Starting phenix.real_space_refine on Tue Dec 12 03:34:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/12_2023/6pqq_20451_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/12_2023/6pqq_20451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/12_2023/6pqq_20451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/12_2023/6pqq_20451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/12_2023/6pqq_20451_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/12_2023/6pqq_20451_updated.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 28 5.49 5 S 136 5.16 5 C 13200 2.51 5 N 3148 2.21 5 O 3504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B ARG 872": "NH1" <-> "NH2" Residue "B GLU 966": "OE1" <-> "OE2" Residue "D ARG 592": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D ARG 852": "NH1" <-> "NH2" Residue "D ARG 872": "NH1" <-> "NH2" Residue "D GLU 966": "OE1" <-> "OE2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "C ARG 872": "NH1" <-> "NH2" Residue "C GLU 966": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20016 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4740 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 20, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4740 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 20, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "D" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4740 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 20, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4740 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 20, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'6OU': 5, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'6OU': 5, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'6OU': 5, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'6OU': 5, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 10.59, per 1000 atoms: 0.53 Number of scatterers: 20016 At special positions: 0 Unit cell: (113.4, 113.4, 147.96, 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 136 16.00 P 28 15.00 O 3504 8.00 N 3148 7.00 C 13200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.29 Conformation dependent library (CDL) restraints added in 3.2 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 4 sheets defined 64.7% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 551 through 557 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.837A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 605 through 610 removed outlier: 3.670A pdb=" N LYS A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 631 through 640 removed outlier: 3.647A pdb=" N PHE A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 695 through 698 No H-bonds generated for 'chain 'A' and resid 695 through 698' Processing helix chain 'A' and resid 701 through 739 removed outlier: 3.760A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 767 through 795 removed outlier: 3.765A pdb=" N PHE A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 822 Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.718A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 891 removed outlier: 5.095A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 901 through 913 removed outlier: 4.749A pdb=" N LEU A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 921 No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 923 through 927 Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 951 through 986 removed outlier: 4.228A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 974 " --> pdb=" O HIS A 970 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 998 Processing helix chain 'A' and resid 1015 through 1024 Processing helix chain 'A' and resid 1041 through 1071 Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 485 through 491 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 517 through 524 Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.838A pdb=" N ASN B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 600 Processing helix chain 'B' and resid 605 through 610 removed outlier: 3.669A pdb=" N LYS B 610 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 628 Processing helix chain 'B' and resid 631 through 640 removed outlier: 3.647A pdb=" N PHE B 640 " --> pdb=" O VAL B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 691 Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 701 through 739 removed outlier: 3.759A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 767 through 795 removed outlier: 3.765A pdb=" N PHE B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 822 Proline residue: B 821 - end of helix Processing helix chain 'B' and resid 828 through 852 removed outlier: 3.718A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 891 removed outlier: 5.096A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 898 No H-bonds generated for 'chain 'B' and resid 896 through 898' Processing helix chain 'B' and resid 901 through 913 removed outlier: 4.748A pdb=" N LEU B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 921 No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 923 through 927 Processing helix chain 'B' and resid 934 through 947 Processing helix chain 'B' and resid 951 through 986 removed outlier: 4.228A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 971 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 998 Processing helix chain 'B' and resid 1015 through 1024 Processing helix chain 'B' and resid 1041 through 1071 Processing helix chain 'D' and resid 447 through 455 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 485 through 491 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 517 through 524 Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 538 through 540 No H-bonds generated for 'chain 'D' and resid 538 through 540' Processing helix chain 'D' and resid 551 through 557 Processing helix chain 'D' and resid 561 through 569 Processing helix chain 'D' and resid 583 through 590 removed outlier: 3.838A pdb=" N ASN D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 600 Processing helix chain 'D' and resid 605 through 610 removed outlier: 3.670A pdb=" N LYS D 610 " --> pdb=" O ASP D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 628 Processing helix chain 'D' and resid 631 through 640 removed outlier: 3.648A pdb=" N PHE D 640 " --> pdb=" O VAL D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 691 Processing helix chain 'D' and resid 695 through 698 No H-bonds generated for 'chain 'D' and resid 695 through 698' Processing helix chain 'D' and resid 701 through 739 removed outlier: 3.760A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE D 716 " --> pdb=" O LEU D 712 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 767 through 795 removed outlier: 3.765A pdb=" N PHE D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 822 Proline residue: D 821 - end of helix Processing helix chain 'D' and resid 828 through 852 removed outlier: 3.718A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG D 852 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 891 removed outlier: 5.095A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 898 No H-bonds generated for 'chain 'D' and resid 896 through 898' Processing helix chain 'D' and resid 901 through 913 removed outlier: 4.748A pdb=" N LEU D 913 " --> pdb=" O PHE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 921 No H-bonds generated for 'chain 'D' and resid 918 through 921' Processing helix chain 'D' and resid 923 through 927 Processing helix chain 'D' and resid 934 through 947 Processing helix chain 'D' and resid 951 through 986 removed outlier: 4.228A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 971 " --> pdb=" O VAL D 967 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS D 974 " --> pdb=" O HIS D 970 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 998 Processing helix chain 'D' and resid 1015 through 1024 Processing helix chain 'D' and resid 1041 through 1071 Processing helix chain 'C' and resid 447 through 455 Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 485 through 491 Processing helix chain 'C' and resid 495 through 503 Processing helix chain 'C' and resid 517 through 524 Processing helix chain 'C' and resid 527 through 534 Processing helix chain 'C' and resid 538 through 540 No H-bonds generated for 'chain 'C' and resid 538 through 540' Processing helix chain 'C' and resid 551 through 557 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.838A pdb=" N ASN C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 600 Processing helix chain 'C' and resid 605 through 610 removed outlier: 3.669A pdb=" N LYS C 610 " --> pdb=" O ASP C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 628 Processing helix chain 'C' and resid 631 through 640 removed outlier: 3.647A pdb=" N PHE C 640 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 691 Processing helix chain 'C' and resid 695 through 698 No H-bonds generated for 'chain 'C' and resid 695 through 698' Processing helix chain 'C' and resid 701 through 739 removed outlier: 3.760A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE C 716 " --> pdb=" O LEU C 712 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 767 through 795 removed outlier: 3.765A pdb=" N PHE C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 822 Proline residue: C 821 - end of helix Processing helix chain 'C' and resid 828 through 852 removed outlier: 3.718A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG C 852 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 891 removed outlier: 5.096A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 901 through 913 removed outlier: 4.749A pdb=" N LEU C 913 " --> pdb=" O PHE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 921 No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 923 through 927 Processing helix chain 'C' and resid 934 through 947 Processing helix chain 'C' and resid 951 through 986 removed outlier: 4.227A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 971 " --> pdb=" O VAL C 967 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER C 972 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 973 " --> pdb=" O LYS C 969 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 974 " --> pdb=" O HIS C 970 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 998 Processing helix chain 'C' and resid 1015 through 1024 Processing helix chain 'C' and resid 1041 through 1071 Processing sheet with id= A, first strand: chain 'A' and resid 642 through 644 Processing sheet with id= B, first strand: chain 'B' and resid 642 through 644 Processing sheet with id= C, first strand: chain 'D' and resid 642 through 644 Processing sheet with id= D, first strand: chain 'C' and resid 642 through 644 1000 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 7.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3012 1.30 - 1.43: 5112 1.43 - 1.56: 11738 1.56 - 1.69: 274 1.69 - 1.81: 268 Bond restraints: 20404 Sorted by residual: bond pdb=" O2 LBN D1202 " pdb=" P1 LBN D1202 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" O2 LBN B1202 " pdb=" P1 LBN B1202 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" O2 LBN A1202 " pdb=" P1 LBN A1202 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" O2 LBN C1202 " pdb=" P1 LBN C1202 " ideal model delta sigma weight residual 1.650 1.790 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" O2 LBN B1201 " pdb=" P1 LBN B1201 " ideal model delta sigma weight residual 1.650 1.783 -0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 20399 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 460 105.81 - 112.87: 10799 112.87 - 119.94: 7418 119.94 - 127.00: 8524 127.00 - 134.06: 271 Bond angle restraints: 27472 Sorted by residual: angle pdb=" N ILE A 611 " pdb=" CA ILE A 611 " pdb=" C ILE A 611 " ideal model delta sigma weight residual 108.12 122.55 -14.43 1.34e+00 5.57e-01 1.16e+02 angle pdb=" N ILE C 611 " pdb=" CA ILE C 611 " pdb=" C ILE C 611 " ideal model delta sigma weight residual 108.12 122.54 -14.42 1.34e+00 5.57e-01 1.16e+02 angle pdb=" N ILE B 611 " pdb=" CA ILE B 611 " pdb=" C ILE B 611 " ideal model delta sigma weight residual 108.12 122.53 -14.41 1.34e+00 5.57e-01 1.16e+02 angle pdb=" N ILE D 611 " pdb=" CA ILE D 611 " pdb=" C ILE D 611 " ideal model delta sigma weight residual 108.12 122.52 -14.40 1.34e+00 5.57e-01 1.15e+02 angle pdb=" C ILE D 611 " pdb=" CA ILE D 611 " pdb=" CB ILE D 611 " ideal model delta sigma weight residual 111.35 105.60 5.75 1.09e+00 8.42e-01 2.79e+01 ... (remaining 27467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 11992 35.71 - 71.42: 360 71.42 - 107.12: 64 107.12 - 142.83: 28 142.83 - 178.54: 32 Dihedral angle restraints: 12476 sinusoidal: 5356 harmonic: 7120 Sorted by residual: dihedral pdb=" C19 6OU D1205 " pdb=" C20 6OU D1205 " pdb=" C21 6OU D1205 " pdb=" O22 6OU D1205 " ideal model delta sinusoidal sigma weight residual -59.00 119.54 -178.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU C1205 " pdb=" C20 6OU C1205 " pdb=" C21 6OU C1205 " pdb=" O22 6OU C1205 " ideal model delta sinusoidal sigma weight residual -59.00 119.54 -178.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU A1205 " pdb=" C20 6OU A1205 " pdb=" C21 6OU A1205 " pdb=" O22 6OU A1205 " ideal model delta sinusoidal sigma weight residual -59.00 119.53 -178.53 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3042 0.134 - 0.269: 70 0.269 - 0.403: 0 0.403 - 0.538: 8 0.538 - 0.672: 12 Chirality restraints: 3132 Sorted by residual: chirality pdb=" C20 6OU D1205 " pdb=" C19 6OU D1205 " pdb=" C21 6OU D1205 " pdb=" O30 6OU D1205 " both_signs ideal model delta sigma weight residual False 2.35 3.02 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C20 6OU C1205 " pdb=" C19 6OU C1205 " pdb=" C21 6OU C1205 " pdb=" O30 6OU C1205 " both_signs ideal model delta sigma weight residual False 2.35 3.02 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C20 6OU A1205 " pdb=" C19 6OU A1205 " pdb=" C21 6OU A1205 " pdb=" O30 6OU A1205 " both_signs ideal model delta sigma weight residual False 2.35 3.02 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 3129 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 820 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO C 821 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 821 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 821 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 820 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO B 821 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 821 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 821 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 820 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO A 821 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 821 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 821 " -0.038 5.00e-02 4.00e+02 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 5764 2.83 - 3.35: 17761 3.35 - 3.87: 31513 3.87 - 4.38: 36324 4.38 - 4.90: 61681 Nonbonded interactions: 153043 Sorted by model distance: nonbonded pdb=" O ILE D 810 " pdb=" OG1 THR D 814 " model vdw 2.316 2.440 nonbonded pdb=" O ILE A 810 " pdb=" OG1 THR A 814 " model vdw 2.316 2.440 nonbonded pdb=" O ILE C 810 " pdb=" OG1 THR C 814 " model vdw 2.316 2.440 nonbonded pdb=" O ILE B 810 " pdb=" OG1 THR B 814 " model vdw 2.316 2.440 nonbonded pdb=" O MET B 744 " pdb=" NE1 TRP B 832 " model vdw 2.392 2.520 ... (remaining 153038 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.650 Check model and map are aligned: 0.270 Set scattering table: 0.190 Process input model: 49.660 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.110 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:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.141 20404 Z= 0.674 Angle : 1.262 14.804 27472 Z= 0.561 Chirality : 0.070 0.672 3132 Planarity : 0.007 0.068 3304 Dihedral : 21.090 178.540 7844 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.20 % Allowed : 3.77 % Favored : 96.03 % 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: -3.37 (0.14), residues: 2376 helix: -2.18 (0.09), residues: 1720 sheet: -0.88 (0.68), residues: 68 loop : -1.79 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 832 HIS 0.010 0.002 HIS A 589 PHE 0.019 0.002 PHE D 888 TYR 0.033 0.003 TYR C 842 ARG 0.005 0.001 ARG D 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 487 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 491 average time/residue: 1.3716 time to fit residues: 755.7077 Evaluate side-chains 227 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 2.106 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.7910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 0.4980 chunk 217 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 476 ASN A 512 HIS A 519 HIS A 644 HIS A 700 HIS A 805 ASN A 907 GLN A 983 HIS B 451 HIS B 476 ASN B 512 HIS B 519 HIS B 549 ASN B 644 HIS B 700 HIS B 805 ASN B 907 GLN B 983 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 ASN D 512 HIS D 519 HIS D 693 ASN D 700 HIS D 805 ASN D 907 GLN D 983 HIS C 451 HIS C 460 ASN C 476 ASN C 512 HIS C 519 HIS C 644 HIS C 700 HIS C 747 ASN C 983 HIS ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20404 Z= 0.160 Angle : 0.574 8.417 27472 Z= 0.273 Chirality : 0.039 0.147 3132 Planarity : 0.005 0.060 3304 Dihedral : 23.816 177.988 3472 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.73 % Allowed : 15.18 % Favored : 82.09 % 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: -0.92 (0.16), residues: 2376 helix: -0.32 (0.12), residues: 1728 sheet: -0.21 (0.73), residues: 68 loop : -1.10 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 832 HIS 0.003 0.001 HIS D 494 PHE 0.010 0.001 PHE B 823 TYR 0.013 0.001 TYR C 842 ARG 0.012 0.001 ARG D 975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 247 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 17 residues processed: 284 average time/residue: 1.2582 time to fit residues: 406.1531 Evaluate side-chains 211 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 2.081 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.2140 time to fit residues: 3.5336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS A 570 HIS A 722 ASN B 460 ASN B 570 HIS B 722 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN D 494 HIS D 570 HIS D 644 HIS D 722 ASN D 855 ASN C 570 HIS C 589 HIS C 805 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20404 Z= 0.384 Angle : 0.689 9.620 27472 Z= 0.331 Chirality : 0.045 0.162 3132 Planarity : 0.005 0.058 3304 Dihedral : 22.314 166.538 3472 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.66 % Allowed : 14.83 % Favored : 80.51 % 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: 0.08 (0.17), residues: 2376 helix: 0.44 (0.12), residues: 1744 sheet: 0.28 (0.78), residues: 68 loop : -0.88 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 993 HIS 0.007 0.002 HIS D 494 PHE 0.024 0.002 PHE B 888 TYR 0.017 0.002 TYR C 706 ARG 0.006 0.001 ARG D 975 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 198 time to evaluate : 2.366 Fit side-chains outliers start: 94 outliers final: 28 residues processed: 268 average time/residue: 1.1804 time to fit residues: 364.5122 Evaluate side-chains 197 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 2.233 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 6 average time/residue: 0.3763 time to fit residues: 6.2925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 0.0870 chunk 62 optimal weight: 9.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN A 722 ASN A 747 ASN A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 ASN B 747 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 747 ASN D1047 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 590 ASN C 739 ASN C 979 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20404 Z= 0.158 Angle : 0.542 8.292 27472 Z= 0.261 Chirality : 0.039 0.151 3132 Planarity : 0.004 0.059 3304 Dihedral : 21.633 173.661 3472 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.52 % Allowed : 15.92 % Favored : 80.56 % 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: 0.82 (0.17), residues: 2376 helix: 1.05 (0.12), residues: 1740 sheet: 0.61 (0.76), residues: 68 loop : -0.85 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 832 HIS 0.003 0.001 HIS D 589 PHE 0.008 0.001 PHE C 823 TYR 0.010 0.001 TYR D 842 ARG 0.009 0.000 ARG B 996 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 187 time to evaluate : 2.271 Fit side-chains outliers start: 71 outliers final: 31 residues processed: 239 average time/residue: 1.2676 time to fit residues: 345.8932 Evaluate side-chains 193 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 23 residues processed: 8 average time/residue: 0.8333 time to fit residues: 11.1132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.0050 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN B 619 ASN B1047 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20404 Z= 0.170 Angle : 0.537 8.822 27472 Z= 0.256 Chirality : 0.039 0.149 3132 Planarity : 0.004 0.050 3304 Dihedral : 20.988 172.185 3472 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.87 % Allowed : 16.12 % Favored : 80.01 % 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: 1.24 (0.18), residues: 2376 helix: 1.35 (0.13), residues: 1740 sheet: 0.92 (0.77), residues: 68 loop : -0.72 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 832 HIS 0.004 0.001 HIS B 481 PHE 0.008 0.001 PHE C 823 TYR 0.009 0.001 TYR D 842 ARG 0.009 0.000 ARG B 996 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 179 time to evaluate : 2.228 Fit side-chains outliers start: 78 outliers final: 37 residues processed: 233 average time/residue: 1.2276 time to fit residues: 329.0331 Evaluate side-chains 203 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 27 residues processed: 10 average time/residue: 0.6047 time to fit residues: 10.8412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.0470 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20404 Z= 0.253 Angle : 0.586 9.788 27472 Z= 0.277 Chirality : 0.041 0.170 3132 Planarity : 0.004 0.048 3304 Dihedral : 20.480 170.969 3472 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.12 % Allowed : 17.01 % Favored : 79.86 % 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: 1.33 (0.18), residues: 2376 helix: 1.40 (0.13), residues: 1748 sheet: 0.99 (0.76), residues: 68 loop : -0.65 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 832 HIS 0.004 0.001 HIS C 494 PHE 0.020 0.001 PHE B 877 TYR 0.010 0.001 TYR C 706 ARG 0.011 0.001 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 172 time to evaluate : 2.317 Fit side-chains outliers start: 63 outliers final: 35 residues processed: 221 average time/residue: 1.1889 time to fit residues: 302.6246 Evaluate side-chains 201 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 2.226 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 25 residues processed: 10 average time/residue: 0.5764 time to fit residues: 10.2492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.0570 chunk 26 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20404 Z= 0.151 Angle : 0.535 9.164 27472 Z= 0.252 Chirality : 0.039 0.158 3132 Planarity : 0.003 0.048 3304 Dihedral : 20.003 172.096 3472 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.33 % Allowed : 17.66 % Favored : 80.01 % 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: 1.58 (0.18), residues: 2376 helix: 1.62 (0.13), residues: 1740 sheet: 1.15 (0.77), residues: 68 loop : -0.69 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 515 HIS 0.004 0.000 HIS B 481 PHE 0.014 0.001 PHE B 877 TYR 0.011 0.001 TYR D 842 ARG 0.007 0.000 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 185 time to evaluate : 2.229 Fit side-chains outliers start: 47 outliers final: 30 residues processed: 219 average time/residue: 1.2016 time to fit residues: 302.0912 Evaluate side-chains 202 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 23 residues processed: 7 average time/residue: 0.4212 time to fit residues: 7.2149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20404 Z= 0.184 Angle : 0.553 10.673 27472 Z= 0.260 Chirality : 0.039 0.176 3132 Planarity : 0.003 0.044 3304 Dihedral : 19.641 175.071 3472 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.28 % Allowed : 17.91 % Favored : 79.81 % 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: 1.66 (0.18), residues: 2376 helix: 1.66 (0.13), residues: 1744 sheet: 1.19 (0.77), residues: 68 loop : -0.59 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 809 HIS 0.004 0.001 HIS D 481 PHE 0.017 0.001 PHE B 877 TYR 0.009 0.001 TYR D 842 ARG 0.014 0.001 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 2.296 Fit side-chains outliers start: 46 outliers final: 31 residues processed: 208 average time/residue: 1.2485 time to fit residues: 298.6154 Evaluate side-chains 198 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 2.106 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 23 residues processed: 8 average time/residue: 0.7229 time to fit residues: 10.4635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 7.9990 chunk 221 optimal weight: 0.6980 chunk 202 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20404 Z= 0.189 Angle : 0.559 10.105 27472 Z= 0.265 Chirality : 0.039 0.162 3132 Planarity : 0.003 0.045 3304 Dihedral : 19.289 177.869 3472 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.08 % Allowed : 18.45 % Favored : 79.46 % 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: 1.69 (0.18), residues: 2376 helix: 1.68 (0.13), residues: 1744 sheet: 1.15 (0.77), residues: 68 loop : -0.56 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 515 HIS 0.004 0.001 HIS D 481 PHE 0.010 0.001 PHE B 877 TYR 0.009 0.001 TYR D 842 ARG 0.014 0.000 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 2.240 Fit side-chains outliers start: 42 outliers final: 31 residues processed: 205 average time/residue: 1.1983 time to fit residues: 282.8174 Evaluate side-chains 201 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 2.224 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 24 residues processed: 7 average time/residue: 0.3517 time to fit residues: 6.6224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 147 optimal weight: 0.0070 chunk 116 optimal weight: 0.9980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20404 Z= 0.152 Angle : 0.547 11.289 27472 Z= 0.257 Chirality : 0.039 0.151 3132 Planarity : 0.003 0.046 3304 Dihedral : 18.894 179.470 3472 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.88 % Allowed : 18.80 % Favored : 79.32 % 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: 1.75 (0.18), residues: 2376 helix: 1.75 (0.13), residues: 1736 sheet: 1.16 (0.76), residues: 68 loop : -0.62 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 809 HIS 0.002 0.000 HIS C 719 PHE 0.011 0.001 PHE C 877 TYR 0.010 0.001 TYR D 842 ARG 0.012 0.000 ARG A 996 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 2.204 Fit side-chains outliers start: 38 outliers final: 21 residues processed: 217 average time/residue: 1.1898 time to fit residues: 298.8960 Evaluate side-chains 195 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 2.276 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.2079 time to fit residues: 3.7619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9990 chunk 202 optimal weight: 0.0470 chunk 58 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 195 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.120531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.086433 restraints weight = 32119.885| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.53 r_work: 0.2952 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20404 Z= 0.150 Angle : 0.545 10.123 27472 Z= 0.257 Chirality : 0.038 0.155 3132 Planarity : 0.003 0.044 3304 Dihedral : 18.474 179.699 3472 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.44 % Allowed : 19.30 % Favored : 79.27 % 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: 1.82 (0.18), residues: 2376 helix: 1.79 (0.13), residues: 1740 sheet: 1.22 (0.77), residues: 68 loop : -0.55 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 515 HIS 0.003 0.000 HIS C1062 PHE 0.016 0.001 PHE B 877 TYR 0.012 0.001 TYR D1049 ARG 0.011 0.000 ARG A 996 =============================================================================== Job complete usr+sys time: 6326.18 seconds wall clock time: 113 minutes 22.03 seconds (6802.03 seconds total)