Starting phenix.real_space_refine on Sun Aug 24 02:22:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc4_15962/08_2025/8bc4_15962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc4_15962/08_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_15962/08_2025/8bc4_15962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc4_15962/08_2025/8bc4_15962.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc4_15962/08_2025/8bc4_15962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc4_15962/08_2025/8bc4_15962.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 7, 'ASP:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 1} 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: {'GLU:plan': 10, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} 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: {'GLU:plan': 9, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 1} 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: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} 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: {'GLU:plan': 7, 'ASP:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1} 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: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 1} 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: {'GLU:plan': 7, 'ASP:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 1} 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: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1} 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: {'GLU:plan': 8, 'ASP:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 2} 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: {'GLU:plan': 8, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 1} 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: 3.99, per 1000 atoms: 0.24 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: 1.45 Conformation dependent library (CDL) restraints added in 715.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.49 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: 3.04 Time building geometry restraints manager: 1.90 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: 3.300 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.910 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.450 ------------------------------------------------------------------------------- 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 : 4.83 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.011 0.001 ARG A 14 TYR 0.024 0.003 TYR D 148 PHE 0.030 0.002 PHE A 103 TRP 0.016 0.002 TRP I 214 HIS 0.009 0.002 HIS E 200 Details of bonding type rmsd covalent geometry : bond 0.01453 (16561) covalent geometry : angle 2.01252 (22640) hydrogen bonds : bond 0.25533 ( 781) hydrogen bonds : angle 10.01726 ( 2340) 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 : 0.518 Fit side-chains revert: symmetry clash REVERT: A 26 THR cc_start: 0.7874 (p) cc_final: 0.7673 (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: 0.7429 (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: 0.7305 (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: 0.7248 (t) REVERT: E 218 VAL cc_start: 0.3650 (OUTLIER) cc_final: 0.3167 (m) REVERT: F 46 PHE cc_start: 0.7345 (m-10) cc_final: 0.7124 (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: 0.6171 (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: 0.6820 (t80) REVERT: H 192 ASP cc_start: 0.7849 (m-30) cc_final: 0.7266 (m-30) REVERT: J 49 GLU cc_start: 0.6475 (tp30) cc_final: 0.6272 (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: 0.4950 time to fit residues: 331.5761 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 : 0.518 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 85 ASN A 111 ASN A 150 GLN A 172 ASN A 199 GLN A 200 HIS B 34 ASN B 85 ASN B 120 GLN B 160 ASN B 172 ASN B 200 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN 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 199 GLN 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 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 G 216 ASN H 31 HIS H 63 ASN H 85 ASN H 172 ASN I 63 ASN I 65 HIS I 85 ASN J 65 HIS J 162 ASN J 172 ASN J 200 HIS J 212 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135542 restraints weight = 19788.866| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 0.88 r_work: 0.3507 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16570 Z= 0.166 Angle : 0.596 7.406 22640 Z= 0.318 Chirality : 0.047 0.187 2585 Planarity : 0.005 0.040 2926 Dihedral : 8.496 71.471 2469 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.83 % Allowed : 17.50 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.16), residues: 2127 helix: -0.64 (0.13), residues: 1327 sheet: -1.53 (0.24), residues: 318 loop : -1.16 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 171 TYR 0.015 0.002 TYR I 159 PHE 0.021 0.002 PHE C 191 TRP 0.012 0.001 TRP B 214 HIS 0.011 0.002 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00377 (16561) covalent geometry : angle 0.59644 (22640) hydrogen bonds : bond 0.05158 ( 781) hydrogen bonds : angle 5.17182 ( 2340) Misc. bond : bond 0.00207 ( 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 340 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 297 time to evaluate : 0.650 Fit side-chains REVERT: A 6 ASP cc_start: 0.7553 (t0) cc_final: 0.7329 (t0) REVERT: A 61 GLU cc_start: 0.8230 (tt0) cc_final: 0.7803 (tp30) REVERT: A 94 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6638 (mm-30) REVERT: A 130 LYS cc_start: 0.8304 (tmtt) cc_final: 0.8020 (tptt) REVERT: A 174 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7586 (ttpt) REVERT: A 211 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7144 (mtt180) REVERT: B 61 GLU cc_start: 0.7694 (tt0) cc_final: 0.7474 (tt0) REVERT: C 72 MET cc_start: 0.7726 (mtt) cc_final: 0.7447 (mtt) REVERT: D 33 MET cc_start: 0.7556 (ttp) cc_final: 0.7354 (ptm) REVERT: D 61 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: D 204 ASP cc_start: 0.7235 (m-30) cc_final: 0.6806 (m-30) REVERT: D 208 ASN cc_start: 0.7683 (t0) cc_final: 0.7399 (t0) REVERT: E 30 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6566 (ttp-110) REVERT: E 34 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.6877 (t0) REVERT: E 110 THR cc_start: 0.7684 (p) cc_final: 0.7144 (t) REVERT: E 164 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6984 (mt-10) REVERT: E 218 VAL cc_start: 0.3344 (OUTLIER) cc_final: 0.3014 (m) REVERT: F 94 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6646 (mp0) REVERT: F 192 ASP cc_start: 0.7676 (m-30) cc_final: 0.7137 (p0) REVERT: G 33 MET cc_start: 0.7096 (ttp) cc_final: 0.6827 (tmm) REVERT: G 211 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6972 (mtp-110) REVERT: H 30 ARG cc_start: 0.7342 (ttp80) cc_final: 0.7062 (ttp-110) REVERT: H 122 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7663 (mt) REVERT: H 148 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.6872 (p90) REVERT: H 192 ASP cc_start: 0.8025 (m-30) cc_final: 0.7609 (m-30) REVERT: H 196 GLU cc_start: 0.7830 (mp0) cc_final: 0.7526 (mp0) REVERT: I 130 LYS cc_start: 0.7262 (tmtt) cc_final: 0.6869 (tttt) REVERT: I 142 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.8080 (m) REVERT: J 130 LYS cc_start: 0.7802 (tttm) cc_final: 0.7009 (tppt) REVERT: J 204 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6612 (m-30) outliers start: 43 outliers final: 14 residues processed: 325 average time/residue: 0.5768 time to fit residues: 208.9366 Evaluate side-chains 281 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 164 GLU 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 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 I residue 133 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 204 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 173 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN A 199 GLN B 34 ASN B 111 ASN B 141 ASN B 208 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 199 GLN C 200 HIS D 85 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN F 31 HIS F 65 HIS G 31 HIS G 111 ASN G 175 GLN G 199 GLN G 216 ASN H 65 HIS J 162 ASN J 175 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131178 restraints weight = 20379.876| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 0.92 r_work: 0.3446 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16570 Z= 0.239 Angle : 0.655 6.193 22640 Z= 0.354 Chirality : 0.051 0.229 2585 Planarity : 0.005 0.045 2926 Dihedral : 8.180 62.935 2436 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.82 % Allowed : 15.86 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.17), residues: 2127 helix: 0.25 (0.13), residues: 1320 sheet: -1.21 (0.24), residues: 360 loop : -0.83 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 211 TYR 0.020 0.002 TYR I 159 PHE 0.027 0.003 PHE C 191 TRP 0.013 0.002 TRP G 20 HIS 0.010 0.003 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00562 (16561) covalent geometry : angle 0.65519 (22640) hydrogen bonds : bond 0.06049 ( 781) hydrogen bonds : angle 5.07534 ( 2340) Misc. bond : bond 0.00178 ( 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 331 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8252 (tt0) cc_final: 0.7817 (tp30) REVERT: A 94 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6542 (mm-30) REVERT: B 12 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7518 (mt-10) REVERT: B 93 THR cc_start: 0.7879 (t) cc_final: 0.7631 (p) REVERT: C 122 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7933 (tt) REVERT: C 162 ASN cc_start: 0.7390 (m-40) cc_final: 0.6973 (m-40) REVERT: D 49 GLU cc_start: 0.7480 (tp30) cc_final: 0.7203 (mm-30) REVERT: D 61 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: D 204 ASP cc_start: 0.7367 (m-30) cc_final: 0.7049 (m-30) REVERT: E 30 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6541 (ttp-110) REVERT: E 34 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.6928 (t0) REVERT: E 43 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7102 (mt) REVERT: E 164 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: E 171 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6295 (mmp-170) REVERT: E 218 VAL cc_start: 0.3263 (OUTLIER) cc_final: 0.2861 (m) REVERT: F 178 ASP cc_start: 0.7711 (m-30) cc_final: 0.7386 (m-30) REVERT: F 192 ASP cc_start: 0.7697 (m-30) cc_final: 0.6939 (p0) REVERT: F 196 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: G 211 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6992 (mtp-110) REVERT: H 30 ARG cc_start: 0.7130 (ttp80) cc_final: 0.6824 (ttp-110) REVERT: H 104 GLU cc_start: 0.6766 (tp30) cc_final: 0.6184 (tp30) REVERT: H 122 LEU cc_start: 0.7928 (mt) cc_final: 0.7718 (mt) REVERT: H 192 ASP cc_start: 0.8183 (m-30) cc_final: 0.7808 (m-30) REVERT: I 130 LYS cc_start: 0.7203 (tmtt) cc_final: 0.6850 (tttt) REVERT: J 130 LYS cc_start: 0.7585 (tttm) cc_final: 0.6816 (tppt) REVERT: J 204 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6604 (m-30) outliers start: 58 outliers final: 21 residues processed: 312 average time/residue: 0.5402 time to fit residues: 188.2487 Evaluate side-chains 286 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 61 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 43 LEU Chi-restraints excluded: chain E residue 77 THR 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 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 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 217 THR 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 60 VAL Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 204 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 126 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 195 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 B 34 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 111 ASN C 199 GLN D 123 GLN F 63 ASN G 216 ASN J 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132456 restraints weight = 20205.617| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 0.93 r_work: 0.3472 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16570 Z= 0.144 Angle : 0.520 5.734 22640 Z= 0.281 Chirality : 0.046 0.137 2585 Planarity : 0.004 0.043 2926 Dihedral : 7.496 58.967 2432 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.29 % Allowed : 16.32 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.18), residues: 2127 helix: 0.94 (0.14), residues: 1320 sheet: -0.84 (0.24), residues: 378 loop : -0.57 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 14 TYR 0.014 0.001 TYR I 159 PHE 0.024 0.002 PHE C 191 TRP 0.011 0.001 TRP F 138 HIS 0.005 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00328 (16561) covalent geometry : angle 0.51980 (22640) hydrogen bonds : bond 0.04750 ( 781) hydrogen bonds : angle 4.62410 ( 2340) Misc. bond : bond 0.00146 ( 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 310 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 260 time to evaluate : 0.650 Fit side-chains REVERT: A 6 ASP cc_start: 0.7457 (t0) cc_final: 0.6621 (t70) REVERT: A 61 GLU cc_start: 0.8317 (tt0) cc_final: 0.7794 (tp30) REVERT: C 49 GLU cc_start: 0.6501 (tp30) cc_final: 0.6292 (tp30) REVERT: C 122 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7898 (tt) REVERT: C 162 ASN cc_start: 0.7277 (m-40) cc_final: 0.6854 (m-40) REVERT: D 49 GLU cc_start: 0.7559 (tp30) cc_final: 0.7266 (mm-30) REVERT: D 204 ASP cc_start: 0.7216 (m-30) cc_final: 0.6870 (m-30) REVERT: E 30 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6404 (ttp-110) REVERT: E 34 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.6861 (t0) REVERT: E 43 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7061 (mt) REVERT: E 171 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6505 (mmp-170) REVERT: F 12 GLU cc_start: 0.7646 (tt0) cc_final: 0.7406 (mt-10) REVERT: F 61 GLU cc_start: 0.7586 (tt0) cc_final: 0.7295 (tt0) REVERT: F 178 ASP cc_start: 0.7698 (m-30) cc_final: 0.7411 (m-30) REVERT: F 192 ASP cc_start: 0.7560 (m-30) cc_final: 0.6692 (p0) REVERT: F 196 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: G 94 GLU cc_start: 0.7173 (tp30) cc_final: 0.6258 (tp30) REVERT: G 211 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7385 (mtp180) REVERT: H 30 ARG cc_start: 0.7053 (ttp80) cc_final: 0.6774 (ttp-110) REVERT: H 104 GLU cc_start: 0.6641 (tp30) cc_final: 0.6045 (tp30) REVERT: H 122 LEU cc_start: 0.7876 (mt) cc_final: 0.7643 (mt) REVERT: H 171 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7174 (mmt90) REVERT: H 192 ASP cc_start: 0.8158 (m-30) cc_final: 0.7731 (m-30) REVERT: H 196 GLU cc_start: 0.7865 (mp0) cc_final: 0.7555 (mp0) REVERT: I 130 LYS cc_start: 0.7190 (tmtt) cc_final: 0.6863 (tttt) REVERT: J 130 LYS cc_start: 0.7608 (tttm) cc_final: 0.7055 (mmtp) outliers start: 50 outliers final: 20 residues processed: 292 average time/residue: 0.5194 time to fit residues: 169.8052 Evaluate side-chains 274 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 43 LEU 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 77 THR Chi-restraints excluded: chain E residue 94 GLU 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 208 ASN 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 83 SER Chi-restraints excluded: chain H residue 84 SER 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 187 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 62 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN E 150 GLN F 34 ASN F 111 ASN G 216 ASN H 200 HIS J 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129259 restraints weight = 20378.067| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 0.90 r_work: 0.3436 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 16570 Z= 0.286 Angle : 0.687 8.214 22640 Z= 0.372 Chirality : 0.054 0.272 2585 Planarity : 0.005 0.048 2926 Dihedral : 8.460 67.126 2431 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.88 % Allowed : 16.05 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.17), residues: 2127 helix: 0.55 (0.13), residues: 1327 sheet: -1.06 (0.24), residues: 360 loop : -0.81 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 14 TYR 0.017 0.003 TYR A 159 PHE 0.030 0.003 PHE C 191 TRP 0.014 0.003 TRP H 214 HIS 0.008 0.002 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00680 (16561) covalent geometry : angle 0.68678 (22640) hydrogen bonds : bond 0.06369 ( 781) hydrogen bonds : angle 5.06894 ( 2340) Misc. bond : bond 0.00201 ( 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 317 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 0.641 Fit side-chains REVERT: A 6 ASP cc_start: 0.7627 (t0) cc_final: 0.6919 (t70) REVERT: A 61 GLU cc_start: 0.8238 (tt0) cc_final: 0.7690 (tp30) REVERT: C 2 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8173 (mmtp) REVERT: C 49 GLU cc_start: 0.6711 (tp30) cc_final: 0.6441 (tp30) REVERT: C 122 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7852 (tt) REVERT: D 33 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6855 (ptm) REVERT: D 204 ASP cc_start: 0.7340 (m-30) cc_final: 0.7043 (m-30) REVERT: E 30 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6512 (ttp-110) REVERT: E 34 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.6925 (t0) REVERT: E 49 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6541 (tp30) REVERT: E 164 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6949 (mt-10) REVERT: E 171 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6489 (mmp-170) REVERT: F 12 GLU cc_start: 0.7662 (tt0) cc_final: 0.7416 (mt-10) REVERT: F 61 GLU cc_start: 0.7748 (tt0) cc_final: 0.7437 (tt0) REVERT: F 178 ASP cc_start: 0.7709 (m-30) cc_final: 0.7408 (m-30) REVERT: F 192 ASP cc_start: 0.7569 (m-30) cc_final: 0.6925 (p0) REVERT: F 196 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: G 94 GLU cc_start: 0.7248 (tp30) cc_final: 0.6349 (tp30) REVERT: G 211 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6902 (mtp-110) REVERT: H 30 ARG cc_start: 0.6935 (ttp80) cc_final: 0.6722 (ttp-110) REVERT: H 62 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.6934 (pp) REVERT: H 104 GLU cc_start: 0.6958 (tp30) cc_final: 0.6209 (tp30) REVERT: H 122 LEU cc_start: 0.7883 (mt) cc_final: 0.7643 (mt) REVERT: H 171 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7129 (mmt90) REVERT: H 192 ASP cc_start: 0.8155 (m-30) cc_final: 0.7774 (m-30) REVERT: I 130 LYS cc_start: 0.7199 (tmtt) cc_final: 0.6845 (tttt) REVERT: J 130 LYS cc_start: 0.7593 (tttm) cc_final: 0.7071 (mmtp) REVERT: J 139 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7479 (mtpt) outliers start: 59 outliers final: 30 residues processed: 300 average time/residue: 0.5460 time to fit residues: 183.0512 Evaluate side-chains 289 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 2 LYS 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 D residue 174 LYS Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 94 GLU 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 208 ASN Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 197 SER 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 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 H residue 217 THR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 103 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 93 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 186 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN D 123 GLN D 199 GLN F 63 ASN G 216 ASN J 85 ASN J 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.143542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134943 restraints weight = 20014.659| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 0.90 r_work: 0.3489 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4206 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= 0.124 Angle : 0.497 5.818 22640 Z= 0.268 Chirality : 0.045 0.135 2585 Planarity : 0.004 0.044 2926 Dihedral : 7.281 58.251 2431 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.76 % Allowed : 16.78 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.18), residues: 2127 helix: 1.32 (0.14), residues: 1320 sheet: -0.71 (0.25), residues: 378 loop : -0.43 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 14 TYR 0.012 0.001 TYR G 205 PHE 0.025 0.001 PHE C 191 TRP 0.012 0.001 TRP F 138 HIS 0.003 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00279 (16561) covalent geometry : angle 0.49702 (22640) hydrogen bonds : bond 0.04408 ( 781) hydrogen bonds : angle 4.45270 ( 2340) Misc. bond : bond 0.00119 ( 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 306 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.608 Fit side-chains REVERT: A 6 ASP cc_start: 0.7450 (t0) cc_final: 0.6456 (t70) REVERT: A 61 GLU cc_start: 0.8292 (tt0) cc_final: 0.7758 (tp30) REVERT: B 196 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: C 49 GLU cc_start: 0.6626 (tp30) cc_final: 0.6314 (tp30) REVERT: C 122 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7837 (tt) REVERT: D 204 ASP cc_start: 0.7209 (m-30) cc_final: 0.6839 (m-30) REVERT: E 30 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6409 (ttp-110) REVERT: E 34 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.6944 (t0) REVERT: E 49 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6535 (tp30) REVERT: E 171 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6559 (mmp-170) REVERT: E 215 ASP cc_start: 0.6500 (OUTLIER) cc_final: 0.6040 (m-30) REVERT: F 12 GLU cc_start: 0.7633 (tt0) cc_final: 0.7374 (mt-10) REVERT: F 178 ASP cc_start: 0.7709 (m-30) cc_final: 0.7436 (m-30) REVERT: F 192 ASP cc_start: 0.7476 (m-30) cc_final: 0.6715 (p0) REVERT: F 196 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: G 94 GLU cc_start: 0.7177 (tp30) cc_final: 0.6196 (tp30) REVERT: G 211 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7419 (mtp180) REVERT: H 30 ARG cc_start: 0.6968 (ttp80) cc_final: 0.6713 (ttp-110) REVERT: H 62 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6836 (pp) REVERT: H 104 GLU cc_start: 0.6665 (tp30) cc_final: 0.6035 (tp30) REVERT: H 171 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7112 (mmt90) REVERT: H 192 ASP cc_start: 0.8103 (m-30) cc_final: 0.7711 (m-30) REVERT: H 196 GLU cc_start: 0.7923 (mp0) cc_final: 0.7606 (mp0) REVERT: I 130 LYS cc_start: 0.7218 (tmtt) cc_final: 0.6901 (tttt) REVERT: J 130 LYS cc_start: 0.7512 (tttm) cc_final: 0.6843 (tppt) REVERT: J 139 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7463 (mtpt) outliers start: 42 outliers final: 19 residues processed: 292 average time/residue: 0.5651 time to fit residues: 183.6455 Evaluate side-chains 278 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 43 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C 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 41 THR Chi-restraints excluded: chain E residue 77 THR 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 208 ASN Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 211 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 I residue 90 ILE Chi-restraints excluded: chain I residue 133 SER 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 199 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 76 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 45 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 65 HIS C 31 HIS C 199 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN G 216 ASN ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 ASN J 175 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138970 restraints weight = 19825.566| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 0.90 r_work: 0.3534 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16570 Z= 0.093 Angle : 0.448 6.698 22640 Z= 0.240 Chirality : 0.043 0.134 2585 Planarity : 0.004 0.042 2926 Dihedral : 5.978 55.367 2431 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.64 % Allowed : 18.16 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.19), residues: 2127 helix: 1.74 (0.14), residues: 1334 sheet: -0.61 (0.26), residues: 366 loop : 0.15 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 14 TYR 0.019 0.001 TYR C 15 PHE 0.022 0.001 PHE C 191 TRP 0.011 0.001 TRP F 214 HIS 0.004 0.001 HIS I 31 Details of bonding type rmsd covalent geometry : bond 0.00201 (16561) covalent geometry : angle 0.44808 (22640) hydrogen bonds : bond 0.03529 ( 781) hydrogen bonds : angle 4.07852 ( 2340) Misc. bond : bond 0.00080 ( 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 299 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7405 (t0) cc_final: 0.6228 (t70) REVERT: A 61 GLU cc_start: 0.8301 (tt0) cc_final: 0.7806 (tp30) REVERT: C 49 GLU cc_start: 0.6482 (tp30) cc_final: 0.6231 (tp30) REVERT: D 204 ASP cc_start: 0.7072 (m-30) cc_final: 0.6669 (m-30) REVERT: E 30 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6740 (ttp-110) REVERT: E 34 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7054 (t0) REVERT: E 49 GLU cc_start: 0.6840 (tm-30) cc_final: 0.6474 (tp30) REVERT: E 171 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6552 (mmp-170) REVERT: E 211 ARG cc_start: 0.7015 (mtm-85) cc_final: 0.6527 (mtt180) REVERT: F 12 GLU cc_start: 0.7672 (tt0) cc_final: 0.7385 (mt-10) REVERT: F 178 ASP cc_start: 0.7755 (m-30) cc_final: 0.7470 (m-30) REVERT: G 94 GLU cc_start: 0.7104 (tp30) cc_final: 0.6139 (tp30) REVERT: G 175 GLN cc_start: 0.7567 (mt0) cc_final: 0.7366 (mt0) REVERT: G 211 ARG cc_start: 0.7696 (mtp-110) cc_final: 0.7461 (mtp180) REVERT: H 30 ARG cc_start: 0.6969 (ttp80) cc_final: 0.6713 (ttp-110) REVERT: H 62 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6801 (pp) REVERT: H 192 ASP cc_start: 0.8042 (m-30) cc_final: 0.7646 (m-30) REVERT: H 196 GLU cc_start: 0.7754 (mp0) cc_final: 0.7441 (mp0) REVERT: I 34 ASN cc_start: 0.6793 (m-40) cc_final: 0.6503 (m110) REVERT: I 130 LYS cc_start: 0.7236 (tmtt) cc_final: 0.6953 (tttt) REVERT: J 130 LYS cc_start: 0.7505 (tttm) cc_final: 0.6852 (tppt) outliers start: 25 outliers final: 9 residues processed: 294 average time/residue: 0.5764 time to fit residues: 188.8020 Evaluate side-chains 266 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 253 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 178 ASP 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 171 ARG Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 83 SER 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 98 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 121 optimal weight: 0.1980 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 E 216 ASN F 111 ASN G 158 ASN G 216 ASN I 185 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 = 0.3624 r_free = 0.3624 target = 0.140352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131606 restraints weight = 20215.712| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 0.91 r_work: 0.3455 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16570 Z= 0.205 Angle : 0.589 6.861 22640 Z= 0.318 Chirality : 0.049 0.198 2585 Planarity : 0.005 0.046 2926 Dihedral : 7.131 60.400 2430 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.57 % Allowed : 17.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.18), residues: 2127 helix: 1.38 (0.14), residues: 1327 sheet: -0.74 (0.25), residues: 360 loop : -0.35 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 14 TYR 0.018 0.002 TYR G 15 PHE 0.033 0.002 PHE C 191 TRP 0.014 0.002 TRP F 138 HIS 0.006 0.002 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00480 (16561) covalent geometry : angle 0.58893 (22640) hydrogen bonds : bond 0.05335 ( 781) hydrogen bonds : angle 4.65281 ( 2340) Misc. bond : bond 0.00176 ( 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: 39 poor density : 252 time to evaluate : 0.722 Fit side-chains REVERT: A 6 ASP cc_start: 0.7517 (t0) cc_final: 0.6747 (t70) REVERT: A 61 GLU cc_start: 0.8282 (tt0) cc_final: 0.7820 (tp30) REVERT: C 49 GLU cc_start: 0.6669 (tp30) cc_final: 0.6343 (tp30) REVERT: C 122 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7896 (tt) REVERT: D 49 GLU cc_start: 0.7700 (tp30) cc_final: 0.7471 (mm-30) REVERT: D 204 ASP cc_start: 0.7376 (m-30) cc_final: 0.7052 (m-30) REVERT: E 30 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6871 (ttp-110) REVERT: E 34 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.6905 (t0) REVERT: E 49 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6547 (tp30) REVERT: E 164 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6876 (mt-10) REVERT: E 171 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6532 (mmp-170) REVERT: E 215 ASP cc_start: 0.6443 (OUTLIER) cc_final: 0.5973 (m-30) REVERT: F 12 GLU cc_start: 0.7746 (tt0) cc_final: 0.7419 (mt-10) REVERT: F 94 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: F 178 ASP cc_start: 0.7682 (m-30) cc_final: 0.7387 (m-30) REVERT: G 94 GLU cc_start: 0.7241 (tp30) cc_final: 0.6349 (tp30) REVERT: H 14 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7030 (mtp85) REVERT: H 30 ARG cc_start: 0.6956 (ttp80) cc_final: 0.6709 (ttp-110) REVERT: H 62 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6929 (pp) REVERT: H 104 GLU cc_start: 0.6685 (tp30) cc_final: 0.6083 (tp30) REVERT: H 192 ASP cc_start: 0.8140 (m-30) cc_final: 0.7760 (m-30) REVERT: H 196 GLU cc_start: 0.7807 (mp0) cc_final: 0.7485 (mp0) REVERT: I 130 LYS cc_start: 0.7262 (tmtt) cc_final: 0.6882 (tttt) REVERT: J 130 LYS cc_start: 0.7558 (tttm) cc_final: 0.7052 (mmtp) outliers start: 39 outliers final: 18 residues processed: 280 average time/residue: 0.6268 time to fit residues: 195.4709 Evaluate side-chains 272 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 LEU Chi-restraints excluded: chain B residue 130 LYS 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 41 THR Chi-restraints excluded: chain E residue 77 THR 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 208 ASN Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 122 LEU 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 I residue 119 SER Chi-restraints excluded: chain J residue 122 LEU 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 135 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 216 ASN ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136176 restraints weight = 19964.040| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 0.89 r_work: 0.3514 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16570 Z= 0.107 Angle : 0.473 5.549 22640 Z= 0.254 Chirality : 0.044 0.132 2585 Planarity : 0.004 0.042 2926 Dihedral : 6.229 55.067 2430 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.58 % Allowed : 19.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.18), residues: 2127 helix: 1.75 (0.14), residues: 1327 sheet: -0.57 (0.26), residues: 366 loop : -0.00 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 14 TYR 0.018 0.001 TYR C 15 PHE 0.024 0.001 PHE C 191 TRP 0.011 0.001 TRP F 138 HIS 0.003 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00238 (16561) covalent geometry : angle 0.47334 (22640) hydrogen bonds : bond 0.03920 ( 781) hydrogen bonds : angle 4.22408 ( 2340) Misc. bond : bond 0.00112 ( 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 284 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7373 (t0) cc_final: 0.6312 (t70) REVERT: A 61 GLU cc_start: 0.8300 (tt0) cc_final: 0.7810 (tp30) REVERT: B 61 GLU cc_start: 0.7896 (tt0) cc_final: 0.7649 (tt0) REVERT: C 49 GLU cc_start: 0.6584 (tp30) cc_final: 0.6294 (tp30) REVERT: D 49 GLU cc_start: 0.7634 (tp30) cc_final: 0.7389 (mm-30) REVERT: D 204 ASP cc_start: 0.7035 (m-30) cc_final: 0.6640 (m-30) REVERT: E 30 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6820 (ttp-110) REVERT: E 34 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.6945 (t0) REVERT: E 49 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6504 (tp30) REVERT: E 171 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6526 (mmp-170) REVERT: F 12 GLU cc_start: 0.7726 (tt0) cc_final: 0.7466 (mt-10) REVERT: F 178 ASP cc_start: 0.7717 (m-30) cc_final: 0.7425 (m-30) REVERT: F 192 ASP cc_start: 0.7155 (p0) cc_final: 0.6413 (p0) REVERT: F 196 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: G 49 GLU cc_start: 0.6798 (tp30) cc_final: 0.6595 (tp30) REVERT: G 94 GLU cc_start: 0.7183 (tp30) cc_final: 0.6218 (tp30) REVERT: G 211 ARG cc_start: 0.7742 (mtp-110) cc_final: 0.7510 (mtp180) REVERT: H 30 ARG cc_start: 0.6976 (ttp80) cc_final: 0.6708 (ttp-110) REVERT: H 62 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6830 (pp) REVERT: H 192 ASP cc_start: 0.8046 (m-30) cc_final: 0.7719 (m-30) REVERT: H 196 GLU cc_start: 0.7773 (mp0) cc_final: 0.7434 (mp0) REVERT: I 34 ASN cc_start: 0.6743 (m-40) cc_final: 0.6473 (m110) REVERT: I 130 LYS cc_start: 0.7266 (tmtt) cc_final: 0.6960 (tttt) REVERT: J 130 LYS cc_start: 0.7494 (tttm) cc_final: 0.6830 (tppt) outliers start: 24 outliers final: 15 residues processed: 276 average time/residue: 0.6172 time to fit residues: 189.8885 Evaluate side-chains 276 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 23 ASP 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 171 ARG Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 215 ASP 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 62 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 119 SER 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 84 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 180 optimal weight: 0.0970 chunk 140 optimal weight: 9.9990 chunk 173 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 E 216 ASN G 175 GLN G 216 ASN I 158 ASN J 162 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132833 restraints weight = 20030.344| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 0.92 r_work: 0.3465 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4308 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= 0.155 Angle : 0.535 7.066 22640 Z= 0.287 Chirality : 0.047 0.142 2585 Planarity : 0.004 0.044 2926 Dihedral : 6.592 54.806 2430 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.51 % Allowed : 19.14 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.18), residues: 2127 helix: 1.62 (0.14), residues: 1327 sheet: -0.67 (0.25), residues: 366 loop : -0.17 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 14 TYR 0.014 0.002 TYR G 205 PHE 0.032 0.002 PHE C 191 TRP 0.012 0.001 TRP F 138 HIS 0.004 0.001 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00358 (16561) covalent geometry : angle 0.53536 (22640) hydrogen bonds : bond 0.04721 ( 781) hydrogen bonds : angle 4.45692 ( 2340) Misc. bond : bond 0.00175 ( 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 275 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 0.656 Fit side-chains REVERT: A 6 ASP cc_start: 0.7439 (t0) cc_final: 0.6385 (t70) REVERT: A 61 GLU cc_start: 0.8260 (tt0) cc_final: 0.7797 (tp30) REVERT: C 49 GLU cc_start: 0.6628 (tp30) cc_final: 0.6304 (tp30) REVERT: C 122 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7900 (tt) REVERT: D 49 GLU cc_start: 0.7655 (tp30) cc_final: 0.7425 (mm-30) REVERT: D 204 ASP cc_start: 0.7114 (m-30) cc_final: 0.6748 (m-30) REVERT: E 30 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6885 (ttp-110) REVERT: E 34 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.6877 (t0) REVERT: E 49 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6517 (tp30) REVERT: E 171 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6491 (mmp-170) REVERT: E 215 ASP cc_start: 0.6550 (OUTLIER) cc_final: 0.6050 (m-30) REVERT: F 12 GLU cc_start: 0.7739 (tt0) cc_final: 0.7486 (mt-10) REVERT: F 49 GLU cc_start: 0.6535 (tm-30) cc_final: 0.6071 (pp20) REVERT: F 178 ASP cc_start: 0.7713 (m-30) cc_final: 0.7418 (m-30) REVERT: F 192 ASP cc_start: 0.7315 (p0) cc_final: 0.6635 (p0) REVERT: F 196 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: G 94 GLU cc_start: 0.7232 (tp30) cc_final: 0.6332 (tp30) REVERT: G 211 ARG cc_start: 0.7728 (mtp-110) cc_final: 0.7406 (mtp180) REVERT: H 30 ARG cc_start: 0.6978 (ttp80) cc_final: 0.6721 (ttp-110) REVERT: H 62 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6904 (pp) REVERT: H 192 ASP cc_start: 0.8177 (m-30) cc_final: 0.7786 (m-30) REVERT: H 196 GLU cc_start: 0.7791 (mp0) cc_final: 0.7452 (mp0) REVERT: I 34 ASN cc_start: 0.6768 (m-40) cc_final: 0.6477 (m110) REVERT: I 130 LYS cc_start: 0.7270 (tmtt) cc_final: 0.6907 (tttt) REVERT: J 130 LYS cc_start: 0.7549 (tttm) cc_final: 0.6980 (mmtp) REVERT: J 144 ASP cc_start: 0.8098 (m-30) cc_final: 0.7896 (m-30) outliers start: 23 outliers final: 15 residues processed: 268 average time/residue: 0.6033 time to fit residues: 180.2447 Evaluate side-chains 267 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 77 THR 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 208 ASN Chi-restraints excluded: chain E residue 215 ASP 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 62 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 119 SER 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 13 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 87 optimal weight: 0.0470 chunk 164 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 88 optimal weight: 0.0020 chunk 111 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.9290 ------------------------------------------------------------------------------- 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 E 216 ASN F 111 ASN G 175 GLN G 216 ASN I 158 ASN J 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135041 restraints weight = 19662.187| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 0.88 r_work: 0.3493 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4338 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= 0.137 Angle : 0.513 5.844 22640 Z= 0.276 Chirality : 0.046 0.139 2585 Planarity : 0.004 0.043 2926 Dihedral : 6.547 56.056 2430 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.91 % Allowed : 18.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.18), residues: 2127 helix: 1.65 (0.14), residues: 1327 sheet: -0.65 (0.26), residues: 366 loop : -0.15 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 14 TYR 0.014 0.001 TYR G 205 PHE 0.031 0.002 PHE C 191 TRP 0.012 0.001 TRP F 138 HIS 0.003 0.001 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00314 (16561) covalent geometry : angle 0.51320 (22640) hydrogen bonds : bond 0.04470 ( 781) hydrogen bonds : angle 4.39541 ( 2340) Misc. bond : bond 0.00146 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5009.32 seconds wall clock time: 86 minutes 28.40 seconds (5188.40 seconds total)