Starting phenix.real_space_refine (version: dev) on Thu Feb 23 11:00:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/02_2023/7or0_13036_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/02_2023/7or0_13036.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/02_2023/7or0_13036_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/02_2023/7or0_13036_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/02_2023/7or0_13036_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/02_2023/7or0_13036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/02_2023/7or0_13036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/02_2023/7or0_13036_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/02_2023/7or0_13036_updated.pdb" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 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 Process input model Symmetric amino acids flipped Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1059": "OE1" <-> "OE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 696": "OE1" <-> "OE2" Residue "B PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1059": "OE1" <-> "OE2" Residue "C TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 696": "OE1" <-> "OE2" Residue "C PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1059": "OE1" <-> "OE2" Residue "D TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 696": "OE1" <-> "OE2" Residue "D PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1059": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19869 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 174 Unusual residues: {' CA': 2, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 11.32, per 1000 atoms: 0.57 Number of scatterers: 19869 At special positions: 0 Unit cell: (113.36, 114.45, 148.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 144 16.00 P 32 15.00 O 3620 8.00 N 3168 7.00 C 12900 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1205 " - " ASN A 753 " " NAG B1205 " - " ASN B 753 " " NAG C1205 " - " ASN C 753 " " NAG D1206 " - " ASN D 753 " " NAG E 1 " - " ASN A 747 " " NAG F 1 " - " ASN B 747 " " NAG G 1 " - " ASN C 747 " " NAG H 1 " - " ASN D 747 " Time building additional restraints: 8.08 Conformation dependent library (CDL) restraints added in 2.9 seconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 8 sheets defined 63.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 527 through 535 removed outlier: 3.829A pdb=" N ASP A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 583 through 589 Processing helix chain 'A' and resid 593 through 601 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 631 through 641 removed outlier: 3.687A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N CYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 684 through 692 removed outlier: 3.517A pdb=" N ASN A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) 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: 6.231A pdb=" N PHE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 4.291A 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 791 Processing helix chain 'A' and resid 803 through 818 removed outlier: 3.655A pdb=" N ILE A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.919A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 871 Processing helix chain 'A' and resid 874 through 877 No H-bonds generated for 'chain 'A' and resid 874 through 877' Processing helix chain 'A' and resid 879 through 891 removed outlier: 3.681A pdb=" N ILE A 890 " --> pdb=" O LEU A 886 " (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: 3.661A pdb=" N MET A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 5.088A 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 987 removed outlier: 4.024A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 998 Processing helix chain 'A' and resid 1039 through 1071 Processing helix chain 'B' and resid 448 through 455 Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 485 through 492 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 517 through 524 Processing helix chain 'B' and resid 527 through 535 removed outlier: 3.828A pdb=" N ASP B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 583 through 589 Processing helix chain 'B' and resid 593 through 601 Processing helix chain 'B' and resid 605 through 610 Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 631 through 641 removed outlier: 3.687A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 684 through 692 removed outlier: 3.518A pdb=" N ASN B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) 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: 6.231A pdb=" N PHE B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN B 722 " --> pdb=" O ALA B 718 " (cutoff:3.500A) removed outlier: 4.291A 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 791 Processing helix chain 'B' and resid 803 through 818 removed outlier: 3.655A pdb=" N ILE B 817 " --> pdb=" O THR B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 828 through 852 removed outlier: 3.920A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 871 Processing helix chain 'B' and resid 874 through 877 No H-bonds generated for 'chain 'B' and resid 874 through 877' Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.680A pdb=" N ILE B 890 " --> pdb=" O LEU B 886 " (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: 3.660A pdb=" N MET B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) removed outlier: 5.088A 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 987 removed outlier: 4.024A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 971 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 998 Processing helix chain 'B' and resid 1039 through 1071 Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 459 through 465 Processing helix chain 'C' and resid 485 through 492 Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 517 through 524 Processing helix chain 'C' and resid 527 through 535 removed outlier: 3.829A pdb=" N ASP C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 558 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 583 through 589 Processing helix chain 'C' and resid 593 through 601 Processing helix chain 'C' and resid 605 through 610 Processing helix chain 'C' and resid 622 through 629 Processing helix chain 'C' and resid 631 through 641 removed outlier: 3.687A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 684 through 692 removed outlier: 3.518A pdb=" N ASN C 692 " --> pdb=" O ALA C 688 " (cutoff:3.500A) 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: 6.231A pdb=" N PHE C 716 " --> pdb=" O LEU C 712 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN C 722 " --> pdb=" O ALA C 718 " (cutoff:3.500A) removed outlier: 4.290A 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 791 Processing helix chain 'C' and resid 803 through 818 removed outlier: 3.655A pdb=" N ILE C 817 " --> pdb=" O THR C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 822 No H-bonds generated for 'chain 'C' and resid 820 through 822' Processing helix chain 'C' and resid 828 through 852 removed outlier: 3.920A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG C 852 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 871 Processing helix chain 'C' and resid 874 through 877 No H-bonds generated for 'chain 'C' and resid 874 through 877' Processing helix chain 'C' and resid 879 through 891 removed outlier: 3.680A pdb=" N ILE C 890 " --> pdb=" O LEU C 886 " (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: 3.661A pdb=" N MET C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) removed outlier: 5.089A 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 987 removed outlier: 4.024A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 971 " --> pdb=" O VAL C 967 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER C 972 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 973 " --> pdb=" O LYS C 969 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 998 Processing helix chain 'C' and resid 1039 through 1071 Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'D' and resid 459 through 465 Processing helix chain 'D' and resid 485 through 492 Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 517 through 524 Processing helix chain 'D' and resid 527 through 535 removed outlier: 3.829A pdb=" N ASP D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 558 Processing helix chain 'D' and resid 561 through 569 Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 593 through 601 Processing helix chain 'D' and resid 605 through 610 Processing helix chain 'D' and resid 622 through 629 Processing helix chain 'D' and resid 631 through 641 removed outlier: 3.687A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N CYS D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 684 through 692 removed outlier: 3.518A pdb=" N ASN D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) 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: 6.230A pdb=" N PHE D 716 " --> pdb=" O LEU D 712 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 722 " --> pdb=" O ALA D 718 " (cutoff:3.500A) removed outlier: 4.291A 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 791 Processing helix chain 'D' and resid 803 through 818 removed outlier: 3.655A pdb=" N ILE D 817 " --> pdb=" O THR D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 822 No H-bonds generated for 'chain 'D' and resid 820 through 822' Processing helix chain 'D' and resid 828 through 852 removed outlier: 3.919A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG D 852 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 871 Processing helix chain 'D' and resid 874 through 877 No H-bonds generated for 'chain 'D' and resid 874 through 877' Processing helix chain 'D' and resid 879 through 891 removed outlier: 3.680A pdb=" N ILE D 890 " --> pdb=" O LEU D 886 " (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: 3.661A pdb=" N MET D 912 " --> pdb=" O THR D 908 " (cutoff:3.500A) removed outlier: 5.088A 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 987 removed outlier: 4.023A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 971 " --> pdb=" O VAL D 967 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 998 Processing helix chain 'D' and resid 1039 through 1071 Processing sheet with id= A, first strand: chain 'A' and resid 642 through 644 Processing sheet with id= B, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.229A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 642 through 644 Processing sheet with id= D, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.229A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 642 through 644 Processing sheet with id= F, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.228A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 642 through 644 Processing sheet with id= H, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.228A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2844 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: 5.91 Time building geometry restraints manager: 8.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3044 1.29 - 1.42: 5038 1.42 - 1.55: 11882 1.55 - 1.68: 40 1.68 - 1.81: 232 Bond restraints: 20236 Sorted by residual: bond pdb=" C17 0IG C1201 " pdb=" S 0IG C1201 " ideal model delta sigma weight residual 1.516 1.724 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C17 0IG A1201 " pdb=" S 0IG A1201 " ideal model delta sigma weight residual 1.516 1.724 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C17 0IG B1201 " pdb=" S 0IG B1201 " ideal model delta sigma weight residual 1.516 1.724 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C17 0IG D1202 " pdb=" S 0IG D1202 " ideal model delta sigma weight residual 1.516 1.723 -0.207 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C10 0IG A1201 " pdb=" N5 0IG A1201 " ideal model delta sigma weight residual 1.564 1.371 0.193 2.00e-02 2.50e+03 9.28e+01 ... (remaining 20231 not shown) Histogram of bond angle deviations from ideal: 92.22 - 109.65: 2403 109.65 - 127.09: 24757 127.09 - 144.52: 248 144.52 - 161.95: 0 161.95 - 179.38: 4 Bond angle restraints: 27412 Sorted by residual: angle pdb=" N6 0IG B1201 " pdb=" N7 0IG B1201 " pdb=" N8 0IG B1201 " ideal model delta sigma weight residual 120.00 179.38 -59.38 3.00e+00 1.11e-01 3.92e+02 angle pdb=" N6 0IG A1201 " pdb=" N7 0IG A1201 " pdb=" N8 0IG A1201 " ideal model delta sigma weight residual 120.00 179.34 -59.34 3.00e+00 1.11e-01 3.91e+02 angle pdb=" N6 0IG D1202 " pdb=" N7 0IG D1202 " pdb=" N8 0IG D1202 " ideal model delta sigma weight residual 120.00 179.34 -59.34 3.00e+00 1.11e-01 3.91e+02 angle pdb=" N6 0IG C1201 " pdb=" N7 0IG C1201 " pdb=" N8 0IG C1201 " ideal model delta sigma weight residual 120.00 179.25 -59.25 3.00e+00 1.11e-01 3.90e+02 angle pdb=" C17 0IG C1201 " pdb=" S 0IG C1201 " pdb=" C9 0IG C1201 " ideal model delta sigma weight residual 107.47 92.22 15.25 3.00e+00 1.11e-01 2.58e+01 ... (remaining 27407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11124 18.00 - 36.00: 660 36.00 - 53.99: 148 53.99 - 71.99: 44 71.99 - 89.99: 16 Dihedral angle restraints: 11992 sinusoidal: 4964 harmonic: 7028 Sorted by residual: dihedral pdb=" CA SER A 602 " pdb=" C SER A 602 " pdb=" N LYS A 603 " pdb=" CA LYS A 603 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA SER C 602 " pdb=" C SER C 602 " pdb=" N LYS C 603 " pdb=" CA LYS C 603 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA SER B 602 " pdb=" C SER B 602 " pdb=" N LYS B 603 " pdb=" CA LYS B 603 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 11989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 3164 1.007 - 2.013: 0 2.013 - 3.019: 0 3.019 - 4.026: 0 4.026 - 5.032: 16 Chirality restraints: 3180 Sorted by residual: chirality pdb=" C5 IHP D1201 " pdb=" C4 IHP D1201 " pdb=" C6 IHP D1201 " pdb=" O15 IHP D1201 " both_signs ideal model delta sigma weight residual False -2.42 2.62 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C5 IHP A1206 " pdb=" C4 IHP A1206 " pdb=" C6 IHP A1206 " pdb=" O15 IHP A1206 " both_signs ideal model delta sigma weight residual False -2.42 2.61 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C5 IHP B1206 " pdb=" C4 IHP B1206 " pdb=" C6 IHP B1206 " pdb=" O15 IHP B1206 " both_signs ideal model delta sigma weight residual False -2.42 2.61 -5.03 2.00e-01 2.50e+01 6.32e+02 ... (remaining 3177 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 0IG A1201 " 0.223 2.00e-02 2.50e+03 2.73e-01 1.86e+03 pdb=" C11 0IG A1201 " 0.075 2.00e-02 2.50e+03 pdb=" C12 0IG A1201 " 0.229 2.00e-02 2.50e+03 pdb=" C13 0IG A1201 " 0.082 2.00e-02 2.50e+03 pdb=" C14 0IG A1201 " -0.219 2.00e-02 2.50e+03 pdb=" C15 0IG A1201 " -0.373 2.00e-02 2.50e+03 pdb=" C16 0IG A1201 " -0.227 2.00e-02 2.50e+03 pdb=" N6 0IG A1201 " -0.371 2.00e-02 2.50e+03 pdb=" N7 0IG A1201 " 0.085 2.00e-02 2.50e+03 pdb=" N8 0IG A1201 " 0.496 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0IG B1201 " -0.223 2.00e-02 2.50e+03 2.73e-01 1.86e+03 pdb=" C11 0IG B1201 " -0.075 2.00e-02 2.50e+03 pdb=" C12 0IG B1201 " -0.230 2.00e-02 2.50e+03 pdb=" C13 0IG B1201 " -0.082 2.00e-02 2.50e+03 pdb=" C14 0IG B1201 " 0.219 2.00e-02 2.50e+03 pdb=" C15 0IG B1201 " 0.373 2.00e-02 2.50e+03 pdb=" C16 0IG B1201 " 0.227 2.00e-02 2.50e+03 pdb=" N6 0IG B1201 " 0.371 2.00e-02 2.50e+03 pdb=" N7 0IG B1201 " -0.085 2.00e-02 2.50e+03 pdb=" N8 0IG B1201 " -0.496 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0IG C1201 " -0.223 2.00e-02 2.50e+03 2.73e-01 1.86e+03 pdb=" C11 0IG C1201 " -0.075 2.00e-02 2.50e+03 pdb=" C12 0IG C1201 " -0.230 2.00e-02 2.50e+03 pdb=" C13 0IG C1201 " -0.082 2.00e-02 2.50e+03 pdb=" C14 0IG C1201 " 0.219 2.00e-02 2.50e+03 pdb=" C15 0IG C1201 " 0.373 2.00e-02 2.50e+03 pdb=" C16 0IG C1201 " 0.227 2.00e-02 2.50e+03 pdb=" N6 0IG C1201 " 0.371 2.00e-02 2.50e+03 pdb=" N7 0IG C1201 " -0.085 2.00e-02 2.50e+03 pdb=" N8 0IG C1201 " -0.496 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3288 2.75 - 3.29: 19013 3.29 - 3.83: 30452 3.83 - 4.36: 38340 4.36 - 4.90: 65744 Nonbonded interactions: 156837 Sorted by model distance: nonbonded pdb=" ND2 ASN D 855 " pdb=" O 0IG D1202 " model vdw 2.217 2.520 nonbonded pdb=" ND2 ASN A 855 " pdb=" O 0IG A1201 " model vdw 2.217 2.520 nonbonded pdb=" ND2 ASN C 855 " pdb=" O 0IG C1201 " model vdw 2.217 2.520 nonbonded pdb=" ND2 ASN B 855 " pdb=" O 0IG B1201 " model vdw 2.218 2.520 nonbonded pdb=" O ILE B 916 " pdb=" O HOH B1301 " model vdw 2.270 2.440 ... (remaining 156832 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' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) selection = (chain 'B' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) selection = (chain 'C' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) selection = (chain 'D' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 32 5.49 5 S 144 5.16 5 C 12900 2.51 5 N 3168 2.21 5 O 3620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 6.350 Check model and map are aligned: 0.310 Process input model: 50.920 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 0.208 20236 Z= 0.685 Angle : 1.061 59.381 27412 Z= 0.453 Chirality : 0.354 5.032 3180 Planarity : 0.011 0.273 3296 Dihedral : 13.237 89.988 7424 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.44 % Favored : 94.22 % Rotamer Outliers : 1.15 % 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: -1.99 (0.16), residues: 2352 helix: -0.75 (0.12), residues: 1644 sheet: -0.42 (0.58), residues: 68 loop : -2.64 (0.22), residues: 640 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 2.428 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 211 average time/residue: 1.3408 time to fit residues: 319.8801 Evaluate side-chains 177 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 168 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.3837 time to fit residues: 4.2043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 664 GLN A 855 ASN A1008 ASN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 619 ASN B 664 GLN B 855 ASN B1008 ASN C 481 HIS C 619 ASN C 855 ASN C1008 ASN ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 664 GLN D 855 ASN D1008 ASN ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 20236 Z= 0.231 Angle : 0.643 12.130 27412 Z= 0.292 Chirality : 0.048 0.713 3180 Planarity : 0.004 0.049 3296 Dihedral : 7.876 71.153 2884 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 2.06 % 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: -0.25 (0.17), residues: 2352 helix: 0.57 (0.13), residues: 1624 sheet: 1.72 (0.57), residues: 60 loop : -2.10 (0.24), residues: 668 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 2.431 Fit side-chains outliers start: 43 outliers final: 20 residues processed: 218 average time/residue: 1.3019 time to fit residues: 321.8817 Evaluate side-chains 199 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 2.415 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.4834 time to fit residues: 7.0453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 178 optimal weight: 0.4980 chunk 145 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 0.0030 chunk 212 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN A1008 ASN A1047 GLN B 664 GLN B1008 ASN B1047 GLN C1008 ASN C1047 GLN D 664 GLN D1008 ASN D1047 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 20236 Z= 0.140 Angle : 0.508 8.936 27412 Z= 0.241 Chirality : 0.038 0.177 3180 Planarity : 0.004 0.047 3296 Dihedral : 7.750 69.183 2884 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 2.44 % 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 (0.18), residues: 2352 helix: 1.16 (0.13), residues: 1624 sheet: 2.38 (0.61), residues: 60 loop : -1.65 (0.25), residues: 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 195 time to evaluate : 2.356 Fit side-chains outliers start: 51 outliers final: 20 residues processed: 230 average time/residue: 1.2482 time to fit residues: 327.9228 Evaluate side-chains 194 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 2.437 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.5078 time to fit residues: 7.1796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 112 optimal weight: 0.0020 chunk 204 optimal weight: 0.6980 chunk 61 optimal weight: 0.0870 overall best weight: 0.9570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN B 664 GLN B1008 ASN C 494 HIS D 664 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 20236 Z= 0.164 Angle : 0.503 10.469 27412 Z= 0.240 Chirality : 0.038 0.168 3180 Planarity : 0.004 0.046 3296 Dihedral : 7.668 66.010 2884 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 2.16 % 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: 0.97 (0.18), residues: 2352 helix: 1.45 (0.13), residues: 1620 sheet: 1.53 (0.68), residues: 68 loop : -1.51 (0.25), residues: 664 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 185 time to evaluate : 2.472 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 27 residues processed: 215 average time/residue: 1.3133 time to fit residues: 321.7295 Evaluate side-chains 198 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 2.490 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 16 residues processed: 11 average time/residue: 0.7519 time to fit residues: 13.2098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1008 ASN D 664 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20236 Z= 0.220 Angle : 0.517 9.904 27412 Z= 0.250 Chirality : 0.039 0.162 3180 Planarity : 0.004 0.042 3296 Dihedral : 7.734 65.674 2884 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 2.49 % 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: 1.10 (0.18), residues: 2352 helix: 1.52 (0.13), residues: 1624 sheet: 1.63 (0.68), residues: 68 loop : -1.38 (0.25), residues: 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 183 time to evaluate : 2.587 Fit side-chains outliers start: 52 outliers final: 28 residues processed: 221 average time/residue: 1.3197 time to fit residues: 333.2849 Evaluate side-chains 201 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 2.406 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 7 average time/residue: 0.4617 time to fit residues: 7.3937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 6.9990 chunk 205 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 chunk 189 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1008 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20236 Z= 0.186 Angle : 0.497 9.019 27412 Z= 0.240 Chirality : 0.038 0.161 3180 Planarity : 0.003 0.040 3296 Dihedral : 7.663 66.013 2884 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 2.49 % 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: 1.22 (0.18), residues: 2352 helix: 1.62 (0.13), residues: 1624 sheet: 3.18 (0.75), residues: 48 loop : -1.39 (0.24), residues: 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 174 time to evaluate : 2.621 Fit side-chains outliers start: 52 outliers final: 31 residues processed: 212 average time/residue: 1.3154 time to fit residues: 316.8263 Evaluate side-chains 205 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 2.524 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 24 residues processed: 7 average time/residue: 0.8938 time to fit residues: 10.5291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 0.0870 chunk 138 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 20236 Z= 0.150 Angle : 0.485 9.087 27412 Z= 0.232 Chirality : 0.038 0.162 3180 Planarity : 0.003 0.036 3296 Dihedral : 7.484 65.858 2884 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 2.11 % 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: 1.32 (0.18), residues: 2352 helix: 1.61 (0.13), residues: 1652 sheet: 1.38 (0.64), residues: 80 loop : -1.19 (0.26), residues: 620 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 179 time to evaluate : 2.435 Fit side-chains outliers start: 44 outliers final: 27 residues processed: 214 average time/residue: 1.3515 time to fit residues: 329.3558 Evaluate side-chains 197 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 2.357 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 7 average time/residue: 0.5382 time to fit residues: 8.3110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 20236 Z= 0.145 Angle : 0.482 9.082 27412 Z= 0.231 Chirality : 0.037 0.159 3180 Planarity : 0.003 0.036 3296 Dihedral : 7.324 65.840 2884 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 1.96 % 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: 1.42 (0.18), residues: 2352 helix: 1.66 (0.13), residues: 1656 sheet: 1.40 (0.65), residues: 80 loop : -1.08 (0.26), residues: 616 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 177 time to evaluate : 2.429 Fit side-chains outliers start: 41 outliers final: 30 residues processed: 207 average time/residue: 1.2791 time to fit residues: 302.3546 Evaluate side-chains 206 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 2.434 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 5 average time/residue: 0.3763 time to fit residues: 5.9547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 127 optimal weight: 0.0050 chunk 92 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS C 571 ASN D 494 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 20236 Z= 0.162 Angle : 0.486 9.045 27412 Z= 0.235 Chirality : 0.038 0.158 3180 Planarity : 0.003 0.034 3296 Dihedral : 7.242 65.816 2884 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 1.96 % 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: 1.47 (0.18), residues: 2352 helix: 1.68 (0.13), residues: 1656 sheet: 1.51 (0.66), residues: 80 loop : -1.02 (0.26), residues: 616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 2.461 Fit side-chains outliers start: 41 outliers final: 35 residues processed: 208 average time/residue: 1.3108 time to fit residues: 309.6734 Evaluate side-chains 205 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 2.292 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 28 residues processed: 8 average time/residue: 0.7323 time to fit residues: 10.3530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 216 optimal weight: 0.0980 chunk 187 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20236 Z= 0.204 Angle : 0.511 9.656 27412 Z= 0.246 Chirality : 0.039 0.154 3180 Planarity : 0.003 0.035 3296 Dihedral : 7.289 65.788 2884 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.53 % 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: 1.49 (0.18), residues: 2352 helix: 1.75 (0.13), residues: 1632 sheet: 1.51 (0.66), residues: 80 loop : -1.07 (0.25), residues: 640 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 2.416 Fit side-chains outliers start: 32 outliers final: 28 residues processed: 204 average time/residue: 1.2710 time to fit residues: 297.0555 Evaluate side-chains 201 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 1 average time/residue: 0.2872 time to fit residues: 3.4116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.5980 chunk 172 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 34 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.083756 restraints weight = 27171.249| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.55 r_work: 0.2889 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 20236 Z= 0.143 Angle : 0.485 9.118 27412 Z= 0.233 Chirality : 0.037 0.155 3180 Planarity : 0.003 0.034 3296 Dihedral : 7.105 65.755 2884 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 1.82 % 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: 1.57 (0.18), residues: 2352 helix: 1.74 (0.13), residues: 1656 sheet: 1.60 (0.66), residues: 80 loop : -0.94 (0.26), residues: 616 =============================================================================== Job complete usr+sys time: 6017.19 seconds wall clock time: 107 minutes 48.62 seconds (6468.62 seconds total)