Starting phenix.real_space_refine on Sat Feb 17 21:31:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or1_13037/02_2024/7or1_13037_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or1_13037/02_2024/7or1_13037.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or1_13037/02_2024/7or1_13037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or1_13037/02_2024/7or1_13037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or1_13037/02_2024/7or1_13037_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or1_13037/02_2024/7or1_13037_updated.pdb" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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 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. Process input model Symmetric amino acids flipped Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 1079": "OE1" <-> "OE2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 1079": "OE1" <-> "OE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 1079": "OE1" <-> "OE2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 1079": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 18 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: 18 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: 18 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: 18 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: 10.70, per 1000 atoms: 0.54 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: 7.95 Conformation dependent library (CDL) restraints added in 3.2 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: 4.02 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: 3.817A 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: 4.070A 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: 3.520A 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: 6.210A pdb=" N PHE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.612A 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: 3.906A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) removed outlier: 4.732A 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: 3.669A pdb=" N MET A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 5.083A 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: 4.027A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.818A 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: 4.071A 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: 3.521A 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: 6.210A pdb=" N PHE B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 722 " --> pdb=" O ALA B 718 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.611A 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: 3.906A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) removed outlier: 4.732A 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: 3.668A pdb=" N MET B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) removed outlier: 5.082A 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: 4.026A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 971 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.817A 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: 3.688A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) removed outlier: 4.072A 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: 3.520A 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: 6.209A pdb=" N PHE C 716 " --> pdb=" O LEU C 712 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN C 722 " --> pdb=" O ALA C 718 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.611A 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: 3.905A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.760A 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: 4.199A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.611A 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: 4.731A 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: 3.682A 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: 3.669A pdb=" N MET C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) removed outlier: 5.083A 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: 4.027A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA C 971 " --> pdb=" O VAL C 967 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER C 972 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU C 973 " --> pdb=" O LYS C 969 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.817A 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: 4.071A 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: 3.521A 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: 6.210A pdb=" N PHE D 716 " --> pdb=" O LEU D 712 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN D 722 " --> pdb=" O ALA D 718 " (cutoff:3.500A) removed outlier: 4.293A 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: 3.612A 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: 3.906A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 4.002A 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: 4.611A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) removed outlier: 4.732A 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: 3.669A pdb=" N MET D 912 " --> pdb=" O THR D 908 " (cutoff:3.500A) removed outlier: 5.082A 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: 4.027A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 971 " --> pdb=" O VAL D 967 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) removed outlier: 3.599A 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 655 through 659 Processing sheet with id= B, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.225A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 655 through 659 Processing sheet with id= D, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.225A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 655 through 659 Processing sheet with id= F, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.225A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 655 through 659 Processing sheet with id= H, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.224A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2832 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: 5.72 Time building geometry restraints manager: 8.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 3044 1.27 - 1.41: 4916 1.41 - 1.54: 11966 1.54 - 1.67: 78 1.67 - 1.81: 232 Bond restraints: 20236 Sorted by residual: bond pdb=" N6 0IG A1201 " pdb=" N7 0IG A1201 " ideal model delta sigma weight residual 1.161 1.283 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" N6 0IG C1201 " pdb=" N7 0IG C1201 " ideal model delta sigma weight residual 1.161 1.283 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" N6 0IG D1202 " pdb=" N7 0IG D1202 " ideal model delta sigma weight residual 1.161 1.283 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" N6 0IG B1201 " pdb=" N7 0IG B1201 " ideal model delta sigma weight residual 1.161 1.283 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C5 IHP C1206 " pdb=" O15 IHP C1206 " ideal model delta sigma weight residual 1.389 1.469 -0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 20231 not shown) Histogram of bond angle deviations from ideal: 88.27 - 106.54: 596 106.54 - 124.81: 26472 124.81 - 143.08: 340 143.08 - 161.35: 0 161.35 - 179.62: 4 Bond angle restraints: 27412 Sorted by residual: angle pdb=" C14 0IG D1202 " pdb=" N6 0IG D1202 " pdb=" N7 0IG D1202 " ideal model delta sigma weight residual 130.27 118.19 12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C14 0IG A1201 " pdb=" N6 0IG A1201 " pdb=" N7 0IG A1201 " ideal model delta sigma weight residual 130.27 118.23 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C14 0IG C1201 " pdb=" N6 0IG C1201 " pdb=" N7 0IG C1201 " ideal model delta sigma weight residual 130.27 118.23 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C14 0IG B1201 " pdb=" N6 0IG B1201 " pdb=" N7 0IG B1201 " ideal model delta sigma weight residual 130.27 118.23 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" N6 0IG D1202 " pdb=" N7 0IG D1202 " pdb=" N8 0IG D1202 " ideal model delta sigma weight residual 168.86 179.62 -10.76 3.00e+00 1.11e-01 1.29e+01 ... (remaining 27407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 12036 34.46 - 68.91: 288 68.91 - 103.37: 20 103.37 - 137.83: 48 137.83 - 172.29: 4 Dihedral angle restraints: 12396 sinusoidal: 5368 harmonic: 7028 Sorted by residual: dihedral pdb=" N 0IG B1201 " pdb=" C 0IG B1201 " pdb=" C1 0IG B1201 " pdb=" O 0IG B1201 " ideal model delta sinusoidal sigma weight residual 203.70 31.41 172.29 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N 0IG C1201 " pdb=" C 0IG C1201 " pdb=" C1 0IG C1201 " pdb=" O 0IG C1201 " ideal model delta sinusoidal sigma weight residual 203.70 31.46 172.24 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N 0IG D1202 " pdb=" C 0IG D1202 " pdb=" C1 0IG D1202 " pdb=" O 0IG D1202 " ideal model delta sinusoidal sigma weight residual 203.70 31.51 172.19 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 3164 1.006 - 2.012: 0 2.012 - 3.019: 0 3.019 - 4.025: 0 4.025 - 5.031: 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 2.61 -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 C1206 " pdb=" C4 IHP C1206 " pdb=" C6 IHP C1206 " pdb=" O15 IHP C1206 " 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 C1201 " -0.143 2.00e-02 2.50e+03 1.69e-01 7.12e+02 pdb=" C11 0IG C1201 " -0.043 2.00e-02 2.50e+03 pdb=" C12 0IG C1201 " -0.144 2.00e-02 2.50e+03 pdb=" C13 0IG C1201 " -0.055 2.00e-02 2.50e+03 pdb=" C14 0IG C1201 " 0.136 2.00e-02 2.50e+03 pdb=" C15 0IG C1201 " 0.243 2.00e-02 2.50e+03 pdb=" C16 0IG C1201 " 0.155 2.00e-02 2.50e+03 pdb=" N6 0IG C1201 " 0.209 2.00e-02 2.50e+03 pdb=" N7 0IG C1201 " -0.060 2.00e-02 2.50e+03 pdb=" N8 0IG C1201 " -0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0IG D1202 " 0.142 2.00e-02 2.50e+03 1.69e-01 7.12e+02 pdb=" C11 0IG D1202 " 0.042 2.00e-02 2.50e+03 pdb=" C12 0IG D1202 " 0.145 2.00e-02 2.50e+03 pdb=" C13 0IG D1202 " 0.055 2.00e-02 2.50e+03 pdb=" C14 0IG D1202 " -0.136 2.00e-02 2.50e+03 pdb=" C15 0IG D1202 " -0.244 2.00e-02 2.50e+03 pdb=" C16 0IG D1202 " -0.154 2.00e-02 2.50e+03 pdb=" N6 0IG D1202 " -0.209 2.00e-02 2.50e+03 pdb=" N7 0IG D1202 " 0.059 2.00e-02 2.50e+03 pdb=" N8 0IG D1202 " 0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0IG B1201 " -0.143 2.00e-02 2.50e+03 1.69e-01 7.11e+02 pdb=" C11 0IG B1201 " -0.042 2.00e-02 2.50e+03 pdb=" C12 0IG B1201 " -0.144 2.00e-02 2.50e+03 pdb=" C13 0IG B1201 " -0.055 2.00e-02 2.50e+03 pdb=" C14 0IG B1201 " 0.136 2.00e-02 2.50e+03 pdb=" C15 0IG B1201 " 0.243 2.00e-02 2.50e+03 pdb=" C16 0IG B1201 " 0.154 2.00e-02 2.50e+03 pdb=" N6 0IG B1201 " 0.209 2.00e-02 2.50e+03 pdb=" N7 0IG B1201 " -0.059 2.00e-02 2.50e+03 pdb=" N8 0IG B1201 " -0.299 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4813 2.79 - 3.32: 18711 3.32 - 3.84: 30430 3.84 - 4.37: 38157 4.37 - 4.90: 64555 Nonbonded interactions: 156666 Sorted by model distance: nonbonded pdb=" O ILE B 916 " pdb=" O HOH B1301 " model vdw 2.262 2.440 nonbonded pdb=" O ILE C 916 " pdb=" O HOH C1301 " model vdw 2.288 2.440 nonbonded pdb=" OG SER C 887 " pdb=" OE1 GLN C 940 " model vdw 2.321 2.440 nonbonded pdb=" OG SER A 887 " pdb=" OE1 GLN A 940 " model vdw 2.321 2.440 nonbonded pdb=" OG SER D 887 " pdb=" OE1 GLN D 940 " model vdw 2.321 2.440 ... (remaining 156661 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 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: 1.270 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: 5.810 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 51.610 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.140 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.122 20236 Z= 0.560 Angle : 0.778 12.076 27412 Z= 0.387 Chirality : 0.354 5.031 3180 Planarity : 0.007 0.169 3296 Dihedral : 16.579 172.285 7828 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.95 % Favored : 93.71 % Rotamer: Outliers : 1.72 % Allowed : 6.90 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.16), residues: 2352 helix: -0.75 (0.12), residues: 1644 sheet: -0.04 (0.62), residues: 60 loop : -2.71 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 832 HIS 0.003 0.001 HIS C 983 PHE 0.013 0.002 PHE A 583 TYR 0.013 0.002 TYR A 456 ARG 0.003 0.000 ARG D 464 *********************** 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 230 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 2.177 Fit side-chains REVERT: B 953 MET cc_start: 0.8611 (mmm) cc_final: 0.8344 (mmm) REVERT: B 978 MET cc_start: 0.8081 (mtm) cc_final: 0.7876 (mtp) REVERT: C 862 MET cc_start: 0.8898 (mtt) cc_final: 0.8660 (mtt) REVERT: C 1063 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: D 911 MET cc_start: 0.9088 (mtp) cc_final: 0.8653 (mtp) REVERT: D 912 MET cc_start: 0.8388 (ttm) cc_final: 0.8168 (ttp) REVERT: D 1059 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7508 (mt-10) REVERT: D 1063 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7547 (mp0) outliers start: 36 outliers final: 12 residues processed: 221 average time/residue: 1.3703 time to fit residues: 340.4765 Evaluate side-chains 191 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 1063 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 0.0000 chunk 120 optimal weight: 0.0570 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.4302 ------------------------------------------------------------------------------- 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 A1008 ASN A1047 GLN B 619 ASN B 664 GLN B1008 ASN B1047 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C 664 GLN C1008 ASN C1047 GLN D 619 ASN D 664 GLN D1008 ASN D1047 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20236 Z= 0.139 Angle : 0.578 11.223 27412 Z= 0.264 Chirality : 0.044 0.512 3180 Planarity : 0.004 0.050 3296 Dihedral : 10.515 162.084 3319 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.63 % Allowed : 9.43 % Favored : 88.94 % 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: -0.14 (0.18), residues: 2352 helix: 0.63 (0.13), residues: 1624 sheet: 1.06 (0.62), residues: 60 loop : -1.93 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 832 HIS 0.003 0.000 HIS C 970 PHE 0.007 0.001 PHE C 879 TYR 0.017 0.001 TYR A 655 ARG 0.003 0.000 ARG D1050 *********************** 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 233 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 199 time to evaluate : 2.195 Fit side-chains REVERT: A 1059 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7805 (mt-10) REVERT: B 508 PHE cc_start: 0.9054 (m-80) cc_final: 0.8768 (m-80) REVERT: B 912 MET cc_start: 0.8216 (ttm) cc_final: 0.7935 (ttp) REVERT: C 862 MET cc_start: 0.8873 (mtt) cc_final: 0.8623 (mtt) REVERT: D 744 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7842 (mtm) REVERT: D 1059 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7858 (mt-10) outliers start: 34 outliers final: 16 residues processed: 221 average time/residue: 1.3122 time to fit residues: 328.2369 Evaluate side-chains 187 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 744 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 191 optimal weight: 0.0270 chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1008 ASN B 664 GLN B1008 ASN C 664 GLN C1008 ASN D 664 GLN D1008 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20236 Z= 0.235 Angle : 0.531 9.270 27412 Z= 0.259 Chirality : 0.040 0.263 3180 Planarity : 0.004 0.047 3296 Dihedral : 9.959 156.102 3311 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.83 % Allowed : 9.63 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2352 helix: 1.12 (0.13), residues: 1624 sheet: -0.14 (0.53), residues: 100 loop : -1.74 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 832 HIS 0.003 0.001 HIS A 983 PHE 0.011 0.001 PHE B 583 TYR 0.008 0.001 TYR B 840 ARG 0.007 0.000 ARG C 996 *********************** 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 250 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 191 time to evaluate : 2.541 Fit side-chains REVERT: A 562 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8396 (mppt) REVERT: A 911 MET cc_start: 0.8789 (mtp) cc_final: 0.8563 (mtp) REVERT: A 1059 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 912 MET cc_start: 0.8343 (ttm) cc_final: 0.8013 (ttp) REVERT: C 530 MET cc_start: 0.8406 (mtp) cc_final: 0.8191 (mtp) REVERT: D 651 CYS cc_start: 0.8381 (m) cc_final: 0.8140 (m) REVERT: D 1059 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7860 (mt-10) outliers start: 59 outliers final: 32 residues processed: 229 average time/residue: 1.2738 time to fit residues: 331.8197 Evaluate side-chains 214 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 875 VAL 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: 0.9990 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 664 GLN B1008 ASN C 463 GLN C 664 GLN D 664 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1646 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= 0.158 Angle : 0.468 10.190 27412 Z= 0.230 Chirality : 0.038 0.200 3180 Planarity : 0.004 0.048 3296 Dihedral : 9.399 146.881 3308 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.96 % Allowed : 10.87 % Favored : 87.16 % 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: 0.93 (0.18), residues: 2352 helix: 1.42 (0.13), residues: 1624 sheet: 0.25 (0.54), residues: 100 loop : -1.44 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 832 HIS 0.003 0.000 HIS B 983 PHE 0.008 0.001 PHE D 877 TYR 0.007 0.001 TYR B 706 ARG 0.004 0.000 ARG D1050 *********************** 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 236 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 2.320 Fit side-chains REVERT: A 864 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: A 1059 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 912 MET cc_start: 0.8316 (ttm) cc_final: 0.8008 (ttp) REVERT: C 483 MET cc_start: 0.8787 (mtp) cc_final: 0.8454 (mtm) REVERT: C 530 MET cc_start: 0.8440 (mtp) cc_final: 0.8218 (mtp) REVERT: C 996 ARG cc_start: 0.8775 (mmm-85) cc_final: 0.8575 (mmm-85) REVERT: D 651 CYS cc_start: 0.8411 (m) cc_final: 0.8203 (m) REVERT: D 833 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: D 911 MET cc_start: 0.8638 (mtp) cc_final: 0.8415 (mtp) REVERT: D 1059 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7865 (mt-10) outliers start: 41 outliers final: 14 residues processed: 222 average time/residue: 1.3280 time to fit residues: 333.7067 Evaluate side-chains 199 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 833 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 664 GLN C 494 HIS D 494 HIS D 664 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1838 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= 0.141 Angle : 0.461 10.949 27412 Z= 0.226 Chirality : 0.037 0.189 3180 Planarity : 0.003 0.044 3296 Dihedral : 9.050 141.493 3305 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.58 % Allowed : 11.64 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2352 helix: 1.63 (0.13), residues: 1632 sheet: 1.19 (0.62), residues: 80 loop : -1.26 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 832 HIS 0.002 0.000 HIS B 983 PHE 0.008 0.001 PHE C 877 TYR 0.007 0.001 TYR B 706 ARG 0.005 0.000 ARG D1050 *********************** 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 216 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 2.242 Fit side-chains REVERT: A 1059 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7869 (mt-10) REVERT: B 664 GLN cc_start: 0.8585 (pt0) cc_final: 0.7660 (pm20) REVERT: C 483 MET cc_start: 0.8784 (mtp) cc_final: 0.8493 (mtm) REVERT: C 530 MET cc_start: 0.8506 (mtp) cc_final: 0.8270 (mtp) REVERT: C 992 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8903 (tm) REVERT: D 1059 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7883 (mt-10) outliers start: 33 outliers final: 16 residues processed: 204 average time/residue: 1.2620 time to fit residues: 292.8676 Evaluate side-chains 196 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.5980 chunk 205 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 0.0770 chunk 56 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS B 494 HIS D 664 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20236 Z= 0.147 Angle : 0.448 9.098 27412 Z= 0.221 Chirality : 0.037 0.189 3180 Planarity : 0.003 0.043 3296 Dihedral : 8.881 137.967 3305 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.20 % Allowed : 11.88 % Favored : 85.92 % 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: 1.37 (0.18), residues: 2352 helix: 1.66 (0.13), residues: 1648 sheet: 1.29 (0.63), residues: 80 loop : -1.19 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 832 HIS 0.002 0.000 HIS B 983 PHE 0.008 0.001 PHE C 877 TYR 0.007 0.001 TYR B 706 ARG 0.005 0.000 ARG C 996 *********************** 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 234 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 188 time to evaluate : 2.213 Fit side-chains REVERT: A 864 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: A 1059 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 912 MET cc_start: 0.8241 (ttm) cc_final: 0.7864 (ttp) REVERT: C 483 MET cc_start: 0.8764 (mtp) cc_final: 0.8470 (mtm) REVERT: C 530 MET cc_start: 0.8521 (mtp) cc_final: 0.8264 (mtp) REVERT: C 721 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7412 (mmt) REVERT: D 664 GLN cc_start: 0.8601 (pt0) cc_final: 0.8110 (pm20) REVERT: D 1059 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7880 (mt-10) outliers start: 46 outliers final: 21 residues processed: 217 average time/residue: 1.2989 time to fit residues: 318.8651 Evaluate side-chains 201 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 142 optimal weight: 0.0070 chunk 138 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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: 0.8195 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20236 Z= 0.234 Angle : 0.501 9.249 27412 Z= 0.244 Chirality : 0.039 0.184 3180 Planarity : 0.004 0.040 3296 Dihedral : 9.023 138.078 3302 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.82 % Allowed : 12.69 % Favored : 85.49 % 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: 1.36 (0.18), residues: 2352 helix: 1.68 (0.13), residues: 1632 sheet: 0.55 (0.57), residues: 100 loop : -1.14 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 832 HIS 0.003 0.001 HIS A 983 PHE 0.009 0.001 PHE B 583 TYR 0.010 0.001 TYR A 706 ARG 0.005 0.000 ARG C 996 *********************** 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 216 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 178 time to evaluate : 2.274 Fit side-chains REVERT: A 469 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7863 (pp) REVERT: A 864 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: A 1059 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 1063 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: B 1059 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7802 (mt-10) REVERT: C 483 MET cc_start: 0.8746 (mtp) cc_final: 0.8437 (mtm) REVERT: C 530 MET cc_start: 0.8642 (mtp) cc_final: 0.8389 (mtp) REVERT: D 1059 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7879 (mt-10) outliers start: 38 outliers final: 27 residues processed: 204 average time/residue: 1.2473 time to fit residues: 289.8595 Evaluate side-chains 206 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 7.9990 chunk 90 optimal weight: 0.0470 chunk 135 optimal weight: 0.0870 chunk 68 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 0.0010 chunk 21 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 206 optimal weight: 0.4980 overall best weight: 0.2062 ------------------------------------------------------------------------------- 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: 0.8137 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20236 Z= 0.109 Angle : 0.434 8.468 27412 Z= 0.214 Chirality : 0.037 0.189 3180 Planarity : 0.003 0.037 3296 Dihedral : 8.504 132.214 3299 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.68 % Allowed : 13.12 % Favored : 85.20 % 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: 1.63 (0.18), residues: 2352 helix: 1.80 (0.13), residues: 1656 sheet: 1.47 (0.65), residues: 80 loop : -0.96 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 832 HIS 0.001 0.000 HIS C 983 PHE 0.008 0.001 PHE B 877 TYR 0.007 0.001 TYR D 706 ARG 0.004 0.000 ARG A1050 *********************** 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 225 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 190 time to evaluate : 2.245 Fit side-chains REVERT: A 483 MET cc_start: 0.8809 (mtp) cc_final: 0.8572 (mtm) REVERT: A 1059 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7882 (mt-10) REVERT: B 1059 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7860 (mt-10) REVERT: C 483 MET cc_start: 0.8748 (mtp) cc_final: 0.8443 (mtm) REVERT: C 530 MET cc_start: 0.8580 (mtp) cc_final: 0.8289 (mtp) REVERT: D 1059 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7763 (mm-30) outliers start: 35 outliers final: 18 residues processed: 208 average time/residue: 1.3184 time to fit residues: 310.7718 Evaluate side-chains 195 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 664 GLN C 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20236 Z= 0.295 Angle : 0.531 8.502 27412 Z= 0.259 Chirality : 0.040 0.182 3180 Planarity : 0.004 0.034 3296 Dihedral : 8.880 136.392 3295 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.39 % Allowed : 13.36 % Favored : 85.25 % 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: 1.46 (0.18), residues: 2352 helix: 1.74 (0.13), residues: 1632 sheet: 1.30 (0.64), residues: 80 loop : -1.10 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 832 HIS 0.003 0.001 HIS C 983 PHE 0.012 0.001 PHE A 877 TYR 0.012 0.001 TYR D 706 ARG 0.003 0.000 ARG A1050 *********************** 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 210 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 2.245 Fit side-chains REVERT: B 1059 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 483 MET cc_start: 0.8738 (mtp) cc_final: 0.8412 (mtm) REVERT: C 530 MET cc_start: 0.8683 (mtp) cc_final: 0.8382 (mtp) REVERT: D 1059 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7879 (mt-10) outliers start: 29 outliers final: 21 residues processed: 200 average time/residue: 1.2870 time to fit residues: 293.6485 Evaluate side-chains 197 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 664 GLN C 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20236 Z= 0.181 Angle : 0.479 9.613 27412 Z= 0.236 Chirality : 0.038 0.183 3180 Planarity : 0.004 0.034 3296 Dihedral : 8.703 133.091 3295 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.91 % Allowed : 14.18 % Favored : 84.91 % 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: 1.56 (0.18), residues: 2352 helix: 1.79 (0.13), residues: 1636 sheet: 1.37 (0.64), residues: 80 loop : -1.01 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 832 HIS 0.003 0.000 HIS B 983 PHE 0.009 0.001 PHE C 877 TYR 0.008 0.001 TYR D 706 ARG 0.003 0.000 ARG A1050 ********************** 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 203 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 2.191 Fit side-chains REVERT: B 664 GLN cc_start: 0.8593 (pt0) cc_final: 0.8171 (pm20) REVERT: B 1059 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7893 (mt-10) REVERT: C 483 MET cc_start: 0.8748 (mtp) cc_final: 0.8464 (mtm) REVERT: C 530 MET cc_start: 0.8634 (mtp) cc_final: 0.8373 (mtp) REVERT: D 1059 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7882 (mt-10) outliers start: 19 outliers final: 19 residues processed: 195 average time/residue: 1.3700 time to fit residues: 301.3180 Evaluate side-chains 199 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 187 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081142 restraints weight = 27256.243| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.55 r_work: 0.2879 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20236 Z= 0.218 Angle : 0.497 9.250 27412 Z= 0.244 Chirality : 0.039 0.182 3180 Planarity : 0.004 0.036 3296 Dihedral : 8.762 133.434 3295 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.29 % Allowed : 14.08 % Favored : 84.63 % 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: 1.53 (0.18), residues: 2352 helix: 1.75 (0.13), residues: 1640 sheet: 1.34 (0.64), residues: 80 loop : -0.97 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 832 HIS 0.003 0.001 HIS D 983 PHE 0.011 0.001 PHE A 877 TYR 0.009 0.001 TYR C 706 ARG 0.003 0.000 ARG A1050 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6037.75 seconds wall clock time: 108 minutes 36.64 seconds (6516.64 seconds total)