Starting phenix.real_space_refine on Fri Sep 19 05:22:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ryu_10059/09_2025/6ryu_10059.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ryu_10059/09_2025/6ryu_10059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ryu_10059/09_2025/6ryu_10059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ryu_10059/09_2025/6ryu_10059.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ryu_10059/09_2025/6ryu_10059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ryu_10059/09_2025/6ryu_10059.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 303 5.49 5 Mg 2 5.21 5 S 100 5.16 5 C 13996 2.51 5 N 4285 2.21 5 O 4908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23598 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3036 Classifications: {'DNA': 149} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3070 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "W" Number of atoms: 5608 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 696, 5602 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 664} Chain breaks: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 58 Conformer: "B" Number of residues, atoms: 696, 5602 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 664} Chain breaks: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 5736 Chain: "W" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "V" Number of atoms: 5612 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 696, 5606 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 664} Chain breaks: 3 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 696, 5606 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 664} Chain breaks: 3 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 5740 Chain: "V" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "W" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ANP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ANP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12252 SG CYS W 452 79.094 105.559 50.583 1.00203.58 S ATOM 12276 SG CYS W 455 82.408 105.779 52.056 1.00206.12 S ATOM 12424 SG CYS W 475 82.423 106.747 48.289 1.00191.46 S ATOM 12338 SG CYS W 464 66.270 106.662 46.592 1.00212.42 S ATOM 12359 SG CYS W 467 66.545 103.209 48.025 1.00226.17 S ATOM 12542 SG CYS W 490 69.262 103.711 45.366 1.00221.82 S ATOM 12566 SG CYS W 493 65.846 103.680 44.560 1.00214.26 S ATOM 17920 SG CYS V 452 43.731 120.941 114.187 1.00236.99 S ATOM 17944 SG CYS V 455 40.424 120.483 112.755 1.00241.92 S ATOM 18092 SG CYS V 475 40.405 123.059 115.669 1.00244.27 S ATOM 18006 SG CYS V 464 56.552 123.671 117.314 1.00237.47 S ATOM 18027 SG CYS V 467 56.256 119.946 117.606 1.00245.21 S ATOM 18210 SG CYS V 490 53.535 121.617 119.730 1.00254.04 S ATOM 18234 SG CYS V 493 56.948 121.937 120.482 1.00246.60 S Time building chain proxies: 7.45, per 1000 atoms: 0.32 Number of scatterers: 23598 At special positions: 0 Unit cell: (123.9, 147, 194.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 100 16.00 P 303 15.00 Mg 2 11.99 O 4908 8.00 N 4285 7.00 C 13996 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN V2203 " pdb="ZN ZN V2203 " - pdb=" SG CYS V 455 " pdb="ZN ZN V2203 " - pdb=" SG CYS V 452 " pdb="ZN ZN V2203 " - pdb=" SG CYS V 475 " pdb=" ZN V2204 " pdb="ZN ZN V2204 " - pdb=" SG CYS V 467 " pdb="ZN ZN V2204 " - pdb=" SG CYS V 493 " pdb="ZN ZN V2204 " - pdb=" SG CYS V 490 " pdb="ZN ZN V2204 " - pdb=" SG CYS V 464 " pdb=" ZN W2203 " pdb="ZN ZN W2203 " - pdb=" SG CYS W 455 " pdb="ZN ZN W2203 " - pdb=" SG CYS W 452 " pdb="ZN ZN W2203 " - pdb=" SG CYS W 475 " pdb=" ZN W2204 " pdb="ZN ZN W2204 " - pdb=" SG CYS W 467 " pdb="ZN ZN W2204 " - pdb=" SG CYS W 493 " pdb="ZN ZN W2204 " - pdb=" SG CYS W 490 " pdb="ZN ZN W2204 " - pdb=" SG CYS W 464 " Number of angles added : 12 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 16 sheets defined 48.6% alpha, 7.3% beta 126 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.577A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 107 removed outlier: 3.511A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 114 removed outlier: 3.592A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.773A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 53 through 76 removed outlier: 4.002A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 removed outlier: 4.214A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.515A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.358A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.985A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.783A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.559A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.630A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.242A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.943A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.882A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 87 through 95 removed outlier: 3.786A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 114 removed outlier: 3.537A pdb=" N LEU E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.567A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 53 through 76 removed outlier: 4.001A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 91 removed outlier: 4.213A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.542A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.644A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.551A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.828A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE H 67 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.988A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG H 96 " --> pdb=" O GLN H 92 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.541A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 559 through 564 removed outlier: 3.874A pdb=" N LEU W 563 " --> pdb=" O SER W 559 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU W 564 " --> pdb=" O GLU W 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 559 through 564' Processing helix chain 'W' and resid 567 through 578 removed outlier: 3.648A pdb=" N ARG W 576 " --> pdb=" O ARG W 572 " (cutoff:3.500A) Processing helix chain 'W' and resid 598 through 601 removed outlier: 3.887A pdb=" N LYS W 601 " --> pdb=" O ARG W 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 598 through 601' Processing helix chain 'W' and resid 602 through 610 removed outlier: 4.015A pdb=" N GLU W 610 " --> pdb=" O ALA W 606 " (cutoff:3.500A) Processing helix chain 'W' and resid 648 through 652 removed outlier: 3.629A pdb=" N ALA W 652 " --> pdb=" O TYR W 649 " (cutoff:3.500A) Processing helix chain 'W' and resid 664 through 678 removed outlier: 3.586A pdb=" N MET W 678 " --> pdb=" O HIS W 674 " (cutoff:3.500A) Processing helix chain 'W' and resid 719 through 723 Processing helix chain 'W' and resid 728 through 743 removed outlier: 3.876A pdb=" N GLU W 732 " --> pdb=" O PRO W 728 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY W 733 " --> pdb=" O TYR W 729 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG W 738 " --> pdb=" O LEU W 734 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA W 742 " --> pdb=" O ARG W 738 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN W 743 " --> pdb=" O PHE W 739 " (cutoff:3.500A) Processing helix chain 'W' and resid 758 through 771 removed outlier: 3.537A pdb=" N GLU W 771 " --> pdb=" O SER W 767 " (cutoff:3.500A) Processing helix chain 'W' and resid 786 through 798 Processing helix chain 'W' and resid 809 through 820 removed outlier: 3.991A pdb=" N ARG W 817 " --> pdb=" O ARG W 813 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU W 818 " --> pdb=" O ALA W 814 " (cutoff:3.500A) Processing helix chain 'W' and resid 852 through 858 removed outlier: 4.091A pdb=" N THR W 856 " --> pdb=" O TYR W 852 " (cutoff:3.500A) Processing helix chain 'W' and resid 874 through 880 removed outlier: 3.844A pdb=" N ARG W 877 " --> pdb=" O GLU W 874 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS W 879 " --> pdb=" O HIS W 876 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN W 880 " --> pdb=" O ARG W 877 " (cutoff:3.500A) Processing helix chain 'W' and resid 883 through 891 removed outlier: 3.753A pdb=" N LEU W 889 " --> pdb=" O PHE W 885 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN W 890 " --> pdb=" O PHE W 886 " (cutoff:3.500A) Processing helix chain 'W' and resid 909 through 920 removed outlier: 3.548A pdb=" N PHE W 913 " --> pdb=" O LEU W 909 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS W 914 " --> pdb=" O GLU W 910 " (cutoff:3.500A) Processing helix chain 'W' and resid 927 through 933 removed outlier: 3.900A pdb=" N LEU W 931 " --> pdb=" O LEU W 927 " (cutoff:3.500A) Processing helix chain 'W' and resid 943 through 948 removed outlier: 3.615A pdb=" N HIS W 947 " --> pdb=" O ILE W 943 " (cutoff:3.500A) Processing helix chain 'W' and resid 979 through 991 removed outlier: 3.635A pdb=" N LEU W 990 " --> pdb=" O TYR W 986 " (cutoff:3.500A) Processing helix chain 'W' and resid 1010 through 1015 removed outlier: 3.514A pdb=" N ASP W1014 " --> pdb=" O ASN W1010 " (cutoff:3.500A) Processing helix chain 'W' and resid 1021 through 1024 Processing helix chain 'W' and resid 1025 through 1030 Processing helix chain 'W' and resid 1043 through 1049 removed outlier: 3.853A pdb=" N ARG W1047 " --> pdb=" O SER W1043 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER W1049 " --> pdb=" O LEU W1045 " (cutoff:3.500A) Processing helix chain 'W' and resid 1050 through 1065 removed outlier: 3.933A pdb=" N LEU W1054 " --> pdb=" O GLY W1050 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN W1056 " --> pdb=" O LEU W1052 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS W1057 " --> pdb=" O LEU W1053 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN W1061 " --> pdb=" O LYS W1057 " (cutoff:3.500A) Processing helix chain 'W' and resid 1075 through 1090 removed outlier: 3.515A pdb=" N LEU W1081 " --> pdb=" O LYS W1077 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS W1088 " --> pdb=" O ASP W1084 " (cutoff:3.500A) Processing helix chain 'W' and resid 1101 through 1113 removed outlier: 4.099A pdb=" N GLN W1106 " --> pdb=" O GLY W1102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU W1107 " --> pdb=" O ASN W1103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE W1109 " --> pdb=" O ARG W1105 " (cutoff:3.500A) Processing helix chain 'W' and resid 1150 through 1158 Processing helix chain 'W' and resid 1180 through 1191 removed outlier: 3.546A pdb=" N THR W1185 " --> pdb=" O GLU W1181 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN W1186 " --> pdb=" O GLU W1182 " (cutoff:3.500A) Processing helix chain 'W' and resid 1196 through 1200 Processing helix chain 'W' and resid 1407 through 1414 Processing helix chain 'V' and resid 559 through 564 removed outlier: 3.874A pdb=" N LEU V 563 " --> pdb=" O SER V 559 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU V 564 " --> pdb=" O GLU V 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 559 through 564' Processing helix chain 'V' and resid 567 through 578 removed outlier: 3.648A pdb=" N ARG V 576 " --> pdb=" O ARG V 572 " (cutoff:3.500A) Processing helix chain 'V' and resid 598 through 601 removed outlier: 3.886A pdb=" N LYS V 601 " --> pdb=" O ARG V 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 598 through 601' Processing helix chain 'V' and resid 602 through 610 removed outlier: 4.015A pdb=" N GLU V 610 " --> pdb=" O ALA V 606 " (cutoff:3.500A) Processing helix chain 'V' and resid 648 through 652 removed outlier: 3.631A pdb=" N ALA V 652 " --> pdb=" O TYR V 649 " (cutoff:3.500A) Processing helix chain 'V' and resid 664 through 678 removed outlier: 3.586A pdb=" N MET V 678 " --> pdb=" O HIS V 674 " (cutoff:3.500A) Processing helix chain 'V' and resid 719 through 723 Processing helix chain 'V' and resid 728 through 744 removed outlier: 3.875A pdb=" N GLU V 732 " --> pdb=" O PRO V 728 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY V 733 " --> pdb=" O TYR V 729 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG V 738 " --> pdb=" O LEU V 734 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA V 742 " --> pdb=" O ARG V 738 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN V 743 " --> pdb=" O PHE V 739 " (cutoff:3.500A) Processing helix chain 'V' and resid 758 through 771 removed outlier: 3.537A pdb=" N GLU V 771 " --> pdb=" O SER V 767 " (cutoff:3.500A) Processing helix chain 'V' and resid 786 through 798 Processing helix chain 'V' and resid 809 through 820 removed outlier: 3.991A pdb=" N ARG V 817 " --> pdb=" O ARG V 813 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU V 818 " --> pdb=" O ALA V 814 " (cutoff:3.500A) Processing helix chain 'V' and resid 852 through 858 removed outlier: 4.092A pdb=" N THR V 856 " --> pdb=" O TYR V 852 " (cutoff:3.500A) Processing helix chain 'V' and resid 874 through 880 removed outlier: 3.844A pdb=" N ARG V 877 " --> pdb=" O GLU V 874 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS V 879 " --> pdb=" O HIS V 876 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN V 880 " --> pdb=" O ARG V 877 " (cutoff:3.500A) Processing helix chain 'V' and resid 883 through 891 removed outlier: 3.753A pdb=" N LEU V 889 " --> pdb=" O PHE V 885 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN V 890 " --> pdb=" O PHE V 886 " (cutoff:3.500A) Processing helix chain 'V' and resid 909 through 920 removed outlier: 3.549A pdb=" N PHE V 913 " --> pdb=" O LEU V 909 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS V 914 " --> pdb=" O GLU V 910 " (cutoff:3.500A) Processing helix chain 'V' and resid 927 through 933 removed outlier: 3.900A pdb=" N LEU V 931 " --> pdb=" O LEU V 927 " (cutoff:3.500A) Processing helix chain 'V' and resid 943 through 948 removed outlier: 3.615A pdb=" N HIS V 947 " --> pdb=" O ILE V 943 " (cutoff:3.500A) Processing helix chain 'V' and resid 979 through 991 removed outlier: 3.635A pdb=" N LEU V 990 " --> pdb=" O TYR V 986 " (cutoff:3.500A) Processing helix chain 'V' and resid 1010 through 1015 removed outlier: 3.514A pdb=" N ASP V1014 " --> pdb=" O ASN V1010 " (cutoff:3.500A) Processing helix chain 'V' and resid 1021 through 1024 Processing helix chain 'V' and resid 1025 through 1030 Processing helix chain 'V' and resid 1043 through 1049 removed outlier: 3.854A pdb=" N ARG V1047 " --> pdb=" O SER V1043 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER V1049 " --> pdb=" O LEU V1045 " (cutoff:3.500A) Processing helix chain 'V' and resid 1050 through 1065 removed outlier: 3.933A pdb=" N LEU V1054 " --> pdb=" O GLY V1050 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN V1056 " --> pdb=" O LEU V1052 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS V1057 " --> pdb=" O LEU V1053 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN V1061 " --> pdb=" O LYS V1057 " (cutoff:3.500A) Processing helix chain 'V' and resid 1075 through 1090 removed outlier: 3.515A pdb=" N LEU V1081 " --> pdb=" O LYS V1077 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS V1088 " --> pdb=" O ASP V1084 " (cutoff:3.500A) Processing helix chain 'V' and resid 1101 through 1113 removed outlier: 4.100A pdb=" N GLN V1106 " --> pdb=" O GLY V1102 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU V1107 " --> pdb=" O ASN V1103 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE V1109 " --> pdb=" O ARG V1105 " (cutoff:3.500A) Processing helix chain 'V' and resid 1150 through 1158 Processing helix chain 'V' and resid 1180 through 1191 removed outlier: 3.546A pdb=" N THR V1185 " --> pdb=" O GLU V1181 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN V1186 " --> pdb=" O GLU V1182 " (cutoff:3.500A) Processing helix chain 'V' and resid 1196 through 1200 Processing helix chain 'V' and resid 1407 through 1414 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.328A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.577A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.273A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.039A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.178A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'W' and resid 462 through 463 Processing sheet with id=AA8, first strand: chain 'W' and resid 502 through 510 removed outlier: 5.728A pdb=" N ILE W 505 " --> pdb=" O LYS W 546 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS W 546 " --> pdb=" O ILE W 505 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'W' and resid 624 through 631 removed outlier: 5.279A pdb=" N ILE W 627 " --> pdb=" O LYS W 643 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS W 643 " --> pdb=" O ILE W 627 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN W 629 " --> pdb=" O LEU W 641 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 747 through 750 removed outlier: 3.728A pdb=" N THR W 901 " --> pdb=" O LEU W 749 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU W 870 " --> pdb=" O LEU W 898 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU W 900 " --> pdb=" O LEU W 870 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL W 872 " --> pdb=" O LEU W 900 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE W 778 " --> pdb=" O LEU W 848 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR W 850 " --> pdb=" O PHE W 778 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL W 780 " --> pdb=" O THR W 850 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 969 through 976 removed outlier: 6.190A pdb=" N THR W 970 " --> pdb=" O ILE W1171 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ARG W1173 " --> pdb=" O THR W 970 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU W 972 " --> pdb=" O ARG W1173 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL W1175 " --> pdb=" O LEU W 972 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL W 974 " --> pdb=" O VAL W1175 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL W1141 " --> pdb=" O TYR W1172 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N PHE W1174 " --> pdb=" O VAL W1141 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE W1143 " --> pdb=" O PHE W1174 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N THR W1176 " --> pdb=" O ILE W1143 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL W1069 " --> pdb=" O PHE W1122 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU W1124 " --> pdb=" O VAL W1069 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE W1071 " --> pdb=" O LEU W1124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 462 through 463 Processing sheet with id=AB4, first strand: chain 'V' and resid 502 through 510 removed outlier: 5.729A pdb=" N ILE V 505 " --> pdb=" O LYS V 546 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS V 546 " --> pdb=" O ILE V 505 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'V' and resid 624 through 631 removed outlier: 5.279A pdb=" N ILE V 627 " --> pdb=" O LYS V 643 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS V 643 " --> pdb=" O ILE V 627 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN V 629 " --> pdb=" O LEU V 641 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 747 through 750 removed outlier: 3.728A pdb=" N THR V 901 " --> pdb=" O LEU V 749 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU V 870 " --> pdb=" O LEU V 898 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU V 900 " --> pdb=" O LEU V 870 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL V 872 " --> pdb=" O LEU V 900 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE V 778 " --> pdb=" O LEU V 848 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR V 850 " --> pdb=" O PHE V 778 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL V 780 " --> pdb=" O THR V 850 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'V' and resid 969 through 976 removed outlier: 6.190A pdb=" N THR V 970 " --> pdb=" O ILE V1171 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG V1173 " --> pdb=" O THR V 970 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU V 972 " --> pdb=" O ARG V1173 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL V1175 " --> pdb=" O LEU V 972 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL V 974 " --> pdb=" O VAL V1175 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL V1141 " --> pdb=" O TYR V1172 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N PHE V1174 " --> pdb=" O VAL V1141 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE V1143 " --> pdb=" O PHE V1174 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N THR V1176 " --> pdb=" O ILE V1143 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL V1069 " --> pdb=" O PHE V1122 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU V1124 " --> pdb=" O VAL V1069 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE V1071 " --> pdb=" O LEU V1124 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 616 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5241 1.33 - 1.45: 6629 1.45 - 1.57: 12053 1.57 - 1.69: 611 1.69 - 1.81: 168 Bond restraints: 24702 Sorted by residual: bond pdb=" O3A ANP V2201 " pdb=" PB ANP V2201 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" O3A ANP W2201 " pdb=" PB ANP W2201 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" N3B ANP V2201 " pdb=" PG ANP V2201 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" N3B ANP W2201 " pdb=" PG ANP W2201 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CG LEU V 480 " pdb=" CD2 LEU V 480 " ideal model delta sigma weight residual 1.521 1.673 -0.152 3.30e-02 9.18e+02 2.13e+01 ... (remaining 24697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 34242 3.74 - 7.49: 364 7.49 - 11.23: 44 11.23 - 14.97: 8 14.97 - 18.71: 2 Bond angle restraints: 34660 Sorted by residual: angle pdb=" CA ASN W 826 " pdb=" CB ASN W 826 " pdb=" CG ASN W 826 " ideal model delta sigma weight residual 112.60 119.26 -6.66 1.00e+00 1.00e+00 4.43e+01 angle pdb=" CA ASN V 826 " pdb=" CB ASN V 826 " pdb=" CG ASN V 826 " ideal model delta sigma weight residual 112.60 119.22 -6.62 1.00e+00 1.00e+00 4.39e+01 angle pdb=" C GLY W1003 " pdb=" N ASN W1004 " pdb=" CA ASN W1004 " ideal model delta sigma weight residual 121.70 133.35 -11.65 1.80e+00 3.09e-01 4.19e+01 angle pdb=" C GLY V1003 " pdb=" N ASN V1004 " pdb=" CA ASN V1004 " ideal model delta sigma weight residual 121.70 133.34 -11.64 1.80e+00 3.09e-01 4.19e+01 angle pdb=" C ASN V 826 " pdb=" CA ASN V 826 " pdb=" CB ASN V 826 " ideal model delta sigma weight residual 110.62 120.17 -9.55 1.51e+00 4.39e-01 4.00e+01 ... (remaining 34655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 12658 35.84 - 71.68: 1377 71.68 - 107.52: 54 107.52 - 143.36: 2 143.36 - 179.20: 2 Dihedral angle restraints: 14093 sinusoidal: 7739 harmonic: 6354 Sorted by residual: dihedral pdb=" CA ARG F 23 " pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta harmonic sigma weight residual -180.00 -149.08 -30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual -180.00 -149.18 -30.82 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA LYS V 832 " pdb=" C LYS V 832 " pdb=" N LYS V 833 " pdb=" CA LYS V 833 " ideal model delta harmonic sigma weight residual -180.00 -150.53 -29.47 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 14090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3428 0.085 - 0.169: 341 0.169 - 0.254: 39 0.254 - 0.339: 7 0.339 - 0.423: 8 Chirality restraints: 3823 Sorted by residual: chirality pdb=" CG LEU W 894 " pdb=" CB LEU W 894 " pdb=" CD1 LEU W 894 " pdb=" CD2 LEU W 894 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CG LEU V 894 " pdb=" CB LEU V 894 " pdb=" CD1 LEU V 894 " pdb=" CD2 LEU V 894 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB ILE W 937 " pdb=" CA ILE W 937 " pdb=" CG1 ILE W 937 " pdb=" CG2 ILE W 937 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 3820 not shown) Planarity restraints: 3367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN W 826 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.34e+01 pdb=" C ASN W 826 " -0.063 2.00e-02 2.50e+03 pdb=" O ASN W 826 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA W 827 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN V 826 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C ASN V 826 " -0.063 2.00e-02 2.50e+03 pdb=" O ASN V 826 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA V 827 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO G 80 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.050 5.00e-02 4.00e+02 ... (remaining 3364 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5230 2.79 - 3.32: 19972 3.32 - 3.85: 42382 3.85 - 4.37: 49856 4.37 - 4.90: 76126 Nonbonded interactions: 193566 Sorted by model distance: nonbonded pdb=" OG SER D 61 " pdb=" OXT GLY F 102 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR V 920 " pdb=" OE1 GLU V 922 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR W 920 " pdb=" OE1 GLU W 922 " model vdw 2.280 3.040 nonbonded pdb=" N ASP V 446 " pdb=" OD1 ASP V 446 " model vdw 2.290 3.120 nonbonded pdb=" N ASP W 446 " pdb=" OD1 ASP W 446 " model vdw 2.290 3.120 ... (remaining 193561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } ncs_group { reference = (chain 'V' and (resid 446 through 809 or resid 811 through 931 or (resid 932 thr \ ough 936 and (name N or name CA or name C or name O or name CB )) or resid 937 t \ hrough 2204)) selection = (chain 'W' and (resid 446 through 809 or resid 811 through 2204)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.930 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: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 28.810 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.254 24716 Z= 0.300 Angle : 1.086 27.018 34672 Z= 0.595 Chirality : 0.056 0.423 3823 Planarity : 0.007 0.091 3367 Dihedral : 23.190 179.204 9989 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.64 % Allowed : 5.97 % Favored : 92.39 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.25 (0.13), residues: 2126 helix: -4.28 (0.07), residues: 952 sheet: -2.62 (0.36), residues: 180 loop : -2.68 (0.16), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG W1159 TYR 0.023 0.003 TYR H 80 PHE 0.029 0.003 PHE V1072 TRP 0.029 0.003 TRP W 488 HIS 0.014 0.002 HIS V 914 Details of bonding type rmsd covalent geometry : bond 0.00579 (24702) covalent geometry : angle 1.05704 (34660) hydrogen bonds : bond 0.31799 ( 894) hydrogen bonds : angle 10.87860 ( 2308) metal coordination : bond 0.15391 ( 14) metal coordination : angle 13.39246 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 459 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8893 (tt0) cc_final: 0.8692 (tt0) REVERT: B 88 TYR cc_start: 0.7989 (m-10) cc_final: 0.7480 (m-80) REVERT: C 38 ASN cc_start: 0.8543 (m-40) cc_final: 0.7958 (p0) REVERT: D 68 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7264 (tm-30) REVERT: G 61 GLU cc_start: 0.7451 (tp30) cc_final: 0.7203 (tp30) REVERT: H 40 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8794 (mttm) REVERT: H 51 ILE cc_start: 0.9155 (tt) cc_final: 0.8942 (tt) REVERT: H 65 ASP cc_start: 0.8249 (t0) cc_final: 0.7908 (t0) REVERT: W 550 MET cc_start: 0.6267 (mtt) cc_final: 0.5898 (mtm) REVERT: W 608 MET cc_start: 0.7792 (mmm) cc_final: 0.6929 (tpt) REVERT: W 1123 LEU cc_start: 0.8758 (mt) cc_final: 0.8556 (mp) REVERT: W 1135 LEU cc_start: 0.8166 (mt) cc_final: 0.7929 (mt) REVERT: V 470 SER cc_start: 0.3408 (OUTLIER) cc_final: 0.0565 (t) REVERT: V 504 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8243 (ttpp) REVERT: V 608 MET cc_start: 0.3331 (mmm) cc_final: 0.2409 (mmt) REVERT: V 731 MET cc_start: 0.6653 (mmm) cc_final: 0.6037 (tpp) REVERT: V 764 PHE cc_start: 0.8455 (t80) cc_final: 0.8229 (t80) REVERT: V 768 LEU cc_start: 0.8923 (mp) cc_final: 0.8554 (tt) REVERT: V 826 ASN cc_start: 0.2605 (OUTLIER) cc_final: 0.2257 (p0) REVERT: V 905 LEU cc_start: 0.8248 (mp) cc_final: 0.7840 (pt) REVERT: V 981 MET cc_start: 0.8699 (ttp) cc_final: 0.7254 (mpp) REVERT: V 1120 PHE cc_start: 0.5802 (t80) cc_final: 0.5476 (t80) REVERT: V 1140 THR cc_start: 0.6788 (m) cc_final: 0.6514 (p) REVERT: V 1155 GLN cc_start: 0.8384 (mm110) cc_final: 0.8052 (tp-100) REVERT: V 1186 GLN cc_start: 0.7364 (mm110) cc_final: 0.6456 (tt0) outliers start: 30 outliers final: 10 residues processed: 484 average time/residue: 0.1852 time to fit residues: 133.2630 Evaluate side-chains 259 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 247 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain W residue 489 LEU Chi-restraints excluded: chain W residue 494 THR Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1179 SER Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 460 GLU Chi-restraints excluded: chain V residue 470 SER Chi-restraints excluded: chain V residue 826 ASN Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1179 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS C 104 GLN D 81 ASN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 472 HIS W 575 GLN W 673 ASN W 715 GLN W 743 GLN W 760 GLN W 846 HIS W 880 ASN W 882 GLN W 906 GLN W 908 ASN W 914 HIS W1004 ASN W1056 GLN V 573 ASN V 575 GLN V 637 HIS V 673 ASN V 715 GLN V 826 ASN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 914 HIS V1106 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.088801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.067438 restraints weight = 95049.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068240 restraints weight = 55630.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068476 restraints weight = 42072.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.068804 restraints weight = 35626.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.068852 restraints weight = 31573.911| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24716 Z= 0.218 Angle : 0.773 24.625 34672 Z= 0.411 Chirality : 0.043 0.167 3823 Planarity : 0.006 0.064 3367 Dihedral : 26.580 178.673 5730 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.13 % Allowed : 13.79 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (0.15), residues: 2126 helix: -2.19 (0.13), residues: 1012 sheet: -2.26 (0.37), residues: 162 loop : -2.41 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V1047 TYR 0.028 0.002 TYR V 613 PHE 0.018 0.002 PHE V1122 TRP 0.025 0.002 TRP V 736 HIS 0.013 0.001 HIS V 637 Details of bonding type rmsd covalent geometry : bond 0.00480 (24702) covalent geometry : angle 0.74498 (34660) hydrogen bonds : bond 0.06698 ( 894) hydrogen bonds : angle 4.62789 ( 2308) metal coordination : bond 0.01757 ( 14) metal coordination : angle 11.10890 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8122 (m-10) cc_final: 0.7469 (m-80) REVERT: C 38 ASN cc_start: 0.8531 (m-40) cc_final: 0.7988 (p0) REVERT: D 56 MET cc_start: 0.8551 (tpp) cc_final: 0.8235 (tpp) REVERT: D 68 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7684 (tm-30) REVERT: E 120 MET cc_start: 0.8162 (mtp) cc_final: 0.7940 (mtp) REVERT: F 88 TYR cc_start: 0.7647 (m-80) cc_final: 0.7241 (m-80) REVERT: H 40 LYS cc_start: 0.9324 (mtpt) cc_final: 0.9017 (mtmm) REVERT: H 51 ILE cc_start: 0.9317 (tt) cc_final: 0.9096 (tt) REVERT: W 471 TYR cc_start: 0.4725 (m-80) cc_final: 0.4510 (m-80) REVERT: W 550 MET cc_start: 0.6297 (mtt) cc_final: 0.5861 (mtm) REVERT: W 1058 MET cc_start: 0.7054 (tpp) cc_final: 0.6783 (tpp) REVERT: W 1075 MET cc_start: 0.8348 (mtm) cc_final: 0.7996 (mtp) REVERT: W 1123 LEU cc_start: 0.8609 (mt) cc_final: 0.8334 (mp) REVERT: W 1192 MET cc_start: 0.7207 (mtp) cc_final: 0.6957 (ttm) REVERT: V 645 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7034 (mtm-85) REVERT: V 712 TYR cc_start: 0.5329 (m-80) cc_final: 0.4931 (m-10) REVERT: V 731 MET cc_start: 0.6859 (mmm) cc_final: 0.5871 (tpp) REVERT: V 905 LEU cc_start: 0.8478 (mp) cc_final: 0.8027 (pt) REVERT: V 925 HIS cc_start: 0.7245 (p90) cc_final: 0.7040 (p-80) REVERT: V 956 ARG cc_start: 0.7308 (tpt-90) cc_final: 0.6705 (pmt-80) REVERT: V 1013 MET cc_start: 0.8499 (tpp) cc_final: 0.8228 (tpp) REVERT: V 1039 MET cc_start: 0.7079 (mmt) cc_final: 0.6258 (mmt) REVERT: V 1075 MET cc_start: 0.8128 (mpp) cc_final: 0.7884 (mmm) REVERT: V 1080 ASP cc_start: 0.7895 (m-30) cc_final: 0.7689 (t0) REVERT: V 1131 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6340 (mp) REVERT: V 1186 GLN cc_start: 0.7527 (mm110) cc_final: 0.6598 (tt0) outliers start: 39 outliers final: 25 residues processed: 293 average time/residue: 0.1583 time to fit residues: 72.7242 Evaluate side-chains 235 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain W residue 472 HIS Chi-restraints excluded: chain W residue 494 THR Chi-restraints excluded: chain W residue 605 PHE Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1019 CYS Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG Chi-restraints excluded: chain V residue 844 LYS Chi-restraints excluded: chain V residue 859 MET Chi-restraints excluded: chain V residue 872 VAL Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1131 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 132 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 180 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 568 GLN W1151 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.090044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.069182 restraints weight = 159057.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069331 restraints weight = 88387.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069656 restraints weight = 59609.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.069800 restraints weight = 55106.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069925 restraints weight = 43539.407| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24716 Z= 0.147 Angle : 0.661 16.722 34672 Z= 0.352 Chirality : 0.039 0.167 3823 Planarity : 0.005 0.059 3367 Dihedral : 26.271 174.425 5719 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.81 % Allowed : 16.80 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.16), residues: 2126 helix: -1.15 (0.15), residues: 1026 sheet: -1.88 (0.39), residues: 158 loop : -2.17 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V1159 TYR 0.022 0.001 TYR W 471 PHE 0.028 0.001 PHE V 764 TRP 0.040 0.002 TRP V 797 HIS 0.021 0.001 HIS W 472 Details of bonding type rmsd covalent geometry : bond 0.00315 (24702) covalent geometry : angle 0.64575 (34660) hydrogen bonds : bond 0.04916 ( 894) hydrogen bonds : angle 3.99162 ( 2308) metal coordination : bond 0.00787 ( 14) metal coordination : angle 7.58698 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8658 (tt0) REVERT: B 88 TYR cc_start: 0.7987 (m-10) cc_final: 0.7192 (m-80) REVERT: C 38 ASN cc_start: 0.8382 (m-40) cc_final: 0.7892 (p0) REVERT: D 68 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7737 (tm-30) REVERT: F 88 TYR cc_start: 0.7374 (m-80) cc_final: 0.7162 (m-80) REVERT: H 40 LYS cc_start: 0.9263 (mtpt) cc_final: 0.8984 (mttm) REVERT: W 550 MET cc_start: 0.6314 (mtt) cc_final: 0.5439 (mpp) REVERT: W 608 MET cc_start: 0.7247 (tpp) cc_final: 0.7006 (tpp) REVERT: W 1058 MET cc_start: 0.7366 (tpp) cc_final: 0.7115 (tpp) REVERT: W 1083 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: W 1123 LEU cc_start: 0.8695 (mt) cc_final: 0.8492 (mp) REVERT: W 1192 MET cc_start: 0.7405 (mtp) cc_final: 0.7173 (tpt) REVERT: V 645 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7064 (mtm-85) REVERT: V 712 TYR cc_start: 0.5517 (m-80) cc_final: 0.4937 (m-10) REVERT: V 731 MET cc_start: 0.7093 (mmm) cc_final: 0.6189 (tpp) REVERT: V 764 PHE cc_start: 0.8571 (t80) cc_final: 0.8266 (t80) REVERT: V 809 ASP cc_start: 0.8681 (p0) cc_final: 0.7856 (p0) REVERT: V 905 LEU cc_start: 0.8611 (mp) cc_final: 0.8200 (pt) REVERT: V 1013 MET cc_start: 0.8478 (tpp) cc_final: 0.8231 (tpp) REVERT: V 1039 MET cc_start: 0.7296 (mmt) cc_final: 0.6409 (mmt) REVERT: V 1058 MET cc_start: 0.8442 (ttm) cc_final: 0.7240 (mmp) REVERT: V 1075 MET cc_start: 0.8024 (mpp) cc_final: 0.7621 (mmm) REVERT: V 1170 MET cc_start: 0.6674 (mmt) cc_final: 0.6310 (mmm) REVERT: V 1186 GLN cc_start: 0.7494 (mm110) cc_final: 0.6858 (tt0) outliers start: 33 outliers final: 23 residues processed: 278 average time/residue: 0.1535 time to fit residues: 68.0428 Evaluate side-chains 231 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain W residue 466 THR Chi-restraints excluded: chain W residue 605 PHE Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 818 GLU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1019 CYS Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG Chi-restraints excluded: chain V residue 794 PHE Chi-restraints excluded: chain V residue 844 LYS Chi-restraints excluded: chain V residue 970 THR Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 119 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 743 GLN V 819 ASN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 947 HIS ** V1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.087724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066848 restraints weight = 148163.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066992 restraints weight = 85362.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.067194 restraints weight = 58028.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067329 restraints weight = 54816.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067484 restraints weight = 44335.192| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24716 Z= 0.220 Angle : 0.696 14.633 34672 Z= 0.368 Chirality : 0.041 0.167 3823 Planarity : 0.005 0.058 3367 Dihedral : 26.362 175.294 5718 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.19 % Allowed : 17.46 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.17), residues: 2126 helix: -0.48 (0.16), residues: 1000 sheet: -1.84 (0.38), residues: 166 loop : -2.04 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG V 645 TYR 0.027 0.002 TYR W 649 PHE 0.023 0.002 PHE V 764 TRP 0.029 0.002 TRP V 797 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00492 (24702) covalent geometry : angle 0.68408 (34660) hydrogen bonds : bond 0.05175 ( 894) hydrogen bonds : angle 4.07913 ( 2308) metal coordination : bond 0.00818 ( 14) metal coordination : angle 7.00971 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7511 (mt-10) REVERT: B 88 TYR cc_start: 0.8261 (m-10) cc_final: 0.7519 (m-80) REVERT: D 56 MET cc_start: 0.8514 (tpp) cc_final: 0.8290 (tpp) REVERT: D 68 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7815 (tm-30) REVERT: E 39 HIS cc_start: 0.6188 (p-80) cc_final: 0.5512 (t70) REVERT: F 88 TYR cc_start: 0.7735 (m-80) cc_final: 0.7319 (m-80) REVERT: H 40 LYS cc_start: 0.9259 (mtpt) cc_final: 0.9027 (mttm) REVERT: W 550 MET cc_start: 0.6369 (mtt) cc_final: 0.5341 (mpp) REVERT: W 608 MET cc_start: 0.7296 (tpp) cc_final: 0.7059 (tpp) REVERT: W 837 MET cc_start: 0.3677 (OUTLIER) cc_final: 0.2757 (mmt) REVERT: W 1058 MET cc_start: 0.7345 (tpp) cc_final: 0.7069 (tpp) REVERT: W 1075 MET cc_start: 0.8716 (mtp) cc_final: 0.8474 (mtp) REVERT: W 1083 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: W 1192 MET cc_start: 0.7505 (mtp) cc_final: 0.7273 (tpt) REVERT: V 645 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7181 (mtm-85) REVERT: V 712 TYR cc_start: 0.5532 (m-80) cc_final: 0.5315 (m-10) REVERT: V 731 MET cc_start: 0.7170 (mmm) cc_final: 0.6761 (mmm) REVERT: V 905 LEU cc_start: 0.8599 (mp) cc_final: 0.8153 (pt) REVERT: V 1013 MET cc_start: 0.8401 (tpp) cc_final: 0.8030 (tpp) REVERT: V 1186 GLN cc_start: 0.7538 (mm110) cc_final: 0.6715 (tt0) outliers start: 40 outliers final: 30 residues processed: 249 average time/residue: 0.1633 time to fit residues: 65.2229 Evaluate side-chains 230 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain W residue 466 THR Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 816 ILE Chi-restraints excluded: chain W residue 837 MET Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG Chi-restraints excluded: chain V residue 794 PHE Chi-restraints excluded: chain V residue 844 LYS Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 231 optimal weight: 5.9990 chunk 204 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 472 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.089345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068544 restraints weight = 130469.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068785 restraints weight = 80143.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069399 restraints weight = 49786.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069577 restraints weight = 43051.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069635 restraints weight = 38664.247| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24716 Z= 0.138 Angle : 0.630 12.624 34672 Z= 0.333 Chirality : 0.038 0.159 3823 Planarity : 0.004 0.058 3367 Dihedral : 26.123 175.395 5718 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.81 % Allowed : 18.72 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.18), residues: 2126 helix: 0.02 (0.16), residues: 996 sheet: -1.56 (0.39), residues: 162 loop : -1.90 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 887 TYR 0.025 0.001 TYR V1023 PHE 0.027 0.001 PHE V 764 TRP 0.026 0.001 TRP V 797 HIS 0.006 0.001 HIS V1088 Details of bonding type rmsd covalent geometry : bond 0.00302 (24702) covalent geometry : angle 0.61835 (34660) hydrogen bonds : bond 0.04282 ( 894) hydrogen bonds : angle 3.65732 ( 2308) metal coordination : bond 0.00717 ( 14) metal coordination : angle 6.46239 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7635 (mt-10) REVERT: A 100 LEU cc_start: 0.9120 (mt) cc_final: 0.8866 (mt) REVERT: B 16 LYS cc_start: 0.6330 (pptt) cc_final: 0.5683 (tptp) REVERT: B 23 ARG cc_start: 0.6769 (mtm180) cc_final: 0.6528 (ptt90) REVERT: B 88 TYR cc_start: 0.8349 (m-10) cc_final: 0.7806 (m-80) REVERT: D 68 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7902 (tm-30) REVERT: F 88 TYR cc_start: 0.7683 (m-80) cc_final: 0.7259 (m-80) REVERT: H 40 LYS cc_start: 0.9210 (mtpt) cc_final: 0.8961 (mttm) REVERT: W 550 MET cc_start: 0.6278 (mtt) cc_final: 0.5286 (mpp) REVERT: W 608 MET cc_start: 0.7360 (tpp) cc_final: 0.6910 (tpt) REVERT: W 981 MET cc_start: 0.5140 (mmp) cc_final: 0.4926 (mmp) REVERT: W 1058 MET cc_start: 0.7243 (tpp) cc_final: 0.6996 (tpp) REVERT: W 1075 MET cc_start: 0.8637 (mtp) cc_final: 0.8418 (mtp) REVERT: W 1080 ASP cc_start: 0.7936 (m-30) cc_final: 0.7579 (m-30) REVERT: W 1123 LEU cc_start: 0.8612 (mt) cc_final: 0.8375 (mp) REVERT: V 645 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7265 (mtm-85) REVERT: V 731 MET cc_start: 0.7275 (mmm) cc_final: 0.6814 (tpp) REVERT: V 905 LEU cc_start: 0.8578 (mp) cc_final: 0.8178 (pt) REVERT: V 1013 MET cc_start: 0.8478 (tpp) cc_final: 0.8106 (tpp) REVERT: V 1075 MET cc_start: 0.8053 (mpp) cc_final: 0.7678 (mmm) REVERT: V 1186 GLN cc_start: 0.7289 (mm110) cc_final: 0.6568 (tt0) outliers start: 33 outliers final: 22 residues processed: 263 average time/residue: 0.1474 time to fit residues: 62.9519 Evaluate side-chains 226 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 818 GLU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1124 LEU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG Chi-restraints excluded: chain V residue 844 LYS Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 562 GLN V 715 GLN V 890 ASN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.088428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.067695 restraints weight = 135953.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067853 restraints weight = 80967.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.068216 restraints weight = 54218.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068371 restraints weight = 50882.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068386 restraints weight = 41492.776| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24716 Z= 0.173 Angle : 0.654 14.536 34672 Z= 0.343 Chirality : 0.040 0.320 3823 Planarity : 0.004 0.056 3367 Dihedral : 26.118 174.587 5716 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.24 % Allowed : 19.38 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.18), residues: 2126 helix: 0.09 (0.16), residues: 1027 sheet: -1.41 (0.38), residues: 174 loop : -1.90 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.024 0.002 TYR V1023 PHE 0.024 0.001 PHE V 764 TRP 0.034 0.002 TRP W 488 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (24702) covalent geometry : angle 0.64321 (34660) hydrogen bonds : bond 0.04569 ( 894) hydrogen bonds : angle 3.71523 ( 2308) metal coordination : bond 0.00857 ( 14) metal coordination : angle 6.38378 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7367 (tm-30) REVERT: A 97 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 125 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: B 16 LYS cc_start: 0.6224 (pptt) cc_final: 0.5583 (tptp) REVERT: B 88 TYR cc_start: 0.8206 (m-10) cc_final: 0.7486 (m-80) REVERT: C 92 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7038 (pt0) REVERT: D 68 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7913 (tm-30) REVERT: F 88 TYR cc_start: 0.7728 (m-80) cc_final: 0.7340 (m-80) REVERT: H 40 LYS cc_start: 0.9194 (mtpt) cc_final: 0.8929 (mttm) REVERT: W 550 MET cc_start: 0.6328 (mtt) cc_final: 0.5343 (mpp) REVERT: W 608 MET cc_start: 0.7423 (tpp) cc_final: 0.6980 (tpp) REVERT: W 837 MET cc_start: 0.3410 (OUTLIER) cc_final: 0.2530 (mmt) REVERT: W 981 MET cc_start: 0.5102 (mmp) cc_final: 0.4769 (mmm) REVERT: W 1058 MET cc_start: 0.7257 (tpp) cc_final: 0.6998 (tpp) REVERT: W 1075 MET cc_start: 0.8646 (mtp) cc_final: 0.8440 (mtp) REVERT: W 1083 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: V 449 MET cc_start: 0.3924 (mmt) cc_final: 0.3468 (mtt) REVERT: V 645 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7298 (mtm-85) REVERT: V 731 MET cc_start: 0.7809 (mmm) cc_final: 0.6726 (tpp) REVERT: V 734 LEU cc_start: 0.8687 (tp) cc_final: 0.8308 (pp) REVERT: V 905 LEU cc_start: 0.8603 (mp) cc_final: 0.8164 (pt) REVERT: V 954 MET cc_start: 0.7025 (tmm) cc_final: 0.6733 (ttp) REVERT: V 1186 GLN cc_start: 0.7473 (mm110) cc_final: 0.6613 (tt0) outliers start: 41 outliers final: 27 residues processed: 237 average time/residue: 0.1450 time to fit residues: 55.3512 Evaluate side-chains 229 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 801 MET Chi-restraints excluded: chain W residue 818 GLU Chi-restraints excluded: chain W residue 837 MET Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG Chi-restraints excluded: chain V residue 794 PHE Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1131 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 122 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.088608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068272 restraints weight = 152280.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.068401 restraints weight = 79306.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.068601 restraints weight = 55157.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.068881 restraints weight = 47424.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.068931 restraints weight = 42741.079| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24716 Z= 0.156 Angle : 0.643 12.980 34672 Z= 0.337 Chirality : 0.039 0.323 3823 Planarity : 0.004 0.061 3367 Dihedral : 26.059 175.208 5716 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.08 % Allowed : 19.98 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.18), residues: 2126 helix: 0.33 (0.17), residues: 1015 sheet: -1.07 (0.38), residues: 180 loop : -1.77 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 817 TYR 0.025 0.001 TYR V1023 PHE 0.014 0.001 PHE V 821 TRP 0.024 0.001 TRP W 488 HIS 0.007 0.001 HIS V 472 Details of bonding type rmsd covalent geometry : bond 0.00347 (24702) covalent geometry : angle 0.63343 (34660) hydrogen bonds : bond 0.04207 ( 894) hydrogen bonds : angle 3.60689 ( 2308) metal coordination : bond 0.00746 ( 14) metal coordination : angle 6.05575 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 97 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7635 (mt-10) REVERT: B 88 TYR cc_start: 0.8344 (m-10) cc_final: 0.7759 (m-80) REVERT: D 68 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7908 (tm-30) REVERT: F 88 TYR cc_start: 0.7758 (m-80) cc_final: 0.7326 (m-80) REVERT: H 40 LYS cc_start: 0.9163 (mtpt) cc_final: 0.8934 (mttm) REVERT: W 550 MET cc_start: 0.6302 (mtt) cc_final: 0.5552 (mpp) REVERT: W 608 MET cc_start: 0.7398 (tpp) cc_final: 0.6922 (tpp) REVERT: W 622 MET cc_start: 0.7679 (mmp) cc_final: 0.7436 (mmt) REVERT: W 981 MET cc_start: 0.5098 (mmp) cc_final: 0.4765 (mmm) REVERT: W 1058 MET cc_start: 0.7282 (tpp) cc_final: 0.7013 (tpp) REVERT: W 1080 ASP cc_start: 0.7902 (m-30) cc_final: 0.7607 (m-30) REVERT: W 1083 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8368 (tp30) REVERT: W 1123 LEU cc_start: 0.8701 (mt) cc_final: 0.8448 (mp) REVERT: V 449 MET cc_start: 0.4010 (mmt) cc_final: 0.3510 (mtt) REVERT: V 557 TRP cc_start: 0.5991 (m100) cc_final: 0.5751 (m100) REVERT: V 645 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7315 (mtm-85) REVERT: V 731 MET cc_start: 0.7892 (mmm) cc_final: 0.7608 (mmm) REVERT: V 905 LEU cc_start: 0.8614 (mp) cc_final: 0.8144 (pt) REVERT: V 1013 MET cc_start: 0.8572 (tpp) cc_final: 0.8250 (tmm) REVERT: V 1186 GLN cc_start: 0.7345 (mm110) cc_final: 0.6465 (tt0) outliers start: 38 outliers final: 27 residues processed: 241 average time/residue: 0.1423 time to fit residues: 56.1671 Evaluate side-chains 219 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 801 MET Chi-restraints excluded: chain W residue 818 GLU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1086 LEU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 8 optimal weight: 0.3980 chunk 228 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 876 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.088664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067330 restraints weight = 114327.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068677 restraints weight = 62330.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068859 restraints weight = 41530.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.069184 restraints weight = 36988.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069247 restraints weight = 32097.232| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24716 Z= 0.151 Angle : 0.642 12.603 34672 Z= 0.336 Chirality : 0.039 0.290 3823 Planarity : 0.004 0.055 3367 Dihedral : 26.009 174.685 5716 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.86 % Allowed : 20.47 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.18), residues: 2126 helix: 0.44 (0.17), residues: 1021 sheet: -1.20 (0.35), residues: 212 loop : -1.68 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.026 0.001 TYR V1023 PHE 0.028 0.001 PHE H 67 TRP 0.021 0.001 TRP W 488 HIS 0.006 0.001 HIS V 472 Details of bonding type rmsd covalent geometry : bond 0.00336 (24702) covalent geometry : angle 0.63356 (34660) hydrogen bonds : bond 0.04171 ( 894) hydrogen bonds : angle 3.55061 ( 2308) metal coordination : bond 0.00744 ( 14) metal coordination : angle 5.77322 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7413 (tm-30) REVERT: A 97 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 125 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: B 88 TYR cc_start: 0.8492 (m-10) cc_final: 0.7959 (m-80) REVERT: D 68 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7831 (tm-30) REVERT: E 48 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9237 (mm) REVERT: F 88 TYR cc_start: 0.7698 (m-80) cc_final: 0.7239 (m-80) REVERT: H 40 LYS cc_start: 0.9232 (mtpt) cc_final: 0.8995 (mttm) REVERT: W 550 MET cc_start: 0.6234 (mtt) cc_final: 0.5479 (mpp) REVERT: W 608 MET cc_start: 0.7211 (tpp) cc_final: 0.6748 (tpp) REVERT: W 622 MET cc_start: 0.7749 (mmp) cc_final: 0.7519 (mmt) REVERT: W 981 MET cc_start: 0.5074 (mmp) cc_final: 0.4743 (mmm) REVERT: W 1058 MET cc_start: 0.7282 (tpp) cc_final: 0.6998 (tpp) REVERT: W 1080 ASP cc_start: 0.7988 (m-30) cc_final: 0.7675 (m-30) REVERT: W 1083 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8340 (tp30) REVERT: W 1123 LEU cc_start: 0.8728 (mt) cc_final: 0.8467 (mp) REVERT: V 557 TRP cc_start: 0.6234 (m100) cc_final: 0.6028 (m100) REVERT: V 645 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7295 (mtm-85) REVERT: V 731 MET cc_start: 0.7990 (mmm) cc_final: 0.6863 (tpp) REVERT: V 734 LEU cc_start: 0.8617 (tp) cc_final: 0.8281 (pp) REVERT: V 905 LEU cc_start: 0.8577 (mp) cc_final: 0.8115 (pt) REVERT: V 954 MET cc_start: 0.8118 (ttp) cc_final: 0.7918 (tmm) REVERT: V 1013 MET cc_start: 0.8484 (tpp) cc_final: 0.8274 (tmm) REVERT: V 1039 MET cc_start: 0.7460 (mmp) cc_final: 0.6625 (mmm) REVERT: V 1047 ARG cc_start: 0.7312 (mmm160) cc_final: 0.7054 (tmt170) REVERT: V 1186 GLN cc_start: 0.7340 (mm110) cc_final: 0.6468 (tt0) outliers start: 34 outliers final: 28 residues processed: 235 average time/residue: 0.1510 time to fit residues: 57.2823 Evaluate side-chains 225 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain W residue 624 ILE Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 818 GLU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1086 LEU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG Chi-restraints excluded: chain V residue 973 ILE Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 743 GLN V 876 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.089218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068606 restraints weight = 143190.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069195 restraints weight = 78322.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069157 restraints weight = 49331.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.069455 restraints weight = 50577.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069511 restraints weight = 41411.382| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24716 Z= 0.137 Angle : 0.638 12.645 34672 Z= 0.331 Chirality : 0.038 0.285 3823 Planarity : 0.004 0.056 3367 Dihedral : 25.892 174.860 5716 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.64 % Allowed : 20.96 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.18), residues: 2126 helix: 0.53 (0.17), residues: 1034 sheet: -1.14 (0.36), residues: 212 loop : -1.64 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 817 TYR 0.025 0.001 TYR H 37 PHE 0.023 0.001 PHE V 821 TRP 0.020 0.001 TRP W 488 HIS 0.005 0.001 HIS V1088 Details of bonding type rmsd covalent geometry : bond 0.00302 (24702) covalent geometry : angle 0.62929 (34660) hydrogen bonds : bond 0.03964 ( 894) hydrogen bonds : angle 3.42657 ( 2308) metal coordination : bond 0.00696 ( 14) metal coordination : angle 5.52329 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7304 (tm-30) REVERT: A 125 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: B 84 MET cc_start: 0.8516 (mmt) cc_final: 0.8257 (mmt) REVERT: B 88 TYR cc_start: 0.8429 (m-10) cc_final: 0.7938 (m-80) REVERT: D 68 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7932 (tm-30) REVERT: F 88 TYR cc_start: 0.7709 (m-80) cc_final: 0.7278 (m-80) REVERT: H 40 LYS cc_start: 0.9196 (mtpt) cc_final: 0.8980 (mttm) REVERT: W 550 MET cc_start: 0.6217 (mtt) cc_final: 0.5443 (mpp) REVERT: W 608 MET cc_start: 0.7342 (tpp) cc_final: 0.6855 (tpp) REVERT: W 622 MET cc_start: 0.7641 (mmp) cc_final: 0.7433 (mmt) REVERT: W 981 MET cc_start: 0.5069 (mmp) cc_final: 0.4743 (mmm) REVERT: W 1058 MET cc_start: 0.7327 (tpp) cc_final: 0.7026 (tpp) REVERT: W 1080 ASP cc_start: 0.7941 (m-30) cc_final: 0.7644 (m-30) REVERT: W 1083 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8359 (tp30) REVERT: W 1123 LEU cc_start: 0.8676 (mt) cc_final: 0.8423 (mp) REVERT: V 645 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7335 (mtm-85) REVERT: V 731 MET cc_start: 0.7941 (mmm) cc_final: 0.7651 (mmm) REVERT: V 905 LEU cc_start: 0.8511 (mp) cc_final: 0.8073 (pt) REVERT: V 1039 MET cc_start: 0.7424 (mmp) cc_final: 0.6563 (mmm) REVERT: V 1186 GLN cc_start: 0.7225 (mm110) cc_final: 0.6553 (tt0) outliers start: 30 outliers final: 23 residues processed: 232 average time/residue: 0.1468 time to fit residues: 55.4450 Evaluate side-chains 219 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain W residue 624 ILE Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 801 MET Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1086 LEU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG Chi-restraints excluded: chain V residue 973 ILE Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 199 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 202 optimal weight: 0.0010 chunk 32 optimal weight: 4.9990 chunk 70 optimal weight: 0.0060 chunk 209 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 149 optimal weight: 0.2980 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.6606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 743 GLN ** W 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 876 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.088596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068351 restraints weight = 151890.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068333 restraints weight = 78370.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068728 restraints weight = 55142.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068934 restraints weight = 47884.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.068991 restraints weight = 43100.446| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24716 Z= 0.162 Angle : 0.664 13.395 34672 Z= 0.344 Chirality : 0.039 0.280 3823 Planarity : 0.004 0.054 3367 Dihedral : 25.927 174.770 5716 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.53 % Allowed : 21.40 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.18), residues: 2126 helix: 0.62 (0.17), residues: 1022 sheet: -1.19 (0.36), residues: 214 loop : -1.61 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 817 TYR 0.026 0.001 TYR H 37 PHE 0.020 0.001 PHE H 67 TRP 0.033 0.002 TRP V 557 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00363 (24702) covalent geometry : angle 0.65629 (34660) hydrogen bonds : bond 0.04212 ( 894) hydrogen bonds : angle 3.53771 ( 2308) metal coordination : bond 0.00742 ( 14) metal coordination : angle 5.57035 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4252 Ramachandran restraints generated. 2126 Oldfield, 0 Emsley, 2126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 125 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: B 88 TYR cc_start: 0.8485 (m-10) cc_final: 0.7896 (m-80) REVERT: D 68 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7900 (tm-30) REVERT: F 88 TYR cc_start: 0.7748 (m-80) cc_final: 0.7259 (m-80) REVERT: H 40 LYS cc_start: 0.9208 (mtpt) cc_final: 0.8989 (mttm) REVERT: W 550 MET cc_start: 0.6219 (mtt) cc_final: 0.5462 (mpp) REVERT: W 608 MET cc_start: 0.7237 (tpp) cc_final: 0.6755 (tpt) REVERT: W 981 MET cc_start: 0.5096 (mmp) cc_final: 0.4762 (mmm) REVERT: W 1058 MET cc_start: 0.7296 (tpp) cc_final: 0.6995 (tpp) REVERT: W 1080 ASP cc_start: 0.7981 (m-30) cc_final: 0.7687 (m-30) REVERT: W 1083 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8317 (tp30) REVERT: W 1192 MET cc_start: 0.7583 (tpt) cc_final: 0.7342 (tpt) REVERT: V 645 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7514 (mtm-85) REVERT: V 731 MET cc_start: 0.7942 (mmm) cc_final: 0.7687 (mmm) REVERT: V 905 LEU cc_start: 0.8494 (mp) cc_final: 0.8077 (pt) REVERT: V 1039 MET cc_start: 0.7507 (mmp) cc_final: 0.6615 (mmm) REVERT: V 1186 GLN cc_start: 0.7351 (mm110) cc_final: 0.6566 (tt0) outliers start: 28 outliers final: 24 residues processed: 217 average time/residue: 0.1603 time to fit residues: 56.5208 Evaluate side-chains 217 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain W residue 624 ILE Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 794 PHE Chi-restraints excluded: chain W residue 801 MET Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 920 THR Chi-restraints excluded: chain W residue 955 LEU Chi-restraints excluded: chain W residue 1006 VAL Chi-restraints excluded: chain W residue 1083 GLU Chi-restraints excluded: chain W residue 1086 LEU Chi-restraints excluded: chain W residue 1194 LEU Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG Chi-restraints excluded: chain V residue 973 ILE Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1084 ASP Chi-restraints excluded: chain V residue 1124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 235 optimal weight: 20.0000 chunk 2 optimal weight: 0.0670 chunk 123 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 203 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 947 HIS ** V 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 674 HIS V 846 HIS V 876 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.086033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065518 restraints weight = 149737.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.065815 restraints weight = 77390.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.066156 restraints weight = 53690.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066276 restraints weight = 46706.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.066375 restraints weight = 43100.396| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24716 Z= 0.259 Angle : 0.747 12.258 34672 Z= 0.389 Chirality : 0.043 0.277 3823 Planarity : 0.005 0.052 3367 Dihedral : 26.319 175.653 5716 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.64 % Allowed : 21.35 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.18), residues: 2126 helix: 0.31 (0.16), residues: 1017 sheet: -1.20 (0.39), residues: 186 loop : -1.70 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 116 TYR 0.034 0.002 TYR W 852 PHE 0.022 0.002 PHE V 821 TRP 0.026 0.002 TRP V 557 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00580 (24702) covalent geometry : angle 0.73819 (34660) hydrogen bonds : bond 0.05306 ( 894) hydrogen bonds : angle 4.05402 ( 2308) metal coordination : bond 0.00938 ( 14) metal coordination : angle 6.30871 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3762.88 seconds wall clock time: 65 minutes 47.65 seconds (3947.65 seconds total)