 KXS A1302 " pdb=" N10 KXS A1302 " ideal model delta sigma weight residual 1.355 1.446 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C08 KXS D1302 " pdb=" N10 KXS D1302 " ideal model delta sigma weight residual 1.355 1.446 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" N LYS D 762 " pdb=" CA LYS D 762 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.23e-02 6.61e+03 6.87e+00 ... (remaining 26359 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.87: 382 105.87 - 112.91: 14359 112.91 - 119.95: 8555 119.95 - 126.99: 12312 126.99 - 134.03: 348 Bond angle restraints: 35956 Sorted by residual: angle pdb=" C GLN B 761 " pdb=" N LYS B 762 " pdb=" CA LYS B 762 " ideal model delta sigma weight residual 120.82 131.08 -10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" C GLN C 761 " pdb=" N LYS C 762 " pdb=" CA LYS C 762 " ideal model delta sigma weight residual 120.82 131.07 -10.25 1.50e+00 4.44e-01 4.67e+01 angle pdb=" C GLN D 761 " pdb=" N LYS D 762 " pdb=" CA LYS D 762 " ideal model delta sigma weight residual 120.82 131.05 -10.23 1.50e+00 4.44e-01 4.65e+01 angle pdb=" C GLN A 761 " pdb=" N LYS A 762 " pdb=" CA LYS A 762 " ideal model delta sigma weight residual 120.82 131.05 -10.23 1.50e+00 4.44e-01 4.65e+01 angle pdb=" N GLN C 459 " pdb=" CA GLN C 459 " pdb=" C GLN C 459 " ideal model delta sigma weight residual 111.11 116.63 -5.52 1.20e+00 6.94e-01 2.12e+01 ... (remaining 35951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 14896 21.24 - 42.47: 324 42.47 - 63.71: 28 63.71 - 84.94: 16 84.94 - 106.18: 24 Dihedral angle restraints: 15288 sinusoidal: 5156 harmonic: 10132 Sorted by residual: dihedral pdb=" CA MET A 858 " pdb=" C MET A 858 " pdb=" N LEU A 859 " pdb=" CA LEU A 859 " ideal model delta harmonic sigma weight residual -180.00 -152.23 -27.77 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA MET C 858 " pdb=" C MET C 858 " pdb=" N LEU C 859 " pdb=" CA LEU C 859 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA MET D 858 " pdb=" C MET D 858 " pdb=" N LEU D 859 " pdb=" CA LEU D 859 " ideal model delta harmonic sigma weight residual -180.00 -152.26 -27.74 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 15285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3446 0.060 - 0.121: 695 0.121 - 0.181: 94 0.181 - 0.242: 17 0.242 - 0.302: 4 Chirality restraints: 4256 Sorted by residual: chirality pdb=" CA PHE D 447 " pdb=" N PHE D 447 " pdb=" C PHE D 447 " pdb=" CB PHE D 447 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA PHE C 447 " pdb=" N PHE C 447 " pdb=" C PHE C 447 " pdb=" CB PHE C 447 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA PHE B 447 " pdb=" N PHE B 447 " pdb=" C PHE B 447 " pdb=" CB PHE B 447 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 4253 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 864 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.11e+00 pdb=" C ILE A 864 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE A 864 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 865 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 864 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C ILE D 864 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE D 864 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP D 865 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 864 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C ILE C 864 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE C 864 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP C 865 " 0.017 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 6376 2.78 - 3.31: 24465 3.31 - 3.84: 40242 3.84 - 4.37: 42849 4.37 - 4.90: 73879 Nonbonded interactions: 187811 Sorted by model distance: nonbonded pdb=" OE1 GLU B 782 " pdb=" OH TYR B 793 " model vdw 2.256 2.440 nonbonded pdb=" OE1 GLU D 782 " pdb=" OH TYR D 793 " model vdw 2.256 2.440 nonbonded pdb=" OE1 GLU A 782 " pdb=" OH TYR A 793 " model vdw 2.256 2.440 nonbonded pdb=" OE1 GLU C 782 " pdb=" OH TYR C 793 " model vdw 2.257 2.440 nonbonded pdb=" OG SER B 687 " pdb=" OG SER B 711 " model vdw 2.277 2.440 ... (remaining 187806 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' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.010 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: 0.080 Extract box with map and model: 7.160 Check model and map are aligned: 0.360 Set scattering table: 0.260 Process input model: 66.290 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.007 0.091 26364 Z= 0.432 Angle : 0.981 10.256 35956 Z= 0.576 Chirality : 0.050 0.302 4256 Planarity : 0.008 0.055 4416 Dihedral : 11.764 106.179 8644 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.17 % Allowed : 3.76 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.12), residues: 3160 helix: -1.40 (0.09), residues: 2220 sheet: 0.43 (0.43), residues: 140 loop : -3.36 (0.16), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 876 HIS 0.006 0.002 HIS B 559 PHE 0.038 0.003 PHE A 867 TYR 0.037 0.003 TYR B 772 ARG 0.005 0.001 ARG D 688 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 677 time to evaluate : 2.791 Fit side-chains REVERT: A 744 PHE cc_start: 0.8010 (t80) cc_final: 0.7708 (t80) REVERT: A 761 GLN cc_start: 0.8687 (tt0) cc_final: 0.8216 (pp30) REVERT: A 877 MET cc_start: 0.9115 (tpp) cc_final: 0.8855 (mmm) REVERT: A 895 TRP cc_start: 0.7280 (t-100) cc_final: 0.6958 (t60) REVERT: A 904 TYR cc_start: 0.6901 (p90) cc_final: 0.6655 (p90) REVERT: A 905 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 1048 ASP cc_start: 0.8821 (m-30) cc_final: 0.8560 (m-30) REVERT: B 744 PHE cc_start: 0.8135 (t80) cc_final: 0.7821 (t80) REVERT: B 761 GLN cc_start: 0.8667 (tt0) cc_final: 0.8230 (pp30) REVERT: B 895 TRP cc_start: 0.7170 (t-100) cc_final: 0.6926 (t60) REVERT: B 904 TYR cc_start: 0.6729 (p90) cc_final: 0.6523 (p90) REVERT: B 905 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 1046 ASN cc_start: 0.7744 (t0) cc_final: 0.7542 (t0) REVERT: B 1048 ASP cc_start: 0.8844 (m-30) cc_final: 0.8589 (m-30) REVERT: C 744 PHE cc_start: 0.8131 (t80) cc_final: 0.7822 (t80) REVERT: C 761 GLN cc_start: 0.8665 (tt0) cc_final: 0.8208 (pp30) REVERT: C 877 MET cc_start: 0.9091 (tpp) cc_final: 0.8842 (mmm) REVERT: C 895 TRP cc_start: 0.7185 (t-100) cc_final: 0.6945 (t60) REVERT: C 905 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7675 (mt-10) REVERT: C 1046 ASN cc_start: 0.7742 (t0) cc_final: 0.7542 (t0) REVERT: C 1048 ASP cc_start: 0.8843 (m-30) cc_final: 0.8588 (m-30) REVERT: D 744 PHE cc_start: 0.8144 (t80) cc_final: 0.7832 (t80) REVERT: D 761 GLN cc_start: 0.8664 (tt0) cc_final: 0.8202 (pp30) REVERT: D 877 MET cc_start: 0.9068 (tpp) cc_final: 0.8832 (mmm) REVERT: D 895 TRP cc_start: 0.7191 (t-100) cc_final: 0.6946 (t60) REVERT: D 905 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7539 (mt-10) REVERT: D 1046 ASN cc_start: 0.7748 (t0) cc_final: 0.7542 (t0) REVERT: D 1048 ASP cc_start: 0.8846 (m-30) cc_final: 0.8591 (m-30) outliers start: 4 outliers final: 4 residues processed: 681 average time/residue: 0.3222 time to fit residues: 358.1815 Evaluate side-chains 332 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 328 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain D residue 453 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 4.9990 chunk 257 optimal weight: 40.0000 chunk 142 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 198 optimal weight: 8.9990 chunk 308 optimal weight: 7.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 681 GLN B 173 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 681 GLN C 173 GLN ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 681 GLN D 173 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 ASN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN D 681 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 26364 Z= 0.441 Angle : 0.736 8.652 35956 Z= 0.382 Chirality : 0.042 0.226 4256 Planarity : 0.004 0.030 4416 Dihedral : 11.176 111.823 3768 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.34 % Allowed : 12.01 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3160 helix: 0.44 (0.11), residues: 2216 sheet: 0.53 (0.43), residues: 140 loop : -2.89 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 137 HIS 0.008 0.002 HIS C 559 PHE 0.026 0.002 PHE B1012 TYR 0.021 0.002 TYR B 646 ARG 0.004 0.001 ARG C 828 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 315 time to evaluate : 2.839 Fit side-chains REVERT: A 667 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 701 PHE cc_start: 0.7564 (m-10) cc_final: 0.7068 (m-10) REVERT: A 877 MET cc_start: 0.9271 (tpp) cc_final: 0.9031 (mmm) REVERT: A 897 TRP cc_start: 0.8176 (m-10) cc_final: 0.7965 (m-10) REVERT: A 1003 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8314 (tm-30) REVERT: B 667 GLN cc_start: 0.8458 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 701 PHE cc_start: 0.7573 (m-10) cc_final: 0.7028 (m-10) REVERT: B 877 MET cc_start: 0.9325 (tpp) cc_final: 0.8977 (mmm) REVERT: B 897 TRP cc_start: 0.8170 (m-10) cc_final: 0.7945 (m-10) REVERT: B 1003 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 667 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7861 (tm-30) REVERT: C 701 PHE cc_start: 0.7570 (m-10) cc_final: 0.7047 (m-10) REVERT: C 877 MET cc_start: 0.9264 (tpp) cc_final: 0.9036 (mmm) REVERT: C 897 TRP cc_start: 0.8192 (m-10) cc_final: 0.7973 (m-10) REVERT: C 1003 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8335 (tm-30) REVERT: D 667 GLN cc_start: 0.8451 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 701 PHE cc_start: 0.7574 (m-10) cc_final: 0.7049 (m-10) REVERT: D 877 MET cc_start: 0.9250 (tpp) cc_final: 0.9039 (mmm) REVERT: D 897 TRP cc_start: 0.8220 (m-10) cc_final: 0.8008 (m-10) REVERT: D 1003 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8311 (tm-30) outliers start: 125 outliers final: 86 residues processed: 410 average time/residue: 0.3267 time to fit residues: 225.4499 Evaluate side-chains 379 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 293 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 760 PHE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 760 PHE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 707 CYS Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 40.0000 chunk 95 optimal weight: 10.0000 chunk 256 optimal weight: 40.0000 chunk 210 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 309 optimal weight: 9.9990 chunk 334 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 chunk 306 optimal weight: 2.9990 chunk 105 optimal weight: 0.0970 chunk 248 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 ASN A 844 HIS B 256 ASN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 ASN B 844 HIS C 256 ASN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 ASN C 844 HIS D 256 ASN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 ASN D 844 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26364 Z= 0.262 Angle : 0.574 7.678 35956 Z= 0.295 Chirality : 0.039 0.171 4256 Planarity : 0.003 0.031 4416 Dihedral : 10.350 112.769 3768 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.96 % Allowed : 13.68 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3160 helix: 1.17 (0.11), residues: 2216 sheet: 0.69 (0.44), residues: 140 loop : -2.38 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 682 HIS 0.004 0.001 HIS D 559 PHE 0.022 0.002 PHE B1012 TYR 0.017 0.002 TYR C 904 ARG 0.004 0.000 ARG A1045 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 323 time to evaluate : 2.903 Fit side-chains REVERT: A 667 GLN cc_start: 0.8624 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 701 PHE cc_start: 0.7479 (m-10) cc_final: 0.6984 (m-10) REVERT: A 877 MET cc_start: 0.9274 (tpp) cc_final: 0.8655 (tmm) REVERT: A 897 TRP cc_start: 0.8165 (m-10) cc_final: 0.7956 (m-10) REVERT: A 1048 ASP cc_start: 0.8375 (m-30) cc_final: 0.8154 (m-30) REVERT: A 1058 MET cc_start: 0.9085 (mmp) cc_final: 0.8700 (mmp) REVERT: B 667 GLN cc_start: 0.8652 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 701 PHE cc_start: 0.7540 (m-10) cc_final: 0.7034 (m-10) REVERT: B 782 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8048 (mm-30) REVERT: B 877 MET cc_start: 0.9297 (tpp) cc_final: 0.8605 (tmm) REVERT: B 897 TRP cc_start: 0.8152 (m-10) cc_final: 0.7940 (m-10) REVERT: B 969 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8685 (mm) REVERT: B 1058 MET cc_start: 0.9077 (mmp) cc_final: 0.8702 (mmp) REVERT: C 667 GLN cc_start: 0.8617 (tm-30) cc_final: 0.7906 (tm-30) REVERT: C 701 PHE cc_start: 0.7488 (m-10) cc_final: 0.6991 (m-10) REVERT: C 782 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8060 (mm-30) REVERT: C 877 MET cc_start: 0.9272 (tpp) cc_final: 0.8669 (tmm) REVERT: C 969 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8683 (mm) REVERT: C 1048 ASP cc_start: 0.8395 (m-30) cc_final: 0.8176 (m-30) REVERT: C 1058 MET cc_start: 0.9139 (mmm) cc_final: 0.8247 (mmt) REVERT: D 667 GLN cc_start: 0.8640 (tm-30) cc_final: 0.7922 (tm-30) REVERT: D 701 PHE cc_start: 0.7536 (m-10) cc_final: 0.7055 (m-10) REVERT: D 782 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8089 (mm-30) REVERT: D 877 MET cc_start: 0.9268 (tpp) cc_final: 0.8660 (tmm) REVERT: D 969 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8683 (mm) REVERT: D 1048 ASP cc_start: 0.8387 (m-30) cc_final: 0.8174 (m-30) outliers start: 116 outliers final: 77 residues processed: 410 average time/residue: 0.2911 time to fit residues: 202.6762 Evaluate side-chains 366 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 286 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 707 CYS Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 328 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 294 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN B 785 GLN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 26364 Z= 0.328 Angle : 0.624 7.682 35956 Z= 0.318 Chirality : 0.040 0.162 4256 Planarity : 0.003 0.032 4416 Dihedral : 9.911 116.818 3768 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.45 % Allowed : 15.51 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3160 helix: 1.48 (0.11), residues: 2200 sheet: 0.41 (0.44), residues: 144 loop : -1.99 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 682 HIS 0.005 0.002 HIS C 559 PHE 0.020 0.002 PHE C1012 TYR 0.015 0.002 TYR C 646 ARG 0.003 0.000 ARG B1045 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 291 time to evaluate : 2.721 Fit side-chains REVERT: A 592 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8777 (mp) REVERT: A 667 GLN cc_start: 0.8682 (tm-30) cc_final: 0.7877 (tm-30) REVERT: A 782 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8025 (mm-30) REVERT: A 858 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8098 (ttt) REVERT: B 592 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8759 (mp) REVERT: B 667 GLN cc_start: 0.8678 (tm-30) cc_final: 0.7889 (tm-30) REVERT: B 858 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8145 (ttt) REVERT: C 592 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8768 (mp) REVERT: C 667 GLN cc_start: 0.8683 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 858 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8071 (ttt) REVERT: C 969 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8749 (mm) REVERT: D 592 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8781 (mp) REVERT: D 667 GLN cc_start: 0.8684 (tm-30) cc_final: 0.7893 (tm-30) REVERT: D 858 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8060 (ttt) outliers start: 151 outliers final: 95 residues processed: 397 average time/residue: 0.2904 time to fit residues: 195.0023 Evaluate side-chains 373 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 269 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 975 VAL Chi-restraints excluded: chain D residue 1015 VAL Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 167 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN A 785 GLN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN C 785 GLN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN D 785 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26364 Z= 0.218 Angle : 0.549 8.242 35956 Z= 0.277 Chirality : 0.038 0.161 4256 Planarity : 0.003 0.034 4416 Dihedral : 9.445 115.855 3768 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.77 % Allowed : 16.88 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.15), residues: 3160 helix: 1.77 (0.11), residues: 2196 sheet: 0.55 (0.44), residues: 144 loop : -1.73 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 682 HIS 0.003 0.001 HIS A 844 PHE 0.024 0.001 PHE A 776 TYR 0.012 0.001 TYR C 904 ARG 0.003 0.000 ARG A1045 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 332 time to evaluate : 2.934 Fit side-chains REVERT: A 667 GLN cc_start: 0.8674 (mm-40) cc_final: 0.7815 (tm-30) REVERT: A 678 LEU cc_start: 0.9364 (tp) cc_final: 0.9139 (tp) REVERT: A 858 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8089 (ttt) REVERT: B 667 GLN cc_start: 0.8679 (mm-40) cc_final: 0.7810 (tm-30) REVERT: B 678 LEU cc_start: 0.9351 (tp) cc_final: 0.9128 (tp) REVERT: B 858 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8002 (ttt) REVERT: B 877 MET cc_start: 0.9248 (mmm) cc_final: 0.9020 (mmm) REVERT: B 1003 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8415 (tm-30) REVERT: C 667 GLN cc_start: 0.8684 (mm-40) cc_final: 0.7817 (tm-30) REVERT: C 678 LEU cc_start: 0.9358 (tp) cc_final: 0.9135 (tp) REVERT: C 858 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7992 (ttt) REVERT: C 877 MET cc_start: 0.9302 (tpp) cc_final: 0.9068 (tpp) REVERT: D 667 GLN cc_start: 0.8688 (mm-40) cc_final: 0.7819 (tm-30) REVERT: D 678 LEU cc_start: 0.9366 (tp) cc_final: 0.9145 (tp) REVERT: D 858 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8000 (ttt) REVERT: D 877 MET cc_start: 0.9302 (tpp) cc_final: 0.9071 (tpp) outliers start: 135 outliers final: 97 residues processed: 427 average time/residue: 0.2883 time to fit residues: 210.5513 Evaluate side-chains 393 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 292 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 756 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 707 CYS Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 975 VAL Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1015 VAL Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 328 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 172 optimal weight: 40.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 26364 Z= 0.525 Angle : 0.761 9.261 35956 Z= 0.389 Chirality : 0.044 0.199 4256 Planarity : 0.004 0.032 4416 Dihedral : 9.683 120.369 3768 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 6.88 % Allowed : 17.48 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3160 helix: 1.43 (0.11), residues: 2172 sheet: -0.21 (0.39), residues: 144 loop : -1.92 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 682 HIS 0.007 0.002 HIS B 559 PHE 0.020 0.002 PHE D1012 TYR 0.027 0.002 TYR C 646 ARG 0.002 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 260 time to evaluate : 2.836 Fit side-chains revert: symmetry clash REVERT: A 667 GLN cc_start: 0.8779 (mm-40) cc_final: 0.7973 (tm-30) REVERT: A 744 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8569 (t80) REVERT: A 895 TRP cc_start: 0.7011 (OUTLIER) cc_final: 0.6804 (t60) REVERT: B 667 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8005 (tm-30) REVERT: B 744 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8580 (t80) REVERT: B 877 MET cc_start: 0.9362 (mmm) cc_final: 0.9101 (mmm) REVERT: B 895 TRP cc_start: 0.7101 (OUTLIER) cc_final: 0.6840 (t60) REVERT: C 667 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8003 (tm-30) REVERT: C 744 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8559 (t80) REVERT: C 895 TRP cc_start: 0.7018 (OUTLIER) cc_final: 0.6813 (t60) REVERT: D 601 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8438 (tmm) REVERT: D 667 GLN cc_start: 0.8805 (mm-40) cc_final: 0.7999 (tm-30) REVERT: D 744 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8563 (t80) REVERT: D 895 TRP cc_start: 0.7023 (OUTLIER) cc_final: 0.6821 (t60) outliers start: 161 outliers final: 120 residues processed: 383 average time/residue: 0.3067 time to fit residues: 197.1632 Evaluate side-chains 382 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 253 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 895 TRP Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 993 TRP Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 TRP Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 993 TRP Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 756 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 895 TRP Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 993 TRP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 895 TRP Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 993 TRP Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1015 VAL Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 240 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 chunk 183 optimal weight: 0.0770 chunk 327 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26364 Z= 0.144 Angle : 0.537 9.604 35956 Z= 0.268 Chirality : 0.037 0.211 4256 Planarity : 0.003 0.035 4416 Dihedral : 8.665 115.035 3768 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.72 % Allowed : 20.68 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.15), residues: 3160 helix: 1.93 (0.11), residues: 2184 sheet: 0.22 (0.43), residues: 144 loop : -1.62 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 993 HIS 0.002 0.001 HIS A 259 PHE 0.018 0.001 PHE C 776 TYR 0.012 0.001 TYR C 904 ARG 0.006 0.000 ARG A1045 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 332 time to evaluate : 3.087 Fit side-chains REVERT: A 667 GLN cc_start: 0.8682 (mm-40) cc_final: 0.7777 (tm-30) REVERT: A 678 LEU cc_start: 0.9369 (tp) cc_final: 0.9167 (tp) REVERT: A 710 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8029 (pt) REVERT: A 877 MET cc_start: 0.9264 (tpp) cc_final: 0.9009 (tpp) REVERT: B 667 GLN cc_start: 0.8678 (mm-40) cc_final: 0.7782 (tm-30) REVERT: B 678 LEU cc_start: 0.9355 (tp) cc_final: 0.9147 (tp) REVERT: B 710 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8042 (pt) REVERT: B 858 MET cc_start: 0.8549 (ttm) cc_final: 0.8089 (ttt) REVERT: C 667 GLN cc_start: 0.8676 (mm-40) cc_final: 0.7766 (tm-30) REVERT: C 678 LEU cc_start: 0.9362 (tp) cc_final: 0.9154 (tp) REVERT: C 710 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8032 (pt) REVERT: C 851 ASN cc_start: 0.8904 (t0) cc_final: 0.8700 (t0) REVERT: C 858 MET cc_start: 0.8559 (ttm) cc_final: 0.8106 (ttt) REVERT: C 862 MET cc_start: 0.8661 (mtt) cc_final: 0.8457 (mtt) REVERT: C 1003 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8433 (tm-30) REVERT: D 601 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8419 (tpp) REVERT: D 667 GLN cc_start: 0.8676 (mm-40) cc_final: 0.7765 (tm-30) REVERT: D 678 LEU cc_start: 0.9376 (tp) cc_final: 0.9173 (tp) REVERT: D 710 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7939 (pt) REVERT: D 858 MET cc_start: 0.8551 (ttm) cc_final: 0.8081 (ttt) outliers start: 87 outliers final: 61 residues processed: 398 average time/residue: 0.2874 time to fit residues: 195.3984 Evaluate side-chains 357 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 291 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 993 TRP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 993 TRP Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 993 TRP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 993 TRP Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1015 VAL Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 208 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 257 optimal weight: 40.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26364 Z= 0.322 Angle : 0.616 8.726 35956 Z= 0.312 Chirality : 0.040 0.199 4256 Planarity : 0.003 0.035 4416 Dihedral : 8.451 118.242 3768 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.27 % Allowed : 21.24 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.15), residues: 3160 helix: 1.85 (0.11), residues: 2188 sheet: -0.04 (0.42), residues: 144 loop : -1.82 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 740 HIS 0.006 0.002 HIS A 844 PHE 0.017 0.002 PHE B1012 TYR 0.015 0.001 TYR A 646 ARG 0.003 0.000 ARG D1045 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 284 time to evaluate : 2.956 Fit side-chains REVERT: A 667 GLN cc_start: 0.8689 (mm-40) cc_final: 0.7758 (tm-30) REVERT: A 678 LEU cc_start: 0.9404 (tp) cc_final: 0.9204 (tp) REVERT: A 858 MET cc_start: 0.8657 (ttm) cc_final: 0.8293 (ttt) REVERT: B 667 GLN cc_start: 0.8678 (mm-40) cc_final: 0.7733 (tm-30) REVERT: B 678 LEU cc_start: 0.9394 (tp) cc_final: 0.9192 (tp) REVERT: B 858 MET cc_start: 0.8664 (ttm) cc_final: 0.8222 (ttt) REVERT: B 877 MET cc_start: 0.9294 (mmm) cc_final: 0.9010 (tpt) REVERT: C 667 GLN cc_start: 0.8713 (mm-40) cc_final: 0.7780 (tm-30) REVERT: C 678 LEU cc_start: 0.9402 (tp) cc_final: 0.9197 (tp) REVERT: C 851 ASN cc_start: 0.9018 (t0) cc_final: 0.8774 (t0) REVERT: C 858 MET cc_start: 0.8700 (ttm) cc_final: 0.8122 (ttt) REVERT: C 862 MET cc_start: 0.8725 (mtt) cc_final: 0.8392 (mtt) REVERT: D 601 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8632 (ttt) REVERT: D 667 GLN cc_start: 0.8717 (mm-40) cc_final: 0.7773 (tm-30) REVERT: D 678 LEU cc_start: 0.9410 (tp) cc_final: 0.9208 (tp) REVERT: D 858 MET cc_start: 0.8655 (ttm) cc_final: 0.8198 (ttt) outliers start: 100 outliers final: 78 residues processed: 368 average time/residue: 0.3121 time to fit residues: 196.5850 Evaluate side-chains 343 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 264 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 993 TRP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 993 TRP Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 756 LEU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 993 TRP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 975 VAL Chi-restraints excluded: chain D residue 993 TRP Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1015 VAL Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 7.9990 chunk 313 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 275 optimal weight: 30.0000 chunk 288 optimal weight: 2.9990 chunk 304 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26364 Z= 0.226 Angle : 0.575 9.087 35956 Z= 0.289 Chirality : 0.038 0.195 4256 Planarity : 0.003 0.037 4416 Dihedral : 8.029 117.205 3768 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.68 % Allowed : 22.22 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.15), residues: 3160 helix: 1.91 (0.11), residues: 2188 sheet: 0.10 (0.43), residues: 144 loop : -1.68 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 740 HIS 0.004 0.001 HIS A 844 PHE 0.019 0.001 PHE A 776 TYR 0.011 0.001 TYR D 646 ARG 0.006 0.000 ARG D1045 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 290 time to evaluate : 3.131 Fit side-chains REVERT: A 667 GLN cc_start: 0.8684 (mm-40) cc_final: 0.7719 (tm-30) REVERT: A 782 GLU cc_start: 0.8654 (tp30) cc_final: 0.7997 (tp30) REVERT: B 667 GLN cc_start: 0.8690 (mm-40) cc_final: 0.7727 (tm-30) REVERT: B 678 LEU cc_start: 0.9361 (tp) cc_final: 0.9156 (tp) REVERT: B 858 MET cc_start: 0.8621 (ttm) cc_final: 0.8007 (ttt) REVERT: C 667 GLN cc_start: 0.8719 (mm-40) cc_final: 0.7777 (tm-30) REVERT: C 678 LEU cc_start: 0.9369 (tp) cc_final: 0.9164 (tp) REVERT: C 782 GLU cc_start: 0.8670 (tp30) cc_final: 0.8099 (tp30) REVERT: C 858 MET cc_start: 0.8620 (ttm) cc_final: 0.8338 (ttt) REVERT: D 667 GLN cc_start: 0.8719 (mm-40) cc_final: 0.7775 (tm-30) REVERT: D 678 LEU cc_start: 0.9374 (tp) cc_final: 0.9170 (tp) REVERT: D 858 MET cc_start: 0.8602 (ttm) cc_final: 0.7991 (ttt) REVERT: D 1058 MET cc_start: 0.9067 (mmm) cc_final: 0.8665 (mmt) outliers start: 86 outliers final: 84 residues processed: 358 average time/residue: 0.2864 time to fit residues: 177.7141 Evaluate side-chains 358 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 274 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 993 TRP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 993 TRP Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 756 LEU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 993 TRP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 975 VAL Chi-restraints excluded: chain D residue 993 TRP Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1015 VAL Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 1.9990 chunk 322 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 338 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26364 Z= 0.166 Angle : 0.547 9.338 35956 Z= 0.274 Chirality : 0.037 0.213 4256 Planarity : 0.003 0.038 4416 Dihedral : 7.502 110.650 3768 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.86 % Allowed : 23.03 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.15), residues: 3160 helix: 2.05 (0.11), residues: 2188 sheet: 0.31 (0.44), residues: 144 loop : -1.56 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 740 HIS 0.003 0.001 HIS A 844 PHE 0.014 0.001 PHE A1012 TYR 0.019 0.001 TYR C 646 ARG 0.005 0.000 ARG C1045 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 308 time to evaluate : 2.861 Fit side-chains REVERT: A 667 GLN cc_start: 0.8647 (mm-40) cc_final: 0.7678 (tm-30) REVERT: A 782 GLU cc_start: 0.8643 (tp30) cc_final: 0.8002 (tp30) REVERT: A 851 ASN cc_start: 0.8962 (t0) cc_final: 0.8637 (t0) REVERT: A 1009 THR cc_start: 0.8228 (p) cc_final: 0.8018 (m) REVERT: B 667 GLN cc_start: 0.8629 (mm-40) cc_final: 0.7676 (tm-30) REVERT: B 678 LEU cc_start: 0.9328 (tp) cc_final: 0.9124 (tp) REVERT: B 802 ASP cc_start: 0.8307 (t0) cc_final: 0.7796 (t0) REVERT: C 667 GLN cc_start: 0.8658 (mm-40) cc_final: 0.7686 (tm-30) REVERT: C 678 LEU cc_start: 0.9326 (tp) cc_final: 0.9118 (tp) REVERT: C 782 GLU cc_start: 0.8664 (tp30) cc_final: 0.8086 (tp30) REVERT: C 858 MET cc_start: 0.8436 (ttm) cc_final: 0.7844 (ttt) REVERT: D 667 GLN cc_start: 0.8644 (mm-40) cc_final: 0.7687 (tm-30) REVERT: D 678 LEU cc_start: 0.9345 (tp) cc_final: 0.9141 (tp) REVERT: D 802 ASP cc_start: 0.8281 (t0) cc_final: 0.7763 (t0) outliers start: 67 outliers final: 54 residues processed: 360 average time/residue: 0.2784 time to fit residues: 172.6439 Evaluate side-chains 333 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 279 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 993 TRP Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 756 LEU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 993 TRP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 993 TRP Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 248 optimal weight: 0.0000 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 270 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.115239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.082311 restraints weight = 63751.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.084617 restraints weight = 37701.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.086137 restraints weight = 27158.048| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26364 Z= 0.175 Angle : 0.558 9.242 35956 Z= 0.281 Chirality : 0.037 0.197 4256 Planarity : 0.003 0.039 4416 Dihedral : 7.187 107.528 3760 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.78 % Allowed : 23.68 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.15), residues: 3160 helix: 2.05 (0.11), residues: 2192 sheet: 0.49 (0.45), residues: 144 loop : -1.54 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 740 HIS 0.003 0.001 HIS B 844 PHE 0.019 0.001 PHE A 776 TYR 0.021 0.001 TYR D 646 ARG 0.005 0.000 ARG B1045 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4595.10 seconds wall clock time: 84 minutes 11.61 seconds (5051.61 seconds total)