Starting phenix.real_space_refine on Sun Sep 13 12:40:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ryu_10059/09_2026/6ryu_10059.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ryu_10059/09_2026/6ryu_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_2026/6ryu_10059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ryu_10059/09_2026/6ryu_10059.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ryu_10059/09_2026/6ryu_10059.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ryu_10059/09_2026/6ryu_10059.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ryu_10059/09_2026/6ryu_10059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ryu_10059/09_2026/6ryu_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-2.2.1-6174/lib/python3.11/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: 7.01, per 1000 atoms: 0.30 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: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.20 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: 5.98 Time building geometry restraints manager: 2.77 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: 34239 3.74 - 7.49: 367 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: 12628 35.84 - 71.68: 1365 71.68 - 107.52: 40 107.52 - 143.36: 2 143.36 - 179.20: 2 Dihedral angle restraints: 14037 sinusoidal: 7683 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 14034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3321 0.085 - 0.169: 444 0.169 - 0.254: 43 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: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.730 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.008 0.254 24716 Z= 0.494 Angle : 1.142 27.018 34672 Z= 0.742 Chirality : 0.060 0.423 3823 Planarity : 0.007 0.091 3367 Dihedral : 22.951 179.204 9933 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 are 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/Z covalent geometry : bond 0.00669 / 0.48 (24702) covalent geometry : angle 1.11518 / 0.74 (34660) hydrogen bonds : bond 0.31799 / 20.58 ( 894) hydrogen bonds : angle 10.87860 / 7.46 ( 2308) metal coordination : bond 0.15391 / 9.83 ( 14) metal coordination : angle 13.39246 / 8.71 ( 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 : 0.818 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: symmetry clash REVERT: B 88 TYR cc_start: 0.7989 (m-10) cc_final: 0.7478 (m-80) REVERT: C 38 ASN cc_start: 0.8542 (m-40) cc_final: 0.7958 (p0) REVERT: D 68 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7263 (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: 0.8795 (mttm) REVERT: H 51 ILE cc_start: 0.9155 (tt) cc_final: 0.8944 (tt) REVERT: H 65 ASP cc_start: 0.8249 (t0) cc_final: 0.7907 (t0) REVERT: W 550 MET cc_start: 0.6267 (mtt) cc_final: 0.5897 (mtm) REVERT: W 608 MET cc_start: 0.7792 (mmm) cc_final: 0.6926 (tpt) REVERT: W 1123 LEU cc_start: 0.8758 (mt) cc_final: 0.8553 (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: 0.0575 (t) REVERT: V 504 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8251 (ttpp) REVERT: V 608 MET cc_start: 0.3331 (mmm) cc_final: 0.2407 (mmt) REVERT: V 731 MET cc_start: 0.6652 (mmm) cc_final: 0.6037 (tpp) REVERT: V 764 PHE cc_start: 0.8455 (t80) cc_final: 0.8226 (t80) REVERT: V 768 LEU cc_start: 0.8923 (mp) cc_final: 0.8553 (tt) REVERT: V 826 ASN cc_start: 0.2605 (OUTLIER) cc_final: 0.2254 (p0) REVERT: V 905 LEU cc_start: 0.8248 (mp) cc_final: 0.7838 (pt) REVERT: V 981 MET cc_start: 0.8699 (ttp) cc_final: 0.7253 (mpp) REVERT: V 1120 PHE cc_start: 0.5802 (t80) cc_final: 0.5478 (t80) REVERT: V 1140 THR cc_start: 0.6788 (m) cc_final: 0.6509 (p) REVERT: V 1155 GLN cc_start: 0.8384 (mm110) cc_final: 0.8048 (tp-100) REVERT: V 1186 GLN cc_start: 0.7364 (mm110) cc_final: 0.6458 (tt0) outliers start: 30 outliers final: 10 residues processed: 484 average time/residue: 0.2002 time to fit residues: 146.6531 Evaluate side-chains 258 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 246 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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: 20.0000 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: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS C 82 HIS C 104 GLN D 92 GLN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 W1067 HIS V 573 ASN V 637 HIS V 673 ASN V 715 GLN V 743 GLN V 826 ASN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 914 HIS V1005 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.089310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.066426 restraints weight = 98005.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067775 restraints weight = 55055.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068548 restraints weight = 38666.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069003 restraints weight = 32021.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.069085 restraints weight = 28962.549| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24716 Z= 0.208 Angle : 0.874 24.972 34672 Z= 0.460 Chirality : 0.052 0.328 3823 Planarity : 0.006 0.061 3367 Dihedral : 26.548 171.976 5674 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.13 % Allowed : 14.07 % Favored : 83.80 % 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 are not related in a simple way. whole: -3.76 (0.15), residues: 2126 helix: -2.42 (0.13), residues: 1020 sheet: -2.23 (0.38), residues: 164 loop : -2.51 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG V1047 TYR 0.025 0.002 TYR V 613 PHE 0.023 0.002 PHE V1122 TRP 0.041 0.002 TRP V 736 HIS 0.015 0.002 HIS V 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.21 (24702) covalent geometry : angle 0.84918 / 0.46 (34660) hydrogen bonds : bond 0.08516 / 5.55 ( 894) hydrogen bonds : angle 4.90104 / 3.33 ( 2308) metal coordination : bond 0.01220 / 0.87 ( 14) metal coordination : angle 11.08720 / 7.61 ( 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 304 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8078 (m-10) cc_final: 0.7428 (m-80) REVERT: C 38 ASN cc_start: 0.8554 (m-40) cc_final: 0.7916 (p0) REVERT: D 56 MET cc_start: 0.8531 (tpp) cc_final: 0.8179 (tpp) REVERT: D 68 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7559 (tm-30) REVERT: F 74 GLU cc_start: 0.8071 (tp30) cc_final: 0.7721 (tp30) REVERT: F 88 TYR cc_start: 0.7492 (m-80) cc_final: 0.7262 (m-80) REVERT: G 61 GLU cc_start: 0.7441 (tp30) cc_final: 0.7221 (tp30) REVERT: H 40 LYS cc_start: 0.9326 (mtpt) cc_final: 0.8931 (mttm) REVERT: W 550 MET cc_start: 0.6194 (mtt) cc_final: 0.5755 (mtm) REVERT: W 954 MET cc_start: 0.6575 (tmm) cc_final: 0.6231 (tpt) REVERT: W 1058 MET cc_start: 0.6841 (tpp) cc_final: 0.6556 (tpp) REVERT: W 1123 LEU cc_start: 0.8681 (mt) cc_final: 0.8446 (mp) REVERT: V 645 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6940 (mtm-85) REVERT: V 731 MET cc_start: 0.6881 (mmm) cc_final: 0.5935 (tpp) REVERT: V 848 LEU cc_start: 0.8277 (tt) cc_final: 0.8075 (tt) REVERT: V 905 LEU cc_start: 0.8470 (mp) cc_final: 0.8049 (pt) REVERT: V 956 ARG cc_start: 0.7147 (tpt-90) cc_final: 0.6851 (pmt-80) REVERT: V 1039 MET cc_start: 0.6900 (mmt) cc_final: 0.6270 (mmt) REVERT: V 1045 LEU cc_start: 0.7545 (pp) cc_final: 0.7217 (tp) REVERT: V 1062 LEU cc_start: 0.8610 (tt) cc_final: 0.8407 (tp) REVERT: V 1075 MET cc_start: 0.8228 (mpp) cc_final: 0.7956 (mmm) REVERT: V 1131 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6027 (mp) REVERT: V 1155 GLN cc_start: 0.8064 (mm110) cc_final: 0.7681 (tp-100) REVERT: V 1186 GLN cc_start: 0.7538 (mm110) cc_final: 0.6734 (tt0) outliers start: 39 outliers final: 23 residues processed: 295 average time/residue: 0.1761 time to fit residues: 81.4761 Evaluate side-chains 242 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR 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 F residue 30 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 494 THR 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 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 467 CYS Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 645 ARG 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 1084 ASP 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: 0.2980 chunk 216 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 53 optimal weight: 0.0050 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 575 GLN V 743 GLN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 907 ASN ** 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 = 0.3793 r_free = 0.3793 target = 0.089752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068278 restraints weight = 159658.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.068836 restraints weight = 90637.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069194 restraints weight = 53706.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.069403 restraints weight = 48929.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069476 restraints weight = 40681.776| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 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 = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24716 Z= 0.151 Angle : 0.726 21.260 34672 Z= 0.389 Chirality : 0.045 0.260 3823 Planarity : 0.005 0.059 3367 Dihedral : 26.615 175.017 5664 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.59 % Allowed : 16.69 % Favored : 81.72 % 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 are not related in a simple way. whole: -2.77 (0.16), residues: 2126 helix: -1.40 (0.15), residues: 1019 sheet: -1.86 (0.39), residues: 160 loop : -2.25 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 39 TYR 0.026 0.002 TYR V1023 PHE 0.037 0.001 PHE V 764 TRP 0.056 0.002 TRP V 797 HIS 0.016 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (24702) covalent geometry : angle 0.70421 / 0.39 (34660) hydrogen bonds : bond 0.06230 / 3.99 ( 894) hydrogen bonds : angle 4.27630 / 2.93 ( 2308) metal coordination : bond 0.01089 / 0.77 ( 14) metal coordination : angle 9.50074 / 6.44 ( 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 280 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.815 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: B 88 TYR cc_start: 0.7920 (m-10) cc_final: 0.7320 (m-80) REVERT: C 38 ASN cc_start: 0.8463 (m-40) cc_final: 0.7922 (p0) REVERT: D 56 MET cc_start: 0.8441 (tpp) cc_final: 0.8148 (tpp) REVERT: D 68 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7784 (tm-30) REVERT: F 88 TYR cc_start: 0.7439 (m-80) cc_final: 0.7190 (m-80) REVERT: H 40 LYS cc_start: 0.9257 (mtpt) cc_final: 0.8896 (mttm) REVERT: W 550 MET cc_start: 0.6310 (mtt) cc_final: 0.5407 (mpp) REVERT: W 608 MET cc_start: 0.7085 (tpp) cc_final: 0.6684 (tpt) REVERT: W 1058 MET cc_start: 0.7380 (tpp) cc_final: 0.7147 (tpp) REVERT: W 1075 MET cc_start: 0.8445 (mtp) cc_final: 0.8181 (mtp) REVERT: W 1123 LEU cc_start: 0.8602 (mt) cc_final: 0.8393 (mp) REVERT: W 1192 MET cc_start: 0.7259 (mtp) cc_final: 0.7014 (ttm) REVERT: V 731 MET cc_start: 0.6782 (mmm) cc_final: 0.5848 (tpp) REVERT: V 905 LEU cc_start: 0.8665 (mp) cc_final: 0.8195 (pt) REVERT: V 955 LEU cc_start: 0.6895 (tt) cc_final: 0.6662 (tt) REVERT: V 1013 MET cc_start: 0.8465 (tpp) cc_final: 0.8171 (tpp) REVERT: V 1039 MET cc_start: 0.7290 (mmt) cc_final: 0.6405 (mmt) REVERT: V 1075 MET cc_start: 0.8170 (mpp) cc_final: 0.7825 (mmm) REVERT: V 1131 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6261 (mp) REVERT: V 1186 GLN cc_start: 0.7279 (mm110) cc_final: 0.6627 (tt0) outliers start: 29 outliers final: 23 residues processed: 270 average time/residue: 0.1634 time to fit residues: 70.9551 Evaluate side-chains 234 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain W residue 494 THR Chi-restraints excluded: chain W residue 794 PHE 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 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 710 VAL Chi-restraints excluded: chain V residue 844 LYS Chi-restraints excluded: chain V residue 859 MET Chi-restraints excluded: chain V residue 970 THR Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1058 MET Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1131 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 119 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN D 92 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 568 GLN W 743 GLN V 819 ASN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1061 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.089046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.067968 restraints weight = 149429.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068413 restraints weight = 81823.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.068765 restraints weight = 51822.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.068844 restraints weight = 48782.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068928 restraints weight = 41055.783| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24716 Z= 0.159 Angle : 0.719 17.469 34672 Z= 0.380 Chirality : 0.045 0.269 3823 Planarity : 0.005 0.055 3367 Dihedral : 26.677 172.220 5663 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.08 % Allowed : 17.30 % Favored : 80.62 % 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 are not related in a simple way. whole: -2.15 (0.17), residues: 2126 helix: -0.73 (0.15), residues: 1016 sheet: -1.63 (0.40), residues: 162 loop : -2.12 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 49 TYR 0.029 0.002 TYR W 649 PHE 0.022 0.002 PHE V 764 TRP 0.032 0.002 TRP V 797 HIS 0.015 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (24702) covalent geometry : angle 0.70240 / 0.38 (34660) hydrogen bonds : bond 0.05511 / 3.52 ( 894) hydrogen bonds : angle 4.07516 / 2.79 ( 2308) metal coordination : bond 0.00826 / 0.59 ( 14) metal coordination : angle 8.18630 / 5.42 ( 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 260 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 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: B 88 TYR cc_start: 0.8044 (m-10) cc_final: 0.7443 (m-80) REVERT: C 38 ASN cc_start: 0.8463 (m-40) cc_final: 0.7900 (p0) REVERT: D 56 MET cc_start: 0.8534 (tpp) cc_final: 0.8100 (tpp) REVERT: D 68 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7765 (tm-30) REVERT: F 88 TYR cc_start: 0.7480 (m-80) cc_final: 0.7221 (m-80) REVERT: H 40 LYS cc_start: 0.9267 (mtpt) cc_final: 0.9015 (mttm) REVERT: W 550 MET cc_start: 0.6336 (mtt) cc_final: 0.5405 (mpp) REVERT: W 608 MET cc_start: 0.7448 (tpp) cc_final: 0.6941 (tpt) REVERT: W 1058 MET cc_start: 0.7397 (tpp) cc_final: 0.7047 (tpp) REVERT: W 1075 MET cc_start: 0.8550 (mtp) cc_final: 0.8293 (mtp) REVERT: W 1083 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: W 1123 LEU cc_start: 0.8577 (mt) cc_final: 0.8376 (mp) REVERT: W 1192 MET cc_start: 0.7334 (mtp) cc_final: 0.7107 (ttm) REVERT: V 449 MET cc_start: 0.4662 (pmm) cc_final: 0.4269 (mmt) REVERT: V 712 TYR cc_start: 0.5445 (m-80) cc_final: 0.4823 (m-10) REVERT: V 731 MET cc_start: 0.7015 (mmm) cc_final: 0.6000 (tpp) REVERT: V 796 MET cc_start: 0.7214 (tpt) cc_final: 0.6938 (tpp) REVERT: V 809 ASP cc_start: 0.8676 (p0) cc_final: 0.8018 (p0) REVERT: V 905 LEU cc_start: 0.8576 (mp) cc_final: 0.8171 (pt) REVERT: V 1013 MET cc_start: 0.8502 (tpp) cc_final: 0.8186 (tpp) REVERT: V 1075 MET cc_start: 0.8191 (mpp) cc_final: 0.7913 (mmm) REVERT: V 1186 GLN cc_start: 0.7430 (mm110) cc_final: 0.6729 (tt0) outliers start: 38 outliers final: 29 residues processed: 249 average time/residue: 0.1625 time to fit residues: 65.3855 Evaluate side-chains 234 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 THR 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 E residue 100 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU 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 605 PHE 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 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 970 THR Chi-restraints excluded: chain V residue 1006 VAL Chi-restraints excluded: chain V residue 1011 VAL Chi-restraints excluded: chain V residue 1058 MET Chi-restraints excluded: chain V residue 1082 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 106 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 204 optimal weight: 0.6980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 743 GLN ** W1021 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.089973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068868 restraints weight = 133505.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069211 restraints weight = 76580.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069946 restraints weight = 49752.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.070029 restraints weight = 40563.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.070091 restraints weight = 37892.198| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 24716 Z= 0.132 Angle : 0.665 14.692 34672 Z= 0.357 Chirality : 0.043 0.283 3823 Planarity : 0.004 0.055 3367 Dihedral : 26.547 172.435 5662 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.19 % Allowed : 18.12 % Favored : 79.69 % 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 are not related in a simple way. whole: -1.70 (0.17), residues: 2126 helix: -0.24 (0.16), residues: 1021 sheet: -1.49 (0.41), residues: 162 loop : -2.05 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.028 0.001 TYR V1023 PHE 0.032 0.001 PHE V 764 TRP 0.039 0.002 TRP W 488 HIS 0.013 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (24702) covalent geometry : angle 0.65294 / 0.36 (34660) hydrogen bonds : bond 0.04923 / 3.18 ( 894) hydrogen bonds : angle 3.77432 / 2.58 ( 2308) metal coordination : bond 0.00743 / 0.54 ( 14) metal coordination : angle 6.85712 / 4.45 ( 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 265 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.811 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: A 100 LEU cc_start: 0.9071 (mt) cc_final: 0.8867 (mt) REVERT: B 68 ASP cc_start: 0.8223 (m-30) cc_final: 0.7349 (m-30) REVERT: B 88 TYR cc_start: 0.8026 (m-10) cc_final: 0.7305 (m-80) REVERT: B 92 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7256 (tmm-80) REVERT: C 38 ASN cc_start: 0.8341 (m-40) cc_final: 0.7842 (p0) REVERT: C 92 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6746 (pt0) REVERT: D 56 MET cc_start: 0.8511 (tpp) cc_final: 0.8094 (tpp) REVERT: D 68 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7755 (tm-30) REVERT: E 106 ASP cc_start: 0.7050 (m-30) cc_final: 0.6821 (m-30) REVERT: E 120 MET cc_start: 0.8210 (mtp) cc_final: 0.7968 (mtp) REVERT: F 74 GLU cc_start: 0.7991 (tp30) cc_final: 0.7790 (tp30) REVERT: F 88 TYR cc_start: 0.7404 (m-80) cc_final: 0.7100 (m-80) REVERT: H 40 LYS cc_start: 0.9224 (mtpt) cc_final: 0.8965 (mttm) REVERT: W 550 MET cc_start: 0.6289 (mtt) cc_final: 0.5411 (mpp) REVERT: W 608 MET cc_start: 0.7400 (tpp) cc_final: 0.6927 (tpp) REVERT: W 622 MET cc_start: 0.7290 (mmp) cc_final: 0.7043 (mmt) REVERT: W 837 MET cc_start: 0.3504 (OUTLIER) cc_final: 0.2426 (mmt) REVERT: W 1058 MET cc_start: 0.7378 (tpp) cc_final: 0.7053 (tpp) REVERT: W 1075 MET cc_start: 0.8548 (mtp) cc_final: 0.8321 (mtp) REVERT: W 1080 ASP cc_start: 0.7995 (m-30) cc_final: 0.7670 (m-30) REVERT: W 1083 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: W 1192 MET cc_start: 0.7313 (mtp) cc_final: 0.7094 (ttm) REVERT: V 449 MET cc_start: 0.4606 (pmm) cc_final: 0.4276 (mmt) REVERT: V 623 MET cc_start: 0.8189 (tpp) cc_final: 0.7920 (tpp) REVERT: V 712 TYR cc_start: 0.5276 (m-80) cc_final: 0.4684 (m-10) REVERT: V 731 MET cc_start: 0.6928 (mmm) cc_final: 0.5803 (tpp) REVERT: V 905 LEU cc_start: 0.8580 (mp) cc_final: 0.8217 (pt) REVERT: V 1013 MET cc_start: 0.8449 (tpp) cc_final: 0.8200 (tpp) REVERT: V 1075 MET cc_start: 0.7964 (mpp) cc_final: 0.7503 (mmm) REVERT: V 1186 GLN cc_start: 0.7254 (mm110) cc_final: 0.6604 (tt0) outliers start: 40 outliers final: 24 residues processed: 255 average time/residue: 0.1633 time to fit residues: 67.2103 Evaluate side-chains 231 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 68 GLU 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 949 MET 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 467 CYS Chi-restraints excluded: chain V residue 510 TRP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 0.5980 chunk 235 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN W 743 GLN ** W1021 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.089070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.067960 restraints weight = 135988.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.068384 restraints weight = 78099.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068632 restraints weight = 50380.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068769 restraints weight = 46890.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068917 restraints weight = 40099.289| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4028 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= 0.154 Angle : 0.675 13.728 34672 Z= 0.357 Chirality : 0.044 0.526 3823 Planarity : 0.004 0.053 3367 Dihedral : 26.591 170.682 5662 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.46 % Allowed : 19.38 % Favored : 78.16 % 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 are not related in a simple way. whole: -1.43 (0.18), residues: 2126 helix: 0.08 (0.16), residues: 1014 sheet: -1.52 (0.40), residues: 162 loop : -1.98 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W1068 TYR 0.028 0.002 TYR W 649 PHE 0.031 0.001 PHE V 764 TRP 0.022 0.001 TRP V 797 HIS 0.011 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (24702) covalent geometry : angle 0.66477 / 0.36 (34660) hydrogen bonds : bond 0.05058 / 3.23 ( 894) hydrogen bonds : angle 3.79862 / 2.60 ( 2308) metal coordination : bond 0.00717 / 0.53 ( 14) metal coordination : angle 6.43193 / 4.24 ( 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 253 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 88 TYR cc_start: 0.8185 (m-10) cc_final: 0.7547 (m-80) REVERT: B 92 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7565 (tmm-80) REVERT: C 38 ASN cc_start: 0.8403 (m-40) cc_final: 0.7918 (p0) REVERT: D 56 MET cc_start: 0.8584 (tpp) cc_final: 0.8138 (tpp) REVERT: D 68 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7784 (tm-30) REVERT: E 120 MET cc_start: 0.8279 (mtp) cc_final: 0.7968 (mtp) REVERT: F 88 TYR cc_start: 0.7544 (m-80) cc_final: 0.7139 (m-80) REVERT: H 40 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8996 (mttm) REVERT: W 550 MET cc_start: 0.6359 (mtt) cc_final: 0.5385 (mpp) REVERT: W 608 MET cc_start: 0.7390 (tpp) cc_final: 0.6903 (tpp) REVERT: W 622 MET cc_start: 0.7385 (mmp) cc_final: 0.7152 (mmt) REVERT: W 1013 MET cc_start: 0.8858 (tpp) cc_final: 0.8604 (tpp) REVERT: W 1058 MET cc_start: 0.7494 (tpp) cc_final: 0.7203 (tpp) REVERT: W 1075 MET cc_start: 0.8655 (mtp) cc_final: 0.8433 (mtp) REVERT: W 1080 ASP cc_start: 0.7911 (m-30) cc_final: 0.7604 (m-30) REVERT: W 1083 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7804 (tp30) REVERT: W 1192 MET cc_start: 0.7477 (mtp) cc_final: 0.7242 (ttm) REVERT: V 449 MET cc_start: 0.4615 (pmm) cc_final: 0.4192 (mmt) REVERT: V 623 MET cc_start: 0.8178 (tpp) cc_final: 0.7923 (tpp) REVERT: V 712 TYR cc_start: 0.5401 (m-80) cc_final: 0.5086 (m-10) REVERT: V 731 MET cc_start: 0.7067 (mmm) cc_final: 0.6538 (mmm) REVERT: V 905 LEU cc_start: 0.8608 (mp) cc_final: 0.8175 (pt) REVERT: V 1013 MET cc_start: 0.8452 (tpp) cc_final: 0.8153 (tpp) REVERT: V 1075 MET cc_start: 0.8053 (mpp) cc_final: 0.7639 (mmm) REVERT: V 1186 GLN cc_start: 0.7448 (mm110) cc_final: 0.6612 (tt0) outliers start: 45 outliers final: 33 residues processed: 241 average time/residue: 0.1642 time to fit residues: 64.1191 Evaluate side-chains 234 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 B residue 92 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR 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 E residue 100 LEU Chi-restraints excluded: chain F residue 57 VAL 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 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 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 1194 LEU Chi-restraints excluded: chain V residue 446 ASP Chi-restraints excluded: chain V residue 467 CYS Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 624 ILE Chi-restraints excluded: chain V residue 764 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 122 optimal weight: 0.0870 chunk 196 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 234 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 448 HIS ** W1021 HIS ** 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** ** 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 = 0.3792 r_free = 0.3792 target = 0.089818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068819 restraints weight = 153005.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069470 restraints weight = 79991.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.069765 restraints weight = 50871.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.070076 restraints weight = 46302.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070075 restraints weight = 40872.992| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24716 Z= 0.127 Angle : 0.641 12.168 34672 Z= 0.344 Chirality : 0.042 0.281 3823 Planarity : 0.004 0.065 3367 Dihedral : 26.486 170.954 5662 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.75 % Allowed : 20.20 % Favored : 78.05 % 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 are not related in a simple way. whole: -1.16 (0.18), residues: 2126 helix: 0.33 (0.16), residues: 1014 sheet: -1.18 (0.41), residues: 154 loop : -1.92 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.027 0.001 TYR V1023 PHE 0.023 0.001 PHE V 764 TRP 0.016 0.001 TRP V 736 HIS 0.010 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (24702) covalent geometry : angle 0.63140 / 0.34 (34660) hydrogen bonds : bond 0.04605 / 2.97 ( 894) hydrogen bonds : angle 3.60049 / 2.46 ( 2308) metal coordination : bond 0.00675 / 0.51 ( 14) metal coordination : angle 5.97529 / 3.94 ( 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 249 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 68 ASP cc_start: 0.8386 (m-30) cc_final: 0.7443 (m-30) REVERT: B 88 TYR cc_start: 0.8135 (m-10) cc_final: 0.7501 (m-80) REVERT: B 92 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7421 (tmm-80) REVERT: C 38 ASN cc_start: 0.8342 (m-40) cc_final: 0.7878 (p0) REVERT: D 56 MET cc_start: 0.8495 (tpp) cc_final: 0.8070 (tpp) REVERT: D 68 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7803 (tm-30) REVERT: E 105 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7117 (tm-30) REVERT: E 120 MET cc_start: 0.8250 (mtp) cc_final: 0.7964 (mtp) REVERT: E 123 ASP cc_start: 0.8535 (m-30) cc_final: 0.8310 (m-30) REVERT: F 88 TYR cc_start: 0.7622 (m-80) cc_final: 0.7201 (m-80) REVERT: H 40 LYS cc_start: 0.9217 (mtpt) cc_final: 0.8960 (mttm) REVERT: W 448 HIS cc_start: 0.3451 (OUTLIER) cc_final: 0.1195 (p90) REVERT: W 550 MET cc_start: 0.6273 (mtt) cc_final: 0.5341 (mpp) REVERT: W 608 MET cc_start: 0.7432 (tpp) cc_final: 0.7058 (tpp) REVERT: W 1023 TYR cc_start: 0.8211 (m-10) cc_final: 0.7763 (m-80) REVERT: W 1058 MET cc_start: 0.7405 (tpp) cc_final: 0.7138 (tpp) REVERT: W 1075 MET cc_start: 0.8476 (mtp) cc_final: 0.8243 (mtp) REVERT: W 1080 ASP cc_start: 0.7938 (m-30) cc_final: 0.7662 (m-30) REVERT: W 1083 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: V 449 MET cc_start: 0.4882 (pmm) cc_final: 0.4226 (mmt) REVERT: V 469 SER cc_start: 0.5202 (m) cc_final: 0.4599 (p) REVERT: V 623 MET cc_start: 0.8121 (tpp) cc_final: 0.7879 (tpp) REVERT: V 873 ASP cc_start: 0.7908 (t0) cc_final: 0.7665 (t0) REVERT: V 905 LEU cc_start: 0.8568 (mp) cc_final: 0.8201 (pt) REVERT: V 1013 MET cc_start: 0.8448 (tpp) cc_final: 0.8119 (tpp) REVERT: V 1039 MET cc_start: 0.7466 (mmt) cc_final: 0.6527 (mmm) REVERT: V 1075 MET cc_start: 0.7990 (mpp) cc_final: 0.7694 (mmm) REVERT: V 1186 GLN cc_start: 0.7409 (mm110) cc_final: 0.6543 (tt0) outliers start: 32 outliers final: 19 residues processed: 244 average time/residue: 0.1595 time to fit residues: 63.4872 Evaluate side-chains 224 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL 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 448 HIS Chi-restraints excluded: chain W residue 747 THR 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 1194 LEU Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 624 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 8 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 161 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 122 optimal weight: 0.0000 chunk 123 optimal weight: 0.0000 overall best weight: 0.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS W 448 HIS ** W1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1151 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.090252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.067480 restraints weight = 113180.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068807 restraints weight = 59836.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069510 restraints weight = 40328.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070139 restraints weight = 32969.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070443 restraints weight = 29212.711| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24716 Z= 0.122 Angle : 0.648 12.043 34672 Z= 0.344 Chirality : 0.042 0.432 3823 Planarity : 0.004 0.053 3367 Dihedral : 26.419 170.348 5660 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.03 % Allowed : 20.25 % Favored : 77.72 % 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 are not related in a simple way. whole: -1.11 (0.18), residues: 2126 helix: 0.33 (0.16), residues: 1038 sheet: -1.17 (0.40), residues: 154 loop : -1.90 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 71 TYR 0.026 0.001 TYR V1023 PHE 0.028 0.001 PHE V 764 TRP 0.015 0.001 TRP V 736 HIS 0.038 0.001 HIS W 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (24702) covalent geometry : angle 0.63921 / 0.34 (34660) hydrogen bonds : bond 0.04529 / 2.93 ( 894) hydrogen bonds : angle 3.52085 / 2.41 ( 2308) metal coordination : bond 0.00747 / 0.52 ( 14) metal coordination : angle 5.83181 / 3.85 ( 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 249 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7236 (tm-30) REVERT: A 125 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7919 (mp10) REVERT: B 16 LYS cc_start: 0.6208 (pptt) cc_final: 0.5706 (tptp) REVERT: B 68 ASP cc_start: 0.8286 (m-30) cc_final: 0.7478 (m-30) REVERT: B 92 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7338 (tmm-80) REVERT: C 38 ASN cc_start: 0.8391 (m-40) cc_final: 0.7916 (p0) REVERT: D 56 MET cc_start: 0.8481 (tpp) cc_final: 0.8014 (tpp) REVERT: E 120 MET cc_start: 0.8255 (mtp) cc_final: 0.7982 (mtp) REVERT: E 123 ASP cc_start: 0.8497 (m-30) cc_final: 0.8270 (m-30) REVERT: F 88 TYR cc_start: 0.7457 (m-80) cc_final: 0.7102 (m-80) REVERT: H 40 LYS cc_start: 0.9205 (mtpt) cc_final: 0.8990 (mttm) REVERT: W 550 MET cc_start: 0.6220 (mtt) cc_final: 0.5290 (mpp) REVERT: W 608 MET cc_start: 0.7367 (tpp) cc_final: 0.7049 (tpp) REVERT: W 1058 MET cc_start: 0.7207 (tpp) cc_final: 0.6979 (tpp) REVERT: W 1075 MET cc_start: 0.8481 (mtp) cc_final: 0.8274 (mtp) REVERT: W 1080 ASP cc_start: 0.7870 (m-30) cc_final: 0.7577 (m-30) REVERT: W 1083 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: V 469 SER cc_start: 0.3684 (m) cc_final: 0.3133 (p) REVERT: V 543 PHE cc_start: 0.7109 (m-10) cc_final: 0.6706 (m-80) REVERT: V 623 MET cc_start: 0.8290 (tpp) cc_final: 0.8017 (tpp) REVERT: V 873 ASP cc_start: 0.7951 (t0) cc_final: 0.7668 (t0) REVERT: V 905 LEU cc_start: 0.8590 (mp) cc_final: 0.8158 (pt) REVERT: V 1013 MET cc_start: 0.8384 (tpp) cc_final: 0.8118 (tpp) REVERT: V 1039 MET cc_start: 0.7317 (mmt) cc_final: 0.6328 (mmt) REVERT: V 1047 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6823 (ptp90) REVERT: V 1075 MET cc_start: 0.7910 (mpp) cc_final: 0.7465 (mmm) REVERT: V 1186 GLN cc_start: 0.7320 (mm110) cc_final: 0.6481 (tt0) outliers start: 37 outliers final: 29 residues processed: 242 average time/residue: 0.1599 time to fit residues: 63.2208 Evaluate side-chains 233 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 57 SER 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 H residue 68 GLU Chi-restraints excluded: chain W residue 466 THR Chi-restraints excluded: chain W residue 624 ILE Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 801 MET Chi-restraints excluded: chain W residue 811 ASP 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 1194 LEU Chi-restraints excluded: chain V residue 467 CYS Chi-restraints excluded: chain V residue 510 TRP Chi-restraints excluded: chain V residue 624 ILE 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 1047 ARG Chi-restraints excluded: chain V residue 1082 LEU Chi-restraints excluded: chain V residue 1084 ASP 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: 0.5980 chunk 84 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 0.0870 chunk 53 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 overall best weight: 2.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN W 947 HIS 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** ** 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 = 0.3761 r_free = 0.3761 target = 0.088464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.067944 restraints weight = 142654.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068291 restraints weight = 76406.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068724 restraints weight = 50227.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.068906 restraints weight = 45249.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068948 restraints weight = 39795.311| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24716 Z= 0.180 Angle : 0.708 15.026 34672 Z= 0.369 Chirality : 0.045 0.327 3823 Planarity : 0.005 0.052 3367 Dihedral : 26.602 170.602 5660 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.81 % Allowed : 20.42 % Favored : 77.78 % 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 are not related in a simple way. whole: -1.14 (0.18), residues: 2126 helix: 0.32 (0.16), residues: 1029 sheet: -1.55 (0.37), residues: 178 loop : -1.83 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 35 TYR 0.023 0.002 TYR V1023 PHE 0.041 0.002 PHE W 913 TRP 0.018 0.002 TRP V 736 HIS 0.008 0.001 HIS W 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (24702) covalent geometry : angle 0.70013 / 0.37 (34660) hydrogen bonds : bond 0.05150 / 3.29 ( 894) hydrogen bonds : angle 3.75914 / 2.57 ( 2308) metal coordination : bond 0.00758 / 0.56 ( 14) metal coordination : angle 5.84609 / 3.92 ( 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 239 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 16 LYS cc_start: 0.6139 (pptt) cc_final: 0.5549 (tptp) REVERT: B 88 TYR cc_start: 0.8424 (m-10) cc_final: 0.7866 (m-80) REVERT: D 56 MET cc_start: 0.8556 (tpp) cc_final: 0.8126 (tpp) REVERT: E 120 MET cc_start: 0.8356 (mtp) cc_final: 0.8006 (mtp) REVERT: F 88 TYR cc_start: 0.7661 (m-80) cc_final: 0.7296 (m-80) REVERT: H 40 LYS cc_start: 0.9216 (mtpt) cc_final: 0.9014 (mttm) REVERT: W 550 MET cc_start: 0.6295 (mtt) cc_final: 0.5321 (mpp) REVERT: W 608 MET cc_start: 0.7422 (tpp) cc_final: 0.6980 (tpp) REVERT: W 1058 MET cc_start: 0.7403 (tpp) cc_final: 0.7133 (tpp) REVERT: W 1075 MET cc_start: 0.8575 (mtp) cc_final: 0.8345 (mtp) REVERT: W 1083 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: V 873 ASP cc_start: 0.8028 (t0) cc_final: 0.7695 (t0) REVERT: V 905 LEU cc_start: 0.8525 (mp) cc_final: 0.8124 (pt) REVERT: V 1013 MET cc_start: 0.8413 (tpp) cc_final: 0.8059 (tpp) REVERT: V 1186 GLN cc_start: 0.7466 (mm110) cc_final: 0.6514 (tt0) outliers start: 33 outliers final: 28 residues processed: 231 average time/residue: 0.1477 time to fit residues: 56.9964 Evaluate side-chains 226 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL 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 H residue 68 GLU Chi-restraints excluded: chain W residue 448 HIS 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 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 624 ILE Chi-restraints excluded: chain V residue 764 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 199 optimal weight: 0.4980 chunk 235 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 0.0370 chunk 209 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 715 GLN ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.088870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.068275 restraints weight = 150694.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068471 restraints weight = 84038.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068908 restraints weight = 53200.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069129 restraints weight = 47843.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.069201 restraints weight = 41592.264| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4550 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 : 0.681 14.180 34672 Z= 0.358 Chirality : 0.043 0.300 3823 Planarity : 0.004 0.052 3367 Dihedral : 26.566 171.006 5660 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.70 % Allowed : 20.63 % 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 are not related in a simple way. whole: -0.99 (0.18), residues: 2126 helix: 0.45 (0.17), residues: 1029 sheet: -1.48 (0.37), residues: 178 loop : -1.77 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.023 0.002 TYR V1023 PHE 0.032 0.002 PHE W 913 TRP 0.017 0.001 TRP V 736 HIS 0.008 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (24702) covalent geometry : angle 0.67202 / 0.36 (34660) hydrogen bonds : bond 0.04695 / 3.01 ( 894) hydrogen bonds : angle 3.66109 / 2.50 ( 2308) metal coordination : bond 0.00774 / 0.58 ( 14) metal coordination : angle 5.98426 / 4.04 ( 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 229 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7368 (tm-30) REVERT: A 125 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: B 16 LYS cc_start: 0.6148 (pptt) cc_final: 0.5604 (tptp) REVERT: B 68 ASP cc_start: 0.8470 (m-30) cc_final: 0.7734 (m-30) REVERT: B 88 TYR cc_start: 0.8389 (m-10) cc_final: 0.7759 (m-80) REVERT: B 92 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7502 (tmm-80) REVERT: C 64 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7575 (mm-30) REVERT: D 56 MET cc_start: 0.8463 (tpp) cc_final: 0.8110 (tpp) REVERT: E 120 MET cc_start: 0.8274 (mtp) cc_final: 0.8015 (mtp) REVERT: F 88 TYR cc_start: 0.7668 (m-80) cc_final: 0.7305 (m-80) REVERT: H 40 LYS cc_start: 0.9205 (mtpt) cc_final: 0.8959 (mttm) REVERT: W 550 MET cc_start: 0.6246 (mtt) cc_final: 0.5311 (mpp) REVERT: W 608 MET cc_start: 0.7396 (tpp) cc_final: 0.6945 (tpp) REVERT: W 837 MET cc_start: 0.3511 (ptp) cc_final: 0.1940 (mmt) REVERT: W 1058 MET cc_start: 0.7408 (tpp) cc_final: 0.7134 (tpp) REVERT: W 1075 MET cc_start: 0.8489 (mtp) cc_final: 0.8288 (mtp) REVERT: W 1080 ASP cc_start: 0.7872 (m-30) cc_final: 0.7568 (m-30) REVERT: W 1083 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: V 873 ASP cc_start: 0.8054 (t0) cc_final: 0.7733 (t0) REVERT: V 905 LEU cc_start: 0.8530 (mp) cc_final: 0.8124 (pt) REVERT: V 1013 MET cc_start: 0.8439 (tpp) cc_final: 0.8088 (tpp) REVERT: V 1186 GLN cc_start: 0.7466 (mm110) cc_final: 0.6501 (tt0) outliers start: 31 outliers final: 26 residues processed: 223 average time/residue: 0.1501 time to fit residues: 55.2943 Evaluate side-chains 225 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL 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 G residue 90 ASP Chi-restraints excluded: chain H residue 68 GLU 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 624 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 235 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 135 optimal weight: 0.0010 chunk 209 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 148 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 669 GLN V 715 GLN V 876 HIS ** V 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1021 HIS ** 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 = 0.3729 r_free = 0.3729 target = 0.086996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.066950 restraints weight = 148763.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066861 restraints weight = 80336.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067213 restraints weight = 57723.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.067513 restraints weight = 46390.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.067579 restraints weight = 42548.039| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4672 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= 0.228 Angle : 0.762 13.809 34672 Z= 0.393 Chirality : 0.047 0.293 3823 Planarity : 0.005 0.049 3367 Dihedral : 26.802 172.052 5660 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.81 % Allowed : 20.80 % 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 are not related in a simple way. whole: -1.13 (0.18), residues: 2126 helix: 0.28 (0.16), residues: 1020 sheet: -1.35 (0.38), residues: 184 loop : -1.78 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG V 453 TYR 0.021 0.002 TYR A 54 PHE 0.031 0.002 PHE W 913 TRP 0.019 0.002 TRP V 508 HIS 0.008 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 (24702) covalent geometry : angle 0.75317 / 0.39 (34660) hydrogen bonds : bond 0.05648 / 3.55 ( 894) hydrogen bonds : angle 4.04358 / 2.77 ( 2308) metal coordination : bond 0.00881 / 0.66 ( 14) metal coordination : angle 6.17689 / 4.15 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4182.52 seconds wall clock time: 73 minutes 13.09 seconds (4393.09 seconds total)