Starting phenix.real_space_refine on Sat Jun 14 16:18:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc4_15962/06_2025/8bc4_15962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc4_15962/06_2025/8bc4_15962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bc4_15962/06_2025/8bc4_15962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc4_15962/06_2025/8bc4_15962.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc4_15962/06_2025/8bc4_15962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc4_15962/06_2025/8bc4_15962.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 10399 2.51 5 N 2679 2.21 5 O 3315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16440 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1607 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1602 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1596 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1617 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1615 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "F" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1613 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 53 Chain: "G" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1604 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "H" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1598 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "I" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1587 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 67 Chain: "J" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1605 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 10.16, per 1000 atoms: 0.62 Number of scatterers: 16440 At special positions: 0 Unit cell: (115.2, 115.2, 86.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 3315 8.00 N 2679 7.00 C 10399 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 2.1 seconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 10 sheets defined 57.5% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.551A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.516A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 removed outlier: 3.627A pdb=" N ALA A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 136 through 142 removed outlier: 3.625A pdb=" N SER A 142 " --> pdb=" O TRP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.628A pdb=" N ASP A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 68 through 73 removed outlier: 3.702A pdb=" N VAL B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 removed outlier: 3.904A pdb=" N LYS B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 118 through 127 removed outlier: 4.145A pdb=" N GLN B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 136 through 142 removed outlier: 3.625A pdb=" N SER B 142 " --> pdb=" O TRP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 200 through 216 removed outlier: 3.698A pdb=" N ASP B 204 " --> pdb=" O HIS B 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.540A pdb=" N TYR C 15 " --> pdb=" O GLU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 68 through 79 Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 117 through 127 removed outlier: 4.082A pdb=" N GLN C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 136 through 142 removed outlier: 3.625A pdb=" N SER C 142 " --> pdb=" O TRP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 190 through 198 Processing helix chain 'C' and resid 200 through 216 removed outlier: 3.627A pdb=" N ASP C 204 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.701A pdb=" N GLY D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 68 through 76 removed outlier: 3.749A pdb=" N GLU D 74 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 75 " --> pdb=" O ASP D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.716A pdb=" N LYS D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 106 Processing helix chain 'D' and resid 117 through 126 removed outlier: 4.243A pdb=" N GLN D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 136 through 142 removed outlier: 3.710A pdb=" N SER D 142 " --> pdb=" O TRP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 172 through 183 Processing helix chain 'D' and resid 190 through 198 Processing helix chain 'D' and resid 200 through 216 removed outlier: 3.628A pdb=" N ASP D 204 " --> pdb=" O HIS D 200 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 50 removed outlier: 3.779A pdb=" N ALA E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 removed outlier: 3.783A pdb=" N THR E 77 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 82 " --> pdb=" O LYS E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 106 Processing helix chain 'E' and resid 117 through 127 removed outlier: 4.022A pdb=" N GLN E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 136 through 142 removed outlier: 3.625A pdb=" N SER E 142 " --> pdb=" O TRP E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 159 Processing helix chain 'E' and resid 172 through 183 removed outlier: 3.596A pdb=" N ILE E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 Processing helix chain 'E' and resid 201 through 216 removed outlier: 3.730A pdb=" N GLY E 206 " --> pdb=" O PHE E 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 28 through 36 removed outlier: 3.701A pdb=" N MET F 33 " --> pdb=" O PRO F 29 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY F 36 " --> pdb=" O ILE F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 68 through 81 removed outlier: 3.645A pdb=" N THR F 77 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 121 through 126 removed outlier: 3.685A pdb=" N ALA F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 142 removed outlier: 3.624A pdb=" N SER F 142 " --> pdb=" O TRP F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 159 Processing helix chain 'F' and resid 172 through 183 Processing helix chain 'F' and resid 190 through 198 Processing helix chain 'F' and resid 200 through 217 removed outlier: 3.627A pdb=" N ASP F 204 " --> pdb=" O HIS F 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.524A pdb=" N ALA G 21 " --> pdb=" O TYR G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 50 Processing helix chain 'G' and resid 68 through 81 Processing helix chain 'G' and resid 93 through 106 Processing helix chain 'G' and resid 124 through 128 removed outlier: 3.610A pdb=" N ILE G 127 " --> pdb=" O PRO G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 142 removed outlier: 3.626A pdb=" N SER G 142 " --> pdb=" O TRP G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 172 through 183 Processing helix chain 'G' and resid 190 through 198 Processing helix chain 'G' and resid 200 through 216 removed outlier: 3.562A pdb=" N ASP G 204 " --> pdb=" O HIS G 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 28 through 36 removed outlier: 3.703A pdb=" N GLY H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 68 through 81 removed outlier: 3.591A pdb=" N LYS H 78 " --> pdb=" O GLU H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 106 Processing helix chain 'H' and resid 118 through 126 removed outlier: 4.017A pdb=" N GLN H 123 " --> pdb=" O SER H 119 " (cutoff:3.500A) Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 150 through 159 Processing helix chain 'H' and resid 172 through 183 Processing helix chain 'H' and resid 190 through 198 Processing helix chain 'H' and resid 200 through 216 removed outlier: 3.625A pdb=" N ASP H 204 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 50 Processing helix chain 'I' and resid 68 through 81 removed outlier: 3.501A pdb=" N GLU I 74 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR I 77 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS I 78 " --> pdb=" O GLU I 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE I 79 " --> pdb=" O GLU I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 106 Processing helix chain 'I' and resid 118 through 127 removed outlier: 4.017A pdb=" N GLN I 123 " --> pdb=" O SER I 119 " (cutoff:3.500A) Proline residue: I 124 - end of helix Processing helix chain 'I' and resid 136 through 141 Processing helix chain 'I' and resid 149 through 159 removed outlier: 3.564A pdb=" N VAL I 153 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 157 " --> pdb=" O VAL I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 183 removed outlier: 3.737A pdb=" N ALA I 180 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 198 removed outlier: 3.566A pdb=" N TYR I 194 " --> pdb=" O GLY I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 202 removed outlier: 7.202A pdb=" N PHE I 202 " --> pdb=" O GLN I 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 199 through 202' Processing helix chain 'I' and resid 203 through 213 Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY J 36 " --> pdb=" O ILE J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 50 Processing helix chain 'J' and resid 68 through 81 removed outlier: 3.840A pdb=" N LYS J 78 " --> pdb=" O GLU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 105 Processing helix chain 'J' and resid 117 through 126 removed outlier: 4.264A pdb=" N GLN J 123 " --> pdb=" O SER J 119 " (cutoff:3.500A) Proline residue: J 124 - end of helix Processing helix chain 'J' and resid 136 through 142 removed outlier: 3.625A pdb=" N SER J 142 " --> pdb=" O TRP J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 172 through 183 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 200 through 216 removed outlier: 3.626A pdb=" N ASP J 204 " --> pdb=" O HIS J 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.089A pdb=" N ILE A 165 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR A 188 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 167 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 132 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR A 110 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER A 133 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL A 112 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN A 111 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 88 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 113 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 90 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL A 115 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A 58 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS A 89 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 60 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.104A pdb=" N GLY B 24 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 25 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU B 61 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 58 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS B 89 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 60 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN B 111 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 88 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR B 113 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 90 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL B 115 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR B 110 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER B 133 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL B 112 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL B 132 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE B 165 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR B 188 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 167 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY C 24 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU C 61 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASN C 111 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 88 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 113 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE C 90 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 115 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR C 110 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER C 133 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL C 112 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 132 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE C 165 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL C 167 " --> pdb=" O THR C 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.243A pdb=" N GLY D 24 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL D 25 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU D 61 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE D 58 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS D 89 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL D 60 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN D 111 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 88 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR D 113 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE D 90 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL D 115 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR D 110 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER D 133 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL D 112 " --> pdb=" O SER D 133 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 132 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE D 165 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL D 167 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.125A pdb=" N GLY E 24 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 25 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLU E 61 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE E 58 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS E 89 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL E 60 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN E 111 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE E 88 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR E 113 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE E 90 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL E 115 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR E 110 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER E 133 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL E 112 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL E 132 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE E 165 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR E 188 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL E 167 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.245A pdb=" N GLY F 24 " --> pdb=" O TYR F 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL F 25 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU F 61 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE F 58 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS F 89 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL F 60 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ASN F 111 " --> pdb=" O PHE F 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE F 88 " --> pdb=" O ASN F 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR F 113 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE F 90 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL F 115 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR F 110 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER F 133 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL F 112 " --> pdb=" O SER F 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 132 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE F 165 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR F 188 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL F 167 " --> pdb=" O THR F 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY G 24 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL G 25 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU G 61 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE G 58 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS G 89 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL G 60 " --> pdb=" O LYS G 89 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASN G 111 " --> pdb=" O PHE G 86 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE G 88 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR G 113 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE G 90 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL G 115 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR G 110 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER G 133 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL G 112 " --> pdb=" O SER G 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL G 132 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE G 165 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR G 188 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL G 167 " --> pdb=" O THR G 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY H 24 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL H 25 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU H 61 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE H 58 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS H 89 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL H 60 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN H 111 " --> pdb=" O PHE H 86 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE H 88 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR H 113 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE H 90 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL H 115 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR H 110 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER H 133 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL H 112 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL H 132 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE H 165 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR H 188 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL H 167 " --> pdb=" O THR H 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY I 24 " --> pdb=" O TYR I 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL I 25 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N GLU I 61 " --> pdb=" O VAL I 25 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN I 111 " --> pdb=" O PHE I 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE I 88 " --> pdb=" O ASN I 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR I 113 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE I 90 " --> pdb=" O THR I 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL I 115 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR I 110 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER I 133 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL I 112 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE I 165 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR I 188 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL I 167 " --> pdb=" O THR I 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY J 24 " --> pdb=" O TYR J 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL J 25 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N GLU J 61 " --> pdb=" O VAL J 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE J 58 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS J 89 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL J 60 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASN J 111 " --> pdb=" O PHE J 86 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE J 88 " --> pdb=" O ASN J 111 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR J 113 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE J 90 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL J 115 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR J 110 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER J 133 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL J 112 " --> pdb=" O SER J 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL J 132 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE J 165 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR J 188 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL J 167 " --> pdb=" O THR J 188 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.43 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2665 1.30 - 1.43: 4710 1.43 - 1.57: 9094 1.57 - 1.70: 27 1.70 - 1.84: 65 Bond restraints: 16561 Sorted by residual: bond pdb=" C2 QC9 H 301 " pdb=" O6 QC9 H 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C2 QC9 J 301 " pdb=" O6 QC9 J 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C2 QC9 F 301 " pdb=" O6 QC9 F 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C2 QC9 C 301 " pdb=" O6 QC9 C 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C2 QC9 A 301 " pdb=" O6 QC9 A 301 " ideal model delta sigma weight residual 1.432 1.292 0.140 2.00e-02 2.50e+03 4.92e+01 ... (remaining 16556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 22431 5.38 - 10.76: 160 10.76 - 16.14: 22 16.14 - 21.52: 9 21.52 - 26.90: 18 Bond angle restraints: 22640 Sorted by residual: angle pdb=" C3 QC9 G 301 " pdb=" C12 QC9 G 301 " pdb=" S13 QC9 G 301 " ideal model delta sigma weight residual 112.26 139.16 -26.90 3.00e+00 1.11e-01 8.04e+01 angle pdb=" C3 QC9 B 301 " pdb=" C12 QC9 B 301 " pdb=" S13 QC9 B 301 " ideal model delta sigma weight residual 112.26 139.10 -26.84 3.00e+00 1.11e-01 8.00e+01 angle pdb=" C3 QC9 H 301 " pdb=" C12 QC9 H 301 " pdb=" S13 QC9 H 301 " ideal model delta sigma weight residual 112.26 139.08 -26.82 3.00e+00 1.11e-01 7.99e+01 angle pdb=" C3 QC9 D 301 " pdb=" C12 QC9 D 301 " pdb=" S13 QC9 D 301 " ideal model delta sigma weight residual 112.26 139.08 -26.82 3.00e+00 1.11e-01 7.99e+01 angle pdb=" C3 QC9 J 301 " pdb=" C12 QC9 J 301 " pdb=" S13 QC9 J 301 " ideal model delta sigma weight residual 112.26 139.07 -26.81 3.00e+00 1.11e-01 7.99e+01 ... (remaining 22635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 8349 17.25 - 34.49: 836 34.49 - 51.74: 306 51.74 - 68.98: 101 68.98 - 86.23: 42 Dihedral angle restraints: 9634 sinusoidal: 3323 harmonic: 6311 Sorted by residual: dihedral pdb=" CD ARG I 171 " pdb=" NE ARG I 171 " pdb=" CZ ARG I 171 " pdb=" NH1 ARG I 171 " ideal model delta sinusoidal sigma weight residual 0.00 85.93 -85.93 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CD ARG G 14 " pdb=" NE ARG G 14 " pdb=" CZ ARG G 14 " pdb=" NH1 ARG G 14 " ideal model delta sinusoidal sigma weight residual 0.00 79.93 -79.93 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CD ARG D 14 " pdb=" NE ARG D 14 " pdb=" CZ ARG D 14 " pdb=" NH1 ARG D 14 " ideal model delta sinusoidal sigma weight residual 0.00 73.27 -73.27 1 1.00e+01 1.00e-02 6.84e+01 ... (remaining 9631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1489 0.092 - 0.184: 942 0.184 - 0.276: 127 0.276 - 0.368: 9 0.368 - 0.460: 18 Chirality restraints: 2585 Sorted by residual: chirality pdb=" C2 QC9 D 301 " pdb=" C1 QC9 D 301 " pdb=" C3 QC9 D 301 " pdb=" O6 QC9 D 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" C2 QC9 A 301 " pdb=" C1 QC9 A 301 " pdb=" C3 QC9 A 301 " pdb=" O6 QC9 A 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C2 QC9 E 301 " pdb=" C1 QC9 E 301 " pdb=" C3 QC9 E 301 " pdb=" O6 QC9 E 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 2582 not shown) Planarity restraints: 2926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 14 " 1.099 9.50e-02 1.11e+02 4.93e-01 1.47e+02 pdb=" NE ARG G 14 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG G 14 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG G 14 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG G 14 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 171 " 1.096 9.50e-02 1.11e+02 4.91e-01 1.45e+02 pdb=" NE ARG I 171 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG I 171 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG I 171 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG I 171 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 14 " 1.066 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARG D 14 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG D 14 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 14 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 14 " 0.023 2.00e-02 2.50e+03 ... (remaining 2923 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4510 2.83 - 3.35: 17262 3.35 - 3.86: 30757 3.86 - 4.38: 38233 4.38 - 4.90: 58920 Nonbonded interactions: 149682 Sorted by model distance: nonbonded pdb=" O LEU D 170 " pdb=" O HOH D 401 " model vdw 2.310 3.040 nonbonded pdb=" O LEU E 170 " pdb=" O HOH E 401 " model vdw 2.310 3.040 nonbonded pdb=" O LEU H 170 " pdb=" O HOH H 401 " model vdw 2.311 3.040 nonbonded pdb=" O LEU A 170 " pdb=" O HOH A 401 " model vdw 2.311 3.040 nonbonded pdb=" O LEU C 170 " pdb=" O HOH C 401 " model vdw 2.311 3.040 ... (remaining 149677 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 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 103 or (resid 104 through 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 138 or (re \ sid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 th \ rough 145 or (resid 146 and (name N or name CA or name C or name O or name CB )) \ or resid 148 or (resid 149 through 151 and (name N or name CA or name C or name \ O or name CB )) or resid 152 through 159 or (resid 160 and (name N or name CA o \ r name C or name O or name CB )) or resid 161 through 163 or (resid 164 and (nam \ e N or name CA or name C or name O or name CB )) or resid 165 through 166 or (re \ sid 167 through 170 and (name N or name CA or name C or name O or name CB )) or \ resid 171 through 173 or (resid 174 and (name N or name CA or name C or name O o \ r name CB )) or resid 175 or (resid 176 through 180 and (name N or name CA or na \ me C or name O or name CB )) or resid 181 through 191 or (resid 192 and (name N \ or name CA or name C or name O or name CB )) or resid 193 through 195 or (resid \ 196 and (name N or name CA or name C or name O or name CB )) or resid 197 throug \ h 210 or (resid 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 217)) selection = (chain 'B' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 138 or (resid 139 and (name N or name CA or name C \ or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 148 or (resid 149 through 151 a \ nd (name N or name CA or name C or name O or name CB )) or resid 152 through 156 \ or (resid 157 and (name N or name CA or name C or name O or name CB )) or resid \ 158 through 159 or (resid 160 and (name N or name CA or name C or name O or nam \ e CB )) or resid 161 or (resid 162 and (name N or name CA or name C or name O or \ name CB )) or resid 163 through 166 or (resid 167 through 170 and (name N or na \ me CA or name C or name O or name CB )) or resid 171 through 173 or (resid 174 a \ nd (name N or name CA or name C or name O or name CB )) or resid 175 or (resid 1 \ 76 through 180 and (name N or name CA or name C or name O or name CB )) or resid \ 181 through 191 or (resid 192 and (name N or name CA or name C or name O or nam \ e CB )) or resid 193 through 195 or (resid 196 and (name N or name CA or name C \ or name O or name CB )) or resid 197 through 203 or (resid 204 and (name N or na \ me CA or name C or name O or name CB )) or resid 205 through 206 or (resid 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 210 \ or (resid 211 and (name N or name CA or name C or name O or name CB )) or resid \ 212 through 217)) selection = (chain 'C' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 52 or (resid 53 throug \ h 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throug \ h 71 or (resid 72 through 75 and (name N or name CA or name C or name O or name \ CB )) or resid 76 through 78 or (resid 79 through 82 and (name N or name CA or n \ ame C or name O or name CB )) or resid 83 or (resid 84 and (name N or name CA or \ name C or name O or name CB )) or resid 85 through 103 or (resid 104 through 10 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 107 through \ 138 or (resid 139 and (name N or name CA or name C or name O or name CB )) or re \ sid 140 through 145 or (resid 146 and (name N or name CA or name C or name O or \ name CB )) or resid 148 or (resid 149 through 151 and (name N or name CA or name \ C or name O or name CB )) or resid 152 through 159 or (resid 160 and (name N or \ name CA or name C or name O or name CB )) or resid 161 or (resid 162 and (name \ N or name CA or name C or name O or name CB )) or resid 163 or (resid 164 and (n \ ame N or name CA or name C or name O or name CB )) or resid 165 through 166 or ( \ resid 167 through 170 and (name N or name CA or name C or name O or name CB )) o \ r resid 171 through 173 or (resid 174 and (name N or name CA or name C or name O \ or name CB )) or resid 175 or (resid 176 through 180 and (name N or name CA or \ name C or name O or name CB )) or resid 181 through 191 or (resid 192 and (name \ N or name CA or name C or name O or name CB )) or resid 193 through 195 or (resi \ d 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 203 or (resid 204 and (name N or name CA or name C or name O or name CB )) o \ r resid 205 through 206 or (resid 207 and (name N or name CA or name C or name O \ or name CB )) or resid 208 through 210 or (resid 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 217)) selection = (chain 'D' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 103 or (resid 104 through 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 138 or (re \ sid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 th \ rough 148 or (resid 149 through 151 and (name N or name CA or name C or name O o \ r name CB )) or resid 152 through 156 or (resid 157 and (name N or name CA or na \ me C or name O or name CB )) or resid 158 through 159 or (resid 160 and (name N \ or name CA or name C or name O or name CB )) or resid 161 or (resid 162 and (nam \ e N or name CA or name C or name O or name CB )) or resid 163 or (resid 164 and \ (name N or name CA or name C or name O or name CB )) or resid 165 through 166 or \ (resid 167 through 170 and (name N or name CA or name C or name O or name CB )) \ or resid 171 through 173 or (resid 174 and (name N or name CA or name C or name \ O or name CB )) or resid 175 through 177 or (resid 178 through 180 and (name N \ or name CA or name C or name O or name CB )) or resid 181 through 186 or (resid \ 187 and (name N or name CA or name C or name O or name CB )) or resid 188 throug \ h 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 195 or (resid 196 and (name N or name CA or name C or name O o \ r name CB )) or resid 197 through 203 or (resid 204 and (name N or name CA or na \ me C or name O or name CB )) or resid 205 through 206 or (resid 207 and (name N \ or name CA or name C or name O or name CB )) or resid 208 through 210 or (resid \ 211 and (name N or name CA or name C or name O or name CB )) or resid 212 throug \ h 217)) selection = (chain 'E' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 52 \ or (resid 53 through 55 and (name N or name CA or name C or name O or name CB ) \ ) or resid 56 through 60 or (resid 61 through 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 78 or (resid 79 through 82 and (na \ me N or name CA or name C or name O or name CB )) or resid 83 or (resid 84 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 through 93 or (r \ esid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 thr \ ough 103 or (resid 104 through 106 and (name N or name CA or name C or name O or \ name CB )) or resid 107 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 or (resid 149 through 1 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 152 through \ 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) or r \ esid 158 through 159 or (resid 160 and (name N or name CA or name C or name O or \ name CB )) or resid 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 or (resid 164 and (name N or name CA or name C or n \ ame O or name CB )) or resid 165 through 166 or (resid 167 through 170 and (name \ N or name CA or name C or name O or name CB )) or resid 171 through 173 or (res \ id 174 and (name N or name CA or name C or name O or name CB )) or resid 175 or \ (resid 176 through 180 and (name N or name CA or name C or name O or name CB )) \ or resid 181 through 186 or (resid 187 and (name N or name CA or name C or name \ O or name CB )) or resid 188 through 191 or (resid 192 and (name N or name CA or \ name C or name O or name CB )) or resid 193 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 203 or (res \ id 204 and (name N or name CA or name C or name O or name CB )) or resid 205 thr \ ough 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 210 or (resid 211 and (name N or name CA or name C or name \ O or name CB )) or resid 212 through 217)) selection = (chain 'F' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 60 \ or (resid 61 through 63 and (name N or name CA or name C or name O or name CB ) \ ) or resid 64 through 71 or (resid 72 through 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 78 or (resid 79 through 82 and (na \ me N or name CA or name C or name O or name CB )) or resid 83 or (resid 84 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 through 93 or (r \ esid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 thr \ ough 103 or (resid 104 through 106 and (name N or name CA or name C or name O or \ name CB )) or resid 107 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 or (resid 149 through 1 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 152 through \ 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) or r \ esid 158 through 161 or (resid 162 and (name N or name CA or name C or name O or \ name CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name \ O or name CB )) or resid 165 through 166 or (resid 167 through 170 and (name N o \ r name CA or name C or name O or name CB )) or resid 171 through 173 or (resid 1 \ 74 and (name N or name CA or name C or name O or name CB )) or resid 175 or (res \ id 176 through 180 and (name N or name CA or name C or name O or name CB )) or r \ esid 181 through 186 or (resid 187 and (name N or name CA or name C or name O or \ name CB )) or resid 188 through 191 or (resid 192 and (name N or name CA or nam \ e C or name O or name CB )) or resid 193 through 195 or (resid 196 and (name N o \ r name CA or name C or name O or name CB )) or resid 197 through 203 or (resid 2 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 205 through \ 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) or r \ esid 208 through 210 or (resid 211 and (name N or name CA or name C or name O or \ name CB )) or resid 212 through 217)) selection = (chain 'G' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 60 or (resid 61 through 63 and (name N or name CA or name C or name O \ or name CB )) or resid 64 through 71 or (resid 72 through 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throu \ gh 82 and (name N or name CA or name C or name O or name CB )) or resid 83 or (r \ esid 84 and (name N or name CA or name C or name O or name CB )) or resid 85 thr \ ough 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or \ resid 95 through 103 or (resid 104 through 106 and (name N or name CA or name C \ or name O or name CB )) or resid 107 through 145 or (resid 146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 148 or (resid 149 through 151 \ and (name N or name CA or name C or name O or name CB )) or resid 152 through 16 \ 1 or (resid 162 and (name N or name CA or name C or name O or name CB )) or resi \ d 163 or (resid 164 and (name N or name CA or name C or name O or name CB )) or \ resid 165 through 166 or (resid 167 through 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 through 175 or (resid 176 through 180 and \ (name N or name CA or name C or name O or name CB )) or resid 181 through 195 or \ (resid 196 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 7 through 203 or (resid 204 and (name N or name CA or name C or name O or name C \ B )) or resid 205 through 206 or (resid 207 and (name N or name CA or name C or \ name O or name CB )) or resid 208 through 210 or (resid 211 and (name N or name \ CA or name C or name O or name CB )) or resid 212 through 217)) selection = (chain 'H' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 103 or (resid 104 through 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 138 or (re \ sid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 th \ rough 149 or (resid 150 through 151 and (name N or name CA or name C or name O o \ r name CB )) or resid 152 through 156 or (resid 157 and (name N or name CA or na \ me C or name O or name CB )) or resid 158 through 159 or (resid 160 and (name N \ or name CA or name C or name O or name CB )) or resid 161 through 163 or (resid \ 164 and (name N or name CA or name C or name O or name CB )) or resid 165 throug \ h 166 or (resid 167 through 170 and (name N or name CA or name C or name O or na \ me CB )) or resid 171 through 173 or (resid 174 and (name N or name CA or name C \ or name O or name CB )) or resid 175 through 177 or (resid 178 through 180 and \ (name N or name CA or name C or name O or name CB )) or resid 181 through 191 or \ (resid 192 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 3 through 195 or (resid 196 and (name N or name CA or name C or name O or name C \ B )) or resid 197 through 203 or (resid 204 and (name N or name CA or name C or \ name O or name CB )) or resid 205 through 206 or (resid 207 and (name N or name \ CA or name C or name O or name CB )) or resid 208 through 217)) selection = (chain 'I' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or r \ esid 83 or (resid 84 and (name N or name CA or name C or name O or name CB )) or \ resid 85 through 93 or (resid 94 and (name N or name CA or name C or name O or \ name CB )) or resid 95 through 103 or (resid 104 through 106 and (name N or name \ CA or name C or name O or name CB )) or resid 107 through 138 or (resid 139 and \ (name N or name CA or name C or name O or name CB )) or resid 140 through 145 o \ r (resid 146 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 48 or (resid 149 through 151 and (name N or name CA or name C or name O or name \ CB )) or resid 152 through 161 or (resid 162 and (name N or name CA or name C or \ name O or name CB )) or resid 163 or (resid 164 and (name N or name CA or name \ C or name O or name CB )) or resid 165 through 173 or (resid 174 and (name N or \ name CA or name C or name O or name CB )) or resid 175 or (resid 176 through 180 \ and (name N or name CA or name C or name O or name CB )) or resid 181 through 1 \ 86 or (resid 187 and (name N or name CA or name C or name O or name CB )) or res \ id 188 through 191 or (resid 192 and (name N or name CA or name C or name O or n \ ame CB )) or resid 193 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 210 or (resid 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 2 \ 17)) selection = (chain 'J' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 60 or (resid 61 through 63 and (name N or name CA or name C or name O \ or name CB )) or resid 64 through 71 or (resid 72 through 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throu \ gh 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throu \ gh 103 or (resid 104 through 106 and (name N or name CA or name C or name O or n \ ame CB )) or resid 107 through 138 or (resid 139 and (name N or name CA or name \ C or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N or \ name CA or name C or name O or name CB )) or resid 148 or (resid 149 through 151 \ and (name N or name CA or name C or name O or name CB )) or resid 152 through 1 \ 59 or (resid 160 and (name N or name CA or name C or name O or name CB )) or res \ id 161 or (resid 162 and (name N or name CA or name C or name O or name CB )) or \ resid 163 or (resid 164 and (name N or name CA or name C or name O or name CB ) \ ) or resid 165 through 166 or (resid 167 through 170 and (name N or name CA or n \ ame C or name O or name CB )) or resid 171 through 173 or (resid 174 and (name N \ or name CA or name C or name O or name CB )) or resid 175 or (resid 176 through \ 180 and (name N or name CA or name C or name O or name CB )) or resid 181 throu \ gh 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) or \ resid 188 through 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB )) or resid 193 through 195 or (resid 196 and (name N or name CA or n \ ame C or name O or name CB )) or resid 197 through 203 or (resid 204 and (name N \ or name CA or name C or name O or name CB )) or resid 205 through 206 or (resid \ 207 and (name N or name CA or name C or name O or name CB )) or resid 208 throu \ gh 210 or (resid 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.310 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.015 0.143 16570 Z= 1.070 Angle : 2.013 26.900 22640 Z= 1.386 Chirality : 0.104 0.460 2585 Planarity : 0.025 0.493 2926 Dihedral : 18.099 86.226 5560 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 10.79 % Allowed : 13.42 % Favored : 75.79 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.13), residues: 2127 helix: -3.32 (0.10), residues: 1283 sheet: -3.05 (0.21), residues: 300 loop : -2.23 (0.21), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 214 HIS 0.009 0.002 HIS E 200 PHE 0.030 0.002 PHE A 103 TYR 0.024 0.003 TYR D 148 ARG 0.011 0.001 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.25533 ( 781) hydrogen bonds : angle 10.01726 ( 2340) covalent geometry : bond 0.01453 (16561) covalent geometry : angle 2.01252 (22640) Misc. bond : bond 0.14080 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 512 time to evaluate : 1.987 Fit side-chains revert: symmetry clash REVERT: A 26 THR cc_start: 0.7874 (p) cc_final: 0.7672 (p) REVERT: A 61 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7678 (tp30) REVERT: A 84 SER cc_start: 0.7239 (p) cc_final: 0.6919 (m) REVERT: C 120 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: D 33 MET cc_start: 0.7631 (ttp) cc_final: 0.7428 (ptm) REVERT: D 204 ASP cc_start: 0.6903 (m-30) cc_final: 0.6484 (m-30) REVERT: D 208 ASN cc_start: 0.7581 (t0) cc_final: 0.7301 (t0) REVERT: E 77 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7856 (m) REVERT: E 110 THR cc_start: 0.7611 (p) cc_final: 0.7249 (t) REVERT: E 218 VAL cc_start: 0.3650 (OUTLIER) cc_final: 0.3166 (m) REVERT: F 46 PHE cc_start: 0.7345 (m-10) cc_final: 0.7125 (m-10) REVERT: F 192 ASP cc_start: 0.7459 (m-30) cc_final: 0.7125 (p0) REVERT: G 12 GLU cc_start: 0.6378 (mt-10) cc_final: 0.6170 (mt-10) REVERT: G 33 MET cc_start: 0.6764 (ttp) cc_final: 0.6394 (tmm) REVERT: H 30 ARG cc_start: 0.7069 (ttp80) cc_final: 0.6705 (ttp-110) REVERT: H 40 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.6124 (pt) REVERT: H 46 PHE cc_start: 0.7905 (m-10) cc_final: 0.7672 (m-10) REVERT: H 94 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5791 (tp30) REVERT: H 122 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7269 (tp) REVERT: H 148 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.6821 (t80) REVERT: H 192 ASP cc_start: 0.7849 (m-30) cc_final: 0.7267 (m-30) REVERT: J 49 GLU cc_start: 0.6475 (tp30) cc_final: 0.6274 (tp30) REVERT: J 130 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7194 (mmtp) outliers start: 164 outliers final: 11 residues processed: 595 average time/residue: 1.1296 time to fit residues: 758.6449 Evaluate side-chains 310 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 290 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain D residue 148 TYR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 124 PRO Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 148 TYR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 208 ASN Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 130 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN A 150 GLN A 172 ASN A 199 GLN A 200 HIS B 34 ASN B 120 GLN B 123 GLN B 160 ASN B 172 ASN C 31 HIS C 111 ASN C 120 GLN C 123 GLN C 172 ASN C 199 GLN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN D 200 HIS E 65 HIS E 85 ASN E 111 ASN E 120 GLN E 162 ASN E 172 ASN E 200 HIS F 34 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN F 172 ASN F 200 HIS F 216 ASN G 85 ASN G 111 ASN G 154 ASN G 162 ASN G 175 GLN G 200 HIS H 63 ASN H 172 ASN I 63 ASN I 85 ASN ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 ASN J 172 ASN J 200 HIS J 212 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140463 restraints weight = 19659.980| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 0.89 r_work: 0.3580 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16570 Z= 0.127 Angle : 0.535 5.999 22640 Z= 0.287 Chirality : 0.044 0.162 2585 Planarity : 0.005 0.067 2926 Dihedral : 8.158 64.356 2469 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.70 % Allowed : 18.03 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2127 helix: -0.53 (0.13), residues: 1321 sheet: -1.44 (0.25), residues: 300 loop : -1.08 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 214 HIS 0.007 0.002 HIS J 200 PHE 0.022 0.002 PHE C 191 TYR 0.010 0.001 TYR H 205 ARG 0.005 0.001 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 781) hydrogen bonds : angle 5.04859 ( 2340) covalent geometry : bond 0.00273 (16561) covalent geometry : angle 0.53494 (22640) Misc. bond : bond 0.00178 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 307 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7631 (t0) cc_final: 0.7383 (t0) REVERT: A 61 GLU cc_start: 0.8117 (tt0) cc_final: 0.7732 (tp30) REVERT: A 94 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6643 (mm-30) REVERT: A 130 LYS cc_start: 0.8222 (tmtt) cc_final: 0.7967 (tptt) REVERT: A 174 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7544 (ttpt) REVERT: A 211 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7042 (mtt180) REVERT: D 61 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: D 204 ASP cc_start: 0.7198 (m-30) cc_final: 0.6766 (m-30) REVERT: D 208 ASN cc_start: 0.7632 (t0) cc_final: 0.7330 (t0) REVERT: E 34 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.6915 (t0) REVERT: E 215 ASP cc_start: 0.6588 (m-30) cc_final: 0.6269 (m-30) REVERT: F 46 PHE cc_start: 0.7199 (m-10) cc_final: 0.6968 (m-10) REVERT: F 94 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6705 (mp0) REVERT: F 192 ASP cc_start: 0.7574 (m-30) cc_final: 0.7146 (p0) REVERT: G 33 MET cc_start: 0.6874 (ttp) cc_final: 0.6654 (tmm) REVERT: H 30 ARG cc_start: 0.7243 (ttp80) cc_final: 0.6958 (ttp-110) REVERT: H 122 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7598 (mt) REVERT: H 192 ASP cc_start: 0.7857 (m-30) cc_final: 0.7498 (m-30) REVERT: H 196 GLU cc_start: 0.7659 (mp0) cc_final: 0.7452 (mp0) REVERT: I 104 GLU cc_start: 0.7167 (tp30) cc_final: 0.6755 (mm-30) REVERT: I 130 LYS cc_start: 0.7220 (tmtt) cc_final: 0.7001 (tptm) REVERT: J 130 LYS cc_start: 0.7768 (tttm) cc_final: 0.7091 (tppt) outliers start: 41 outliers final: 12 residues processed: 332 average time/residue: 1.2562 time to fit residues: 465.2172 Evaluate side-chains 276 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 148 TYR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 0.0770 chunk 105 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 63 ASN A 85 ASN A 199 GLN B 85 ASN B 111 ASN B 185 HIS B 200 HIS C 199 GLN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 HIS F 63 ASN G 111 ASN G 154 ASN G 175 GLN G 216 ASN H 85 ASN I 158 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137263 restraints weight = 19750.019| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 0.87 r_work: 0.3536 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16570 Z= 0.117 Angle : 0.485 5.671 22640 Z= 0.260 Chirality : 0.044 0.129 2585 Planarity : 0.004 0.040 2926 Dihedral : 7.295 59.852 2434 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.63 % Allowed : 17.96 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2127 helix: 0.85 (0.14), residues: 1307 sheet: -1.04 (0.25), residues: 360 loop : -0.37 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 20 HIS 0.004 0.001 HIS B 185 PHE 0.023 0.002 PHE C 191 TYR 0.010 0.001 TYR H 148 ARG 0.005 0.001 ARG G 14 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 781) hydrogen bonds : angle 4.47483 ( 2340) covalent geometry : bond 0.00251 (16561) covalent geometry : angle 0.48494 (22640) Misc. bond : bond 0.00126 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7404 (t0) cc_final: 0.7186 (t0) REVERT: A 14 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7430 (mtp-110) REVERT: A 61 GLU cc_start: 0.8276 (tt0) cc_final: 0.7855 (tp30) REVERT: A 94 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6477 (mm-30) REVERT: A 130 LYS cc_start: 0.8254 (tmtt) cc_final: 0.8003 (mptt) REVERT: A 174 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7599 (ttpt) REVERT: A 211 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7408 (mtt180) REVERT: B 61 GLU cc_start: 0.7815 (tt0) cc_final: 0.7437 (tt0) REVERT: B 196 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: B 216 ASN cc_start: 0.7400 (t0) cc_final: 0.7057 (m-40) REVERT: C 140 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7395 (mt-10) REVERT: C 162 ASN cc_start: 0.7181 (m-40) cc_final: 0.6819 (m-40) REVERT: C 171 ARG cc_start: 0.7481 (mpt90) cc_final: 0.7253 (mmt-90) REVERT: D 204 ASP cc_start: 0.7200 (m-30) cc_final: 0.6782 (m-30) REVERT: D 208 ASN cc_start: 0.7617 (t0) cc_final: 0.7355 (t0) REVERT: E 30 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6383 (ttp-110) REVERT: E 34 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.6878 (t0) REVERT: E 110 THR cc_start: 0.7641 (p) cc_final: 0.7103 (t) REVERT: E 164 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6909 (mt-10) REVERT: E 171 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6537 (mmp-170) REVERT: E 218 VAL cc_start: 0.3261 (OUTLIER) cc_final: 0.2925 (m) REVERT: F 66 LEU cc_start: 0.7040 (mt) cc_final: 0.6738 (mt) REVERT: F 94 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6651 (mp0) REVERT: F 178 ASP cc_start: 0.7665 (m-30) cc_final: 0.7378 (m-30) REVERT: F 192 ASP cc_start: 0.7487 (m-30) cc_final: 0.7272 (p0) REVERT: G 104 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6224 (mm-30) REVERT: G 211 ARG cc_start: 0.7727 (mtp-110) cc_final: 0.7502 (mtp180) REVERT: H 14 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6960 (mtp180) REVERT: H 49 GLU cc_start: 0.7117 (tp30) cc_final: 0.6594 (tp30) REVERT: H 122 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7719 (mt) REVERT: H 148 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.6878 (p90) REVERT: H 192 ASP cc_start: 0.8006 (m-30) cc_final: 0.7601 (m-30) REVERT: H 196 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: I 130 LYS cc_start: 0.7245 (tmtt) cc_final: 0.6914 (tttt) REVERT: J 130 LYS cc_start: 0.7720 (tttm) cc_final: 0.6910 (tppt) outliers start: 40 outliers final: 15 residues processed: 312 average time/residue: 1.2198 time to fit residues: 425.1750 Evaluate side-chains 279 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 148 TYR Chi-restraints excluded: chain H residue 196 GLU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 187 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 144 optimal weight: 0.0010 chunk 167 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 123 GLN B 141 ASN C 85 ASN C 199 GLN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN F 31 HIS F 34 ASN F 65 HIS F 111 ASN F 216 ASN G 175 GLN G 216 ASN I 158 ASN I 212 ASN J 162 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133042 restraints weight = 20047.952| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 0.87 r_work: 0.3472 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16570 Z= 0.164 Angle : 0.542 5.802 22640 Z= 0.293 Chirality : 0.047 0.163 2585 Planarity : 0.004 0.041 2926 Dihedral : 7.517 59.525 2434 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.62 % Allowed : 16.58 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2127 helix: 1.06 (0.14), residues: 1320 sheet: -0.93 (0.25), residues: 360 loop : -0.44 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 20 HIS 0.008 0.002 HIS A 200 PHE 0.025 0.002 PHE C 191 TYR 0.015 0.002 TYR I 159 ARG 0.005 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 781) hydrogen bonds : angle 4.65251 ( 2340) covalent geometry : bond 0.00380 (16561) covalent geometry : angle 0.54231 (22640) Misc. bond : bond 0.00158 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7443 (t0) cc_final: 0.7105 (t0) REVERT: A 14 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7506 (mtp-110) REVERT: A 61 GLU cc_start: 0.8288 (tt0) cc_final: 0.7835 (tp30) REVERT: A 130 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8013 (tptt) REVERT: A 174 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7602 (ttpt) REVERT: B 61 GLU cc_start: 0.7931 (tt0) cc_final: 0.7521 (tt0) REVERT: C 122 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7909 (tt) REVERT: C 162 ASN cc_start: 0.7264 (m-40) cc_final: 0.6850 (m-40) REVERT: D 49 GLU cc_start: 0.7568 (tp30) cc_final: 0.7286 (mm-30) REVERT: D 204 ASP cc_start: 0.7333 (m-30) cc_final: 0.7025 (m-30) REVERT: D 208 ASN cc_start: 0.7645 (t0) cc_final: 0.7421 (t0) REVERT: E 30 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6837 (ttp-110) REVERT: E 34 ASN cc_start: 0.7474 (OUTLIER) cc_final: 0.6860 (t0) REVERT: E 43 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7093 (mt) REVERT: E 171 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6326 (mmp-170) REVERT: E 218 VAL cc_start: 0.3439 (OUTLIER) cc_final: 0.3052 (m) REVERT: F 12 GLU cc_start: 0.7570 (tt0) cc_final: 0.7300 (mt-10) REVERT: F 66 LEU cc_start: 0.7172 (mt) cc_final: 0.6964 (mt) REVERT: F 94 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: F 178 ASP cc_start: 0.7689 (m-30) cc_final: 0.7400 (m-30) REVERT: F 192 ASP cc_start: 0.7552 (m-30) cc_final: 0.6683 (p0) REVERT: F 196 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: G 94 GLU cc_start: 0.7225 (tp30) cc_final: 0.6345 (tp30) REVERT: G 211 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7116 (mtp-110) REVERT: H 14 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7246 (mtp180) REVERT: H 30 ARG cc_start: 0.7095 (ttp80) cc_final: 0.6833 (ttp-110) REVERT: H 192 ASP cc_start: 0.8177 (m-30) cc_final: 0.7740 (m-30) REVERT: H 196 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: I 130 LYS cc_start: 0.7201 (tmtt) cc_final: 0.6886 (tttt) REVERT: J 130 LYS cc_start: 0.7624 (tttm) cc_final: 0.6876 (tppt) outliers start: 55 outliers final: 21 residues processed: 302 average time/residue: 1.1953 time to fit residues: 403.8999 Evaluate side-chains 282 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 196 GLU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 187 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 45 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 173 optimal weight: 0.0270 chunk 10 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 199 GLN C 199 GLN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN G 175 GLN G 216 ASN H 65 HIS J 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135600 restraints weight = 20187.809| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 0.94 r_work: 0.3512 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16570 Z= 0.102 Angle : 0.450 5.650 22640 Z= 0.241 Chirality : 0.044 0.134 2585 Planarity : 0.004 0.040 2926 Dihedral : 6.641 59.068 2430 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.76 % Allowed : 17.37 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.18), residues: 2127 helix: 1.46 (0.14), residues: 1327 sheet: -0.74 (0.26), residues: 360 loop : -0.12 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 214 HIS 0.004 0.001 HIS G 65 PHE 0.024 0.001 PHE C 191 TYR 0.010 0.001 TYR G 205 ARG 0.006 0.000 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 781) hydrogen bonds : angle 4.22872 ( 2340) covalent geometry : bond 0.00222 (16561) covalent geometry : angle 0.44976 (22640) Misc. bond : bond 0.00090 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 1.685 Fit side-chains REVERT: A 6 ASP cc_start: 0.7473 (t0) cc_final: 0.6589 (t70) REVERT: A 14 ARG cc_start: 0.7760 (ttm110) cc_final: 0.7425 (mtp-110) REVERT: A 31 HIS cc_start: 0.7895 (m-70) cc_final: 0.7580 (m170) REVERT: A 61 GLU cc_start: 0.8322 (tt0) cc_final: 0.7843 (tp30) REVERT: A 174 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7541 (ttpt) REVERT: B 61 GLU cc_start: 0.7945 (tt0) cc_final: 0.7573 (tt0) REVERT: C 40 LEU cc_start: 0.7657 (mt) cc_final: 0.7235 (mp) REVERT: C 162 ASN cc_start: 0.7272 (m-40) cc_final: 0.6863 (m-40) REVERT: D 33 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.6991 (tpp) REVERT: D 49 GLU cc_start: 0.7517 (tp30) cc_final: 0.7207 (mm-30) REVERT: D 204 ASP cc_start: 0.7209 (m-30) cc_final: 0.6860 (m-30) REVERT: D 208 ASN cc_start: 0.7578 (t0) cc_final: 0.7332 (t0) REVERT: E 30 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6392 (ttp-110) REVERT: E 34 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.6926 (t0) REVERT: E 171 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6504 (mmp-170) REVERT: E 218 VAL cc_start: 0.3314 (OUTLIER) cc_final: 0.2942 (m) REVERT: F 12 GLU cc_start: 0.7507 (tt0) cc_final: 0.7240 (mt-10) REVERT: F 178 ASP cc_start: 0.7710 (m-30) cc_final: 0.7420 (m-30) REVERT: F 192 ASP cc_start: 0.7512 (m-30) cc_final: 0.7275 (p0) REVERT: G 94 GLU cc_start: 0.7152 (tp30) cc_final: 0.6209 (tp30) REVERT: G 211 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.7492 (mtp180) REVERT: H 14 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6876 (mtp85) REVERT: H 30 ARG cc_start: 0.7045 (ttp80) cc_final: 0.6822 (ttp-110) REVERT: H 192 ASP cc_start: 0.8109 (m-30) cc_final: 0.7675 (m-30) REVERT: H 196 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: I 130 LYS cc_start: 0.7178 (tmtt) cc_final: 0.6857 (tttt) REVERT: I 187 VAL cc_start: 0.6967 (m) cc_final: 0.6696 (m) REVERT: J 130 LYS cc_start: 0.7670 (tttm) cc_final: 0.7017 (tppt) outliers start: 42 outliers final: 15 residues processed: 291 average time/residue: 1.2601 time to fit residues: 408.7588 Evaluate side-chains 272 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 196 GLU Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 187 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 168 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 208 ASN C 199 GLN C 200 HIS D 111 ASN G 175 GLN H 31 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131815 restraints weight = 20293.112| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 0.92 r_work: 0.3457 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16570 Z= 0.199 Angle : 0.572 5.687 22640 Z= 0.310 Chirality : 0.049 0.206 2585 Planarity : 0.005 0.042 2926 Dihedral : 7.460 58.109 2430 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.96 % Allowed : 17.04 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2127 helix: 1.20 (0.14), residues: 1327 sheet: -0.85 (0.25), residues: 360 loop : -0.37 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 214 HIS 0.007 0.002 HIS A 200 PHE 0.029 0.002 PHE C 191 TYR 0.016 0.002 TYR C 15 ARG 0.007 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.05341 ( 781) hydrogen bonds : angle 4.69765 ( 2340) covalent geometry : bond 0.00464 (16561) covalent geometry : angle 0.57224 (22640) Misc. bond : bond 0.00165 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 1.761 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7564 (t0) cc_final: 0.6663 (t70) REVERT: A 14 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7553 (mtp-110) REVERT: A 61 GLU cc_start: 0.8297 (tt0) cc_final: 0.7815 (tp30) REVERT: B 61 GLU cc_start: 0.7903 (tt0) cc_final: 0.7499 (tt0) REVERT: C 49 GLU cc_start: 0.6726 (tp30) cc_final: 0.6458 (tp30) REVERT: C 122 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7928 (tt) REVERT: C 162 ASN cc_start: 0.7303 (m-40) cc_final: 0.6911 (m-40) REVERT: D 33 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6768 (tpp) REVERT: D 204 ASP cc_start: 0.7352 (m-30) cc_final: 0.7043 (m-30) REVERT: D 208 ASN cc_start: 0.7660 (t0) cc_final: 0.7438 (t0) REVERT: E 30 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6848 (ttp-110) REVERT: E 34 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.6920 (t0) REVERT: E 164 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: E 171 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6526 (mmp-170) REVERT: E 207 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7696 (mm) REVERT: E 218 VAL cc_start: 0.3360 (OUTLIER) cc_final: 0.2952 (m) REVERT: F 12 GLU cc_start: 0.7586 (tt0) cc_final: 0.7300 (mt-10) REVERT: F 178 ASP cc_start: 0.7693 (m-30) cc_final: 0.7409 (m-30) REVERT: F 192 ASP cc_start: 0.7565 (m-30) cc_final: 0.6693 (p0) REVERT: F 196 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: G 94 GLU cc_start: 0.7253 (tp30) cc_final: 0.6371 (tp30) REVERT: G 211 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6838 (mtp-110) REVERT: H 14 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7255 (mtp180) REVERT: H 30 ARG cc_start: 0.6997 (ttp80) cc_final: 0.6746 (ttp-110) REVERT: H 62 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6845 (pp) REVERT: H 171 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7065 (mmt90) REVERT: H 192 ASP cc_start: 0.8157 (m-30) cc_final: 0.7785 (m-30) REVERT: I 130 LYS cc_start: 0.7237 (tmtt) cc_final: 0.6875 (tttt) REVERT: J 130 LYS cc_start: 0.7568 (tttm) cc_final: 0.7058 (mmtp) REVERT: J 139 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7386 (mtpt) outliers start: 45 outliers final: 22 residues processed: 279 average time/residue: 1.3137 time to fit residues: 407.6375 Evaluate side-chains 275 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 187 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 83 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 118 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 199 GLN D 123 GLN F 111 ASN G 199 GLN G 216 ASN J 85 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131252 restraints weight = 20313.079| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 0.92 r_work: 0.3453 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16570 Z= 0.187 Angle : 0.562 5.933 22640 Z= 0.304 Chirality : 0.048 0.198 2585 Planarity : 0.004 0.043 2926 Dihedral : 7.429 57.392 2430 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.03 % Allowed : 17.17 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2127 helix: 1.19 (0.14), residues: 1327 sheet: -0.83 (0.25), residues: 360 loop : -0.50 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 20 HIS 0.006 0.002 HIS H 185 PHE 0.029 0.002 PHE C 191 TYR 0.015 0.002 TYR I 159 ARG 0.008 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.05204 ( 781) hydrogen bonds : angle 4.67059 ( 2340) covalent geometry : bond 0.00438 (16561) covalent geometry : angle 0.56234 (22640) Misc. bond : bond 0.00167 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 1.670 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7529 (t0) cc_final: 0.6601 (t70) REVERT: A 14 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7539 (mtp-110) REVERT: A 61 GLU cc_start: 0.8277 (tt0) cc_final: 0.7757 (tp30) REVERT: B 61 GLU cc_start: 0.7913 (tt0) cc_final: 0.7542 (tt0) REVERT: C 49 GLU cc_start: 0.6698 (tp30) cc_final: 0.6372 (tp30) REVERT: C 122 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7914 (tt) REVERT: D 33 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6863 (tpp) REVERT: D 204 ASP cc_start: 0.7251 (m-30) cc_final: 0.6931 (m-30) REVERT: D 208 ASN cc_start: 0.7583 (t0) cc_final: 0.7370 (t0) REVERT: E 30 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6842 (ttp-110) REVERT: E 34 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.6959 (t0) REVERT: E 49 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6550 (tp30) REVERT: E 164 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6893 (mt-10) REVERT: E 171 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6519 (mmp-170) REVERT: E 218 VAL cc_start: 0.3350 (OUTLIER) cc_final: 0.2863 (m) REVERT: F 12 GLU cc_start: 0.7558 (tt0) cc_final: 0.7282 (mt-10) REVERT: F 94 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: F 178 ASP cc_start: 0.7705 (m-30) cc_final: 0.7411 (m-30) REVERT: F 192 ASP cc_start: 0.7548 (m-30) cc_final: 0.6782 (p0) REVERT: F 196 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: G 94 GLU cc_start: 0.7199 (tp30) cc_final: 0.6259 (tp30) REVERT: G 211 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7065 (mtp-110) REVERT: H 14 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7021 (mtp85) REVERT: H 30 ARG cc_start: 0.6961 (ttp80) cc_final: 0.6663 (ttp-110) REVERT: H 62 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6864 (pp) REVERT: H 171 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7413 (mmt90) REVERT: H 192 ASP cc_start: 0.8140 (m-30) cc_final: 0.7739 (m-30) REVERT: H 196 GLU cc_start: 0.7875 (mp0) cc_final: 0.7523 (mp0) REVERT: I 130 LYS cc_start: 0.7225 (tmtt) cc_final: 0.6871 (tttt) REVERT: J 130 LYS cc_start: 0.7539 (tttm) cc_final: 0.6838 (tppt) outliers start: 46 outliers final: 22 residues processed: 284 average time/residue: 1.2547 time to fit residues: 397.5377 Evaluate side-chains 279 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 99 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 199 GLN F 111 ASN G 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135240 restraints weight = 19978.431| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 0.92 r_work: 0.3496 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16570 Z= 0.112 Angle : 0.476 6.530 22640 Z= 0.255 Chirality : 0.044 0.154 2585 Planarity : 0.004 0.041 2926 Dihedral : 6.614 59.800 2430 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.37 % Allowed : 17.76 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2127 helix: 1.68 (0.14), residues: 1320 sheet: -0.72 (0.25), residues: 366 loop : -0.16 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 20 HIS 0.003 0.001 HIS G 65 PHE 0.024 0.001 PHE C 191 TYR 0.012 0.001 TYR G 205 ARG 0.008 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 781) hydrogen bonds : angle 4.28077 ( 2340) covalent geometry : bond 0.00248 (16561) covalent geometry : angle 0.47616 (22640) Misc. bond : bond 0.00153 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7436 (t0) cc_final: 0.6403 (t70) REVERT: A 14 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7479 (mtp-110) REVERT: A 61 GLU cc_start: 0.8268 (tt0) cc_final: 0.7737 (tp30) REVERT: B 61 GLU cc_start: 0.7940 (tt0) cc_final: 0.7565 (tt0) REVERT: C 40 LEU cc_start: 0.7671 (mt) cc_final: 0.7251 (mp) REVERT: C 49 GLU cc_start: 0.6569 (tp30) cc_final: 0.6225 (tp30) REVERT: C 122 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7820 (tt) REVERT: D 33 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6873 (tpp) REVERT: D 204 ASP cc_start: 0.7092 (m-30) cc_final: 0.6741 (m-30) REVERT: D 208 ASN cc_start: 0.7584 (t0) cc_final: 0.7334 (t0) REVERT: E 30 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6428 (ttp-110) REVERT: E 34 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.6908 (t0) REVERT: E 49 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6510 (tp30) REVERT: E 164 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6855 (mt-10) REVERT: E 171 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6511 (mmp-170) REVERT: E 215 ASP cc_start: 0.6441 (m-30) cc_final: 0.6179 (m-30) REVERT: E 218 VAL cc_start: 0.3207 (OUTLIER) cc_final: 0.2823 (m) REVERT: F 12 GLU cc_start: 0.7573 (tt0) cc_final: 0.7311 (mt-10) REVERT: F 94 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: F 178 ASP cc_start: 0.7704 (m-30) cc_final: 0.7408 (m-30) REVERT: F 192 ASP cc_start: 0.7462 (m-30) cc_final: 0.6613 (p0) REVERT: F 196 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: G 94 GLU cc_start: 0.7227 (tp30) cc_final: 0.6259 (tp30) REVERT: G 175 GLN cc_start: 0.7566 (mt0) cc_final: 0.7356 (mt0) REVERT: G 211 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7424 (mtp180) REVERT: H 14 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6921 (mtp85) REVERT: H 30 ARG cc_start: 0.6883 (ttp80) cc_final: 0.6657 (ttp-110) REVERT: H 62 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6850 (pp) REVERT: H 192 ASP cc_start: 0.8078 (m-30) cc_final: 0.7689 (m-30) REVERT: H 196 GLU cc_start: 0.7845 (mp0) cc_final: 0.7455 (mp0) REVERT: I 34 ASN cc_start: 0.6694 (m-40) cc_final: 0.6374 (m110) REVERT: I 130 LYS cc_start: 0.7281 (tmtt) cc_final: 0.6934 (tttt) REVERT: J 130 LYS cc_start: 0.7568 (tttm) cc_final: 0.6900 (tppt) outliers start: 36 outliers final: 15 residues processed: 282 average time/residue: 1.2533 time to fit residues: 394.0936 Evaluate side-chains 274 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 187 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 0.0980 chunk 85 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 144 optimal weight: 40.0000 chunk 181 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 185 HIS C 199 GLN H 200 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133541 restraints weight = 20317.046| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 0.90 r_work: 0.3467 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16570 Z= 0.162 Angle : 0.537 6.776 22640 Z= 0.289 Chirality : 0.047 0.186 2585 Planarity : 0.004 0.042 2926 Dihedral : 7.049 59.670 2430 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.37 % Allowed : 18.42 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.18), residues: 2127 helix: 1.50 (0.14), residues: 1327 sheet: -0.72 (0.25), residues: 360 loop : -0.29 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 214 HIS 0.005 0.001 HIS H 185 PHE 0.031 0.002 PHE C 191 TYR 0.017 0.002 TYR C 15 ARG 0.010 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 781) hydrogen bonds : angle 4.52419 ( 2340) covalent geometry : bond 0.00376 (16561) covalent geometry : angle 0.53716 (22640) Misc. bond : bond 0.00165 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7519 (t0) cc_final: 0.6535 (t70) REVERT: A 14 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7535 (mtp-110) REVERT: A 61 GLU cc_start: 0.8287 (tt0) cc_final: 0.7756 (tp30) REVERT: B 61 GLU cc_start: 0.7924 (tt0) cc_final: 0.7555 (tt0) REVERT: C 49 GLU cc_start: 0.6624 (tp30) cc_final: 0.6342 (tp30) REVERT: C 122 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7945 (tt) REVERT: D 33 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: D 204 ASP cc_start: 0.7202 (m-30) cc_final: 0.6840 (m-30) REVERT: D 208 ASN cc_start: 0.7605 (t0) cc_final: 0.7390 (t0) REVERT: E 30 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6476 (ttp-110) REVERT: E 34 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.6870 (t0) REVERT: E 49 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6550 (tp30) REVERT: E 164 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: E 171 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6525 (mmp-170) REVERT: E 215 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.6205 (m-30) REVERT: E 218 VAL cc_start: 0.3379 (OUTLIER) cc_final: 0.2894 (m) REVERT: F 12 GLU cc_start: 0.7587 (tt0) cc_final: 0.7269 (mt-10) REVERT: F 94 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: F 178 ASP cc_start: 0.7684 (m-30) cc_final: 0.7403 (m-30) REVERT: F 192 ASP cc_start: 0.7505 (m-30) cc_final: 0.6686 (p0) REVERT: F 196 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: G 94 GLU cc_start: 0.7228 (tp30) cc_final: 0.6308 (tp30) REVERT: G 211 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6880 (mtp-110) REVERT: H 14 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6990 (mtp85) REVERT: H 30 ARG cc_start: 0.6938 (ttp80) cc_final: 0.6633 (ttp-110) REVERT: H 62 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6838 (pp) REVERT: H 171 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7329 (mmt90) REVERT: H 192 ASP cc_start: 0.8124 (m-30) cc_final: 0.7743 (m-30) REVERT: H 196 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: I 72 MET cc_start: 0.7153 (mtp) cc_final: 0.6935 (ttm) REVERT: I 130 LYS cc_start: 0.7245 (tmtt) cc_final: 0.6879 (tttt) REVERT: J 130 LYS cc_start: 0.7512 (tttm) cc_final: 0.6846 (tppt) outliers start: 36 outliers final: 18 residues processed: 272 average time/residue: 1.3102 time to fit residues: 396.4792 Evaluate side-chains 277 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 196 GLU Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 101 optimal weight: 0.2980 chunk 155 optimal weight: 0.5980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133505 restraints weight = 20269.063| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 0.92 r_work: 0.3484 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16570 Z= 0.130 Angle : 0.503 5.992 22640 Z= 0.271 Chirality : 0.045 0.135 2585 Planarity : 0.004 0.041 2926 Dihedral : 6.745 57.613 2430 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.17 % Allowed : 18.75 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2127 helix: 1.67 (0.14), residues: 1320 sheet: -0.66 (0.25), residues: 360 loop : -0.19 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 20 HIS 0.003 0.001 HIS C 65 PHE 0.029 0.002 PHE C 191 TYR 0.013 0.001 TYR G 205 ARG 0.010 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 781) hydrogen bonds : angle 4.39792 ( 2340) covalent geometry : bond 0.00296 (16561) covalent geometry : angle 0.50341 (22640) Misc. bond : bond 0.00135 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7471 (t0) cc_final: 0.6412 (t70) REVERT: A 14 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7516 (mtp-110) REVERT: A 61 GLU cc_start: 0.8278 (tt0) cc_final: 0.7727 (tp30) REVERT: B 61 GLU cc_start: 0.7926 (tt0) cc_final: 0.7530 (tt0) REVERT: C 40 LEU cc_start: 0.7678 (mp) cc_final: 0.7460 (mp) REVERT: C 49 GLU cc_start: 0.6620 (tp30) cc_final: 0.6251 (tp30) REVERT: C 122 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7859 (tt) REVERT: D 33 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6869 (tpp) REVERT: D 204 ASP cc_start: 0.7085 (m-30) cc_final: 0.6729 (m-30) REVERT: D 208 ASN cc_start: 0.7559 (t0) cc_final: 0.7318 (t0) REVERT: E 30 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6459 (ttp-110) REVERT: E 34 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.6876 (t0) REVERT: E 49 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6494 (tp30) REVERT: E 164 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: E 171 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6480 (mmp-170) REVERT: E 218 VAL cc_start: 0.3279 (OUTLIER) cc_final: 0.2865 (m) REVERT: F 12 GLU cc_start: 0.7592 (tt0) cc_final: 0.7304 (mt-10) REVERT: F 94 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: F 178 ASP cc_start: 0.7714 (m-30) cc_final: 0.7419 (m-30) REVERT: F 192 ASP cc_start: 0.7477 (m-30) cc_final: 0.6668 (p0) REVERT: F 196 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: G 94 GLU cc_start: 0.7198 (tp30) cc_final: 0.6236 (tp30) REVERT: G 211 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7057 (mtp-110) REVERT: H 14 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7200 (mtp180) REVERT: H 30 ARG cc_start: 0.6932 (ttp80) cc_final: 0.6619 (ttp-110) REVERT: H 62 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6829 (pp) REVERT: H 192 ASP cc_start: 0.8074 (m-30) cc_final: 0.7698 (m-30) REVERT: H 196 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: I 34 ASN cc_start: 0.6705 (m-40) cc_final: 0.6388 (m110) REVERT: I 130 LYS cc_start: 0.7256 (tmtt) cc_final: 0.6902 (tttt) REVERT: J 130 LYS cc_start: 0.7507 (tttm) cc_final: 0.6856 (tppt) outliers start: 33 outliers final: 18 residues processed: 269 average time/residue: 1.2686 time to fit residues: 380.4050 Evaluate side-chains 274 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 196 GLU Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 39 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 135 optimal weight: 0.0370 chunk 9 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 199 GLN G 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.142585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133810 restraints weight = 20224.421| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.92 r_work: 0.3485 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16570 Z= 0.122 Angle : 0.492 6.252 22640 Z= 0.264 Chirality : 0.045 0.134 2585 Planarity : 0.004 0.041 2926 Dihedral : 6.481 51.967 2430 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.17 % Allowed : 18.95 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.18), residues: 2127 helix: 1.73 (0.14), residues: 1327 sheet: -0.61 (0.26), residues: 360 loop : -0.10 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 20 HIS 0.003 0.001 HIS H 185 PHE 0.029 0.001 PHE C 191 TYR 0.015 0.001 TYR H 15 ARG 0.010 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 781) hydrogen bonds : angle 4.33446 ( 2340) covalent geometry : bond 0.00276 (16561) covalent geometry : angle 0.49163 (22640) Misc. bond : bond 0.00127 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11679.73 seconds wall clock time: 201 minutes 52.93 seconds (12112.93 seconds total)