Starting phenix.real_space_refine on Wed Mar 4 20:44:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc4_15962/03_2026/8bc4_15962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc4_15962/03_2026/8bc4_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bc4_15962/03_2026/8bc4_15962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc4_15962/03_2026/8bc4_15962.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bc4_15962/03_2026/8bc4_15962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc4_15962/03_2026/8bc4_15962.map" } 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-dev-5986/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: 3.87, 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: 1.07 Conformation dependent library (CDL) restraints added in 620.5 milliseconds 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: 0.56 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: 2.80 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2665 1.30 - 1.43: 4710 1.43 - 1.57: 9094 1.57 - 1.70: 27 1.70 - 1.84: 65 Bond restraints: 16561 Sorted by residual: bond pdb=" C2 QC9 H 301 " pdb=" O6 QC9 H 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C2 QC9 J 301 " pdb=" O6 QC9 J 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C2 QC9 F 301 " pdb=" O6 QC9 F 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C2 QC9 C 301 " pdb=" O6 QC9 C 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C2 QC9 A 301 " pdb=" O6 QC9 A 301 " ideal model delta sigma weight residual 1.432 1.292 0.140 2.00e-02 2.50e+03 4.92e+01 ... (remaining 16556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 22431 5.38 - 10.76: 160 10.76 - 16.14: 22 16.14 - 21.52: 9 21.52 - 26.90: 18 Bond angle restraints: 22640 Sorted by residual: angle pdb=" C3 QC9 G 301 " pdb=" C12 QC9 G 301 " pdb=" S13 QC9 G 301 " ideal model delta sigma weight residual 112.26 139.16 -26.90 3.00e+00 1.11e-01 8.04e+01 angle pdb=" C3 QC9 B 301 " pdb=" C12 QC9 B 301 " pdb=" S13 QC9 B 301 " ideal model delta sigma weight residual 112.26 139.10 -26.84 3.00e+00 1.11e-01 8.00e+01 angle pdb=" C3 QC9 H 301 " pdb=" C12 QC9 H 301 " pdb=" S13 QC9 H 301 " ideal model delta sigma weight residual 112.26 139.08 -26.82 3.00e+00 1.11e-01 7.99e+01 angle pdb=" C3 QC9 D 301 " pdb=" C12 QC9 D 301 " pdb=" S13 QC9 D 301 " ideal model delta sigma weight residual 112.26 139.08 -26.82 3.00e+00 1.11e-01 7.99e+01 angle pdb=" C3 QC9 J 301 " pdb=" C12 QC9 J 301 " pdb=" S13 QC9 J 301 " ideal model delta sigma weight residual 112.26 139.07 -26.81 3.00e+00 1.11e-01 7.99e+01 ... (remaining 22635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 8349 17.25 - 34.49: 836 34.49 - 51.74: 306 51.74 - 68.98: 101 68.98 - 86.23: 42 Dihedral angle restraints: 9634 sinusoidal: 3323 harmonic: 6311 Sorted by residual: dihedral pdb=" CD ARG I 171 " pdb=" NE ARG I 171 " pdb=" CZ ARG I 171 " pdb=" NH1 ARG I 171 " ideal model delta sinusoidal sigma weight residual 0.00 85.93 -85.93 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CD ARG G 14 " pdb=" NE ARG G 14 " pdb=" CZ ARG G 14 " pdb=" NH1 ARG G 14 " ideal model delta sinusoidal sigma weight residual 0.00 79.93 -79.93 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CD ARG D 14 " pdb=" NE ARG D 14 " pdb=" CZ ARG D 14 " pdb=" NH1 ARG D 14 " ideal model delta sinusoidal sigma weight residual 0.00 73.27 -73.27 1 1.00e+01 1.00e-02 6.84e+01 ... (remaining 9631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1489 0.092 - 0.184: 942 0.184 - 0.276: 127 0.276 - 0.368: 9 0.368 - 0.460: 18 Chirality restraints: 2585 Sorted by residual: chirality pdb=" C2 QC9 D 301 " pdb=" C1 QC9 D 301 " pdb=" C3 QC9 D 301 " pdb=" O6 QC9 D 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" C2 QC9 A 301 " pdb=" C1 QC9 A 301 " pdb=" C3 QC9 A 301 " pdb=" O6 QC9 A 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C2 QC9 E 301 " pdb=" C1 QC9 E 301 " pdb=" C3 QC9 E 301 " pdb=" O6 QC9 E 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 2582 not shown) Planarity restraints: 2926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 14 " 1.099 9.50e-02 1.11e+02 4.93e-01 1.47e+02 pdb=" NE ARG G 14 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG G 14 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG G 14 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG G 14 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 171 " 1.096 9.50e-02 1.11e+02 4.91e-01 1.45e+02 pdb=" NE ARG I 171 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG I 171 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG I 171 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG I 171 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 14 " 1.066 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARG D 14 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG D 14 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 14 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 14 " 0.023 2.00e-02 2.50e+03 ... (remaining 2923 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4510 2.83 - 3.35: 17262 3.35 - 3.86: 30757 3.86 - 4.38: 38233 4.38 - 4.90: 58920 Nonbonded interactions: 149682 Sorted by model distance: nonbonded pdb=" O LEU D 170 " pdb=" O HOH D 401 " model vdw 2.310 3.040 nonbonded pdb=" O LEU E 170 " pdb=" O HOH E 401 " model vdw 2.310 3.040 nonbonded pdb=" O LEU H 170 " pdb=" O HOH H 401 " model vdw 2.311 3.040 nonbonded pdb=" O LEU A 170 " pdb=" O HOH A 401 " model vdw 2.311 3.040 nonbonded pdb=" O LEU C 170 " pdb=" O HOH C 401 " model vdw 2.311 3.040 ... (remaining 149677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 103 or (resid 104 through 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 138 or (re \ sid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 th \ rough 145 or (resid 146 and (name N or name CA or name C or name O or name CB )) \ or resid 148 or (resid 149 through 151 and (name N or name CA or name C or name \ O or name CB )) or resid 152 through 159 or (resid 160 and (name N or name CA o \ r name C or name O or name CB )) or resid 161 through 163 or (resid 164 and (nam \ e N or name CA or name C or name O or name CB )) or resid 165 through 166 or (re \ sid 167 through 170 and (name N or name CA or name C or name O or name CB )) or \ resid 171 through 173 or (resid 174 and (name N or name CA or name C or name O o \ r name CB )) or resid 175 or (resid 176 through 180 and (name N or name CA or na \ me C or name O or name CB )) or resid 181 through 191 or (resid 192 and (name N \ or name CA or name C or name O or name CB )) or resid 193 through 195 or (resid \ 196 and (name N or name CA or name C or name O or name CB )) or resid 197 throug \ h 210 or (resid 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 217)) selection = (chain 'B' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 138 or (resid 139 and (name N or name CA or name C \ or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 148 or (resid 149 through 151 a \ nd (name N or name CA or name C or name O or name CB )) or resid 152 through 156 \ or (resid 157 and (name N or name CA or name C or name O or name CB )) or resid \ 158 through 159 or (resid 160 and (name N or name CA or name C or name O or nam \ e CB )) or resid 161 or (resid 162 and (name N or name CA or name C or name O or \ name CB )) or resid 163 through 166 or (resid 167 through 170 and (name N or na \ me CA or name C or name O or name CB )) or resid 171 through 173 or (resid 174 a \ nd (name N or name CA or name C or name O or name CB )) or resid 175 or (resid 1 \ 76 through 180 and (name N or name CA or name C or name O or name CB )) or resid \ 181 through 191 or (resid 192 and (name N or name CA or name C or name O or nam \ e CB )) or resid 193 through 195 or (resid 196 and (name N or name CA or name C \ or name O or name CB )) or resid 197 through 203 or (resid 204 and (name N or na \ me CA or name C or name O or name CB )) or resid 205 through 206 or (resid 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 210 \ or (resid 211 and (name N or name CA or name C or name O or name CB )) or resid \ 212 through 217)) selection = (chain 'C' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 52 or (resid 53 throug \ h 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throug \ h 71 or (resid 72 through 75 and (name N or name CA or name C or name O or name \ CB )) or resid 76 through 78 or (resid 79 through 82 and (name N or name CA or n \ ame C or name O or name CB )) or resid 83 or (resid 84 and (name N or name CA or \ name C or name O or name CB )) or resid 85 through 103 or (resid 104 through 10 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 107 through \ 138 or (resid 139 and (name N or name CA or name C or name O or name CB )) or re \ sid 140 through 145 or (resid 146 and (name N or name CA or name C or name O or \ name CB )) or resid 148 or (resid 149 through 151 and (name N or name CA or name \ C or name O or name CB )) or resid 152 through 159 or (resid 160 and (name N or \ name CA or name C or name O or name CB )) or resid 161 or (resid 162 and (name \ N or name CA or name C or name O or name CB )) or resid 163 or (resid 164 and (n \ ame N or name CA or name C or name O or name CB )) or resid 165 through 166 or ( \ resid 167 through 170 and (name N or name CA or name C or name O or name CB )) o \ r resid 171 through 173 or (resid 174 and (name N or name CA or name C or name O \ or name CB )) or resid 175 or (resid 176 through 180 and (name N or name CA or \ name C or name O or name CB )) or resid 181 through 191 or (resid 192 and (name \ N or name CA or name C or name O or name CB )) or resid 193 through 195 or (resi \ d 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 203 or (resid 204 and (name N or name CA or name C or name O or name CB )) o \ r resid 205 through 206 or (resid 207 and (name N or name CA or name C or name O \ or name CB )) or resid 208 through 210 or (resid 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 217)) selection = (chain 'D' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 103 or (resid 104 through 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 138 or (re \ sid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 th \ rough 148 or (resid 149 through 151 and (name N or name CA or name C or name O o \ r name CB )) or resid 152 through 156 or (resid 157 and (name N or name CA or na \ me C or name O or name CB )) or resid 158 through 159 or (resid 160 and (name N \ or name CA or name C or name O or name CB )) or resid 161 or (resid 162 and (nam \ e N or name CA or name C or name O or name CB )) or resid 163 or (resid 164 and \ (name N or name CA or name C or name O or name CB )) or resid 165 through 166 or \ (resid 167 through 170 and (name N or name CA or name C or name O or name CB )) \ or resid 171 through 173 or (resid 174 and (name N or name CA or name C or name \ O or name CB )) or resid 175 through 177 or (resid 178 through 180 and (name N \ or name CA or name C or name O or name CB )) or resid 181 through 186 or (resid \ 187 and (name N or name CA or name C or name O or name CB )) or resid 188 throug \ h 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 195 or (resid 196 and (name N or name CA or name C or name O o \ r name CB )) or resid 197 through 203 or (resid 204 and (name N or name CA or na \ me C or name O or name CB )) or resid 205 through 206 or (resid 207 and (name N \ or name CA or name C or name O or name CB )) or resid 208 through 210 or (resid \ 211 and (name N or name CA or name C or name O or name CB )) or resid 212 throug \ h 217)) selection = (chain 'E' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 52 \ or (resid 53 through 55 and (name N or name CA or name C or name O or name CB ) \ ) or resid 56 through 60 or (resid 61 through 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 78 or (resid 79 through 82 and (na \ me N or name CA or name C or name O or name CB )) or resid 83 or (resid 84 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 through 93 or (r \ esid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 thr \ ough 103 or (resid 104 through 106 and (name N or name CA or name C or name O or \ name CB )) or resid 107 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 or (resid 149 through 1 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 152 through \ 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) or r \ esid 158 through 159 or (resid 160 and (name N or name CA or name C or name O or \ name CB )) or resid 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 or (resid 164 and (name N or name CA or name C or n \ ame O or name CB )) or resid 165 through 166 or (resid 167 through 170 and (name \ N or name CA or name C or name O or name CB )) or resid 171 through 173 or (res \ id 174 and (name N or name CA or name C or name O or name CB )) or resid 175 or \ (resid 176 through 180 and (name N or name CA or name C or name O or name CB )) \ or resid 181 through 186 or (resid 187 and (name N or name CA or name C or name \ O or name CB )) or resid 188 through 191 or (resid 192 and (name N or name CA or \ name C or name O or name CB )) or resid 193 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 203 or (res \ id 204 and (name N or name CA or name C or name O or name CB )) or resid 205 thr \ ough 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 210 or (resid 211 and (name N or name CA or name C or name \ O or name CB )) or resid 212 through 217)) selection = (chain 'F' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 60 \ or (resid 61 through 63 and (name N or name CA or name C or name O or name CB ) \ ) or resid 64 through 71 or (resid 72 through 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 78 or (resid 79 through 82 and (na \ me N or name CA or name C or name O or name CB )) or resid 83 or (resid 84 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 through 93 or (r \ esid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 thr \ ough 103 or (resid 104 through 106 and (name N or name CA or name C or name O or \ name CB )) or resid 107 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 or (resid 149 through 1 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 152 through \ 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) or r \ esid 158 through 161 or (resid 162 and (name N or name CA or name C or name O or \ name CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name \ O or name CB )) or resid 165 through 166 or (resid 167 through 170 and (name N o \ r name CA or name C or name O or name CB )) or resid 171 through 173 or (resid 1 \ 74 and (name N or name CA or name C or name O or name CB )) or resid 175 or (res \ id 176 through 180 and (name N or name CA or name C or name O or name CB )) or r \ esid 181 through 186 or (resid 187 and (name N or name CA or name C or name O or \ name CB )) or resid 188 through 191 or (resid 192 and (name N or name CA or nam \ e C or name O or name CB )) or resid 193 through 195 or (resid 196 and (name N o \ r name CA or name C or name O or name CB )) or resid 197 through 203 or (resid 2 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 205 through \ 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) or r \ esid 208 through 210 or (resid 211 and (name N or name CA or name C or name O or \ name CB )) or resid 212 through 217)) selection = (chain 'G' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 60 or (resid 61 through 63 and (name N or name CA or name C or name O \ or name CB )) or resid 64 through 71 or (resid 72 through 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throu \ gh 82 and (name N or name CA or name C or name O or name CB )) or resid 83 or (r \ esid 84 and (name N or name CA or name C or name O or name CB )) or resid 85 thr \ ough 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or \ resid 95 through 103 or (resid 104 through 106 and (name N or name CA or name C \ or name O or name CB )) or resid 107 through 145 or (resid 146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 148 or (resid 149 through 151 \ and (name N or name CA or name C or name O or name CB )) or resid 152 through 16 \ 1 or (resid 162 and (name N or name CA or name C or name O or name CB )) or resi \ d 163 or (resid 164 and (name N or name CA or name C or name O or name CB )) or \ resid 165 through 166 or (resid 167 through 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 through 175 or (resid 176 through 180 and \ (name N or name CA or name C or name O or name CB )) or resid 181 through 195 or \ (resid 196 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 7 through 203 or (resid 204 and (name N or name CA or name C or name O or name C \ B )) or resid 205 through 206 or (resid 207 and (name N or name CA or name C or \ name O or name CB )) or resid 208 through 210 or (resid 211 and (name N or name \ CA or name C or name O or name CB )) or resid 212 through 217)) selection = (chain 'H' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 103 or (resid 104 through 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 138 or (re \ sid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 th \ rough 149 or (resid 150 through 151 and (name N or name CA or name C or name O o \ r name CB )) or resid 152 through 156 or (resid 157 and (name N or name CA or na \ me C or name O or name CB )) or resid 158 through 159 or (resid 160 and (name N \ or name CA or name C or name O or name CB )) or resid 161 through 163 or (resid \ 164 and (name N or name CA or name C or name O or name CB )) or resid 165 throug \ h 166 or (resid 167 through 170 and (name N or name CA or name C or name O or na \ me CB )) or resid 171 through 173 or (resid 174 and (name N or name CA or name C \ or name O or name CB )) or resid 175 through 177 or (resid 178 through 180 and \ (name N or name CA or name C or name O or name CB )) or resid 181 through 191 or \ (resid 192 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 3 through 195 or (resid 196 and (name N or name CA or name C or name O or name C \ B )) or resid 197 through 203 or (resid 204 and (name N or name CA or name C or \ name O or name CB )) or resid 205 through 206 or (resid 207 and (name N or name \ CA or name C or name O or name CB )) or resid 208 through 217)) selection = (chain 'I' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or r \ esid 83 or (resid 84 and (name N or name CA or name C or name O or name CB )) or \ resid 85 through 93 or (resid 94 and (name N or name CA or name C or name O or \ name CB )) or resid 95 through 103 or (resid 104 through 106 and (name N or name \ CA or name C or name O or name CB )) or resid 107 through 138 or (resid 139 and \ (name N or name CA or name C or name O or name CB )) or resid 140 through 145 o \ r (resid 146 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 48 or (resid 149 through 151 and (name N or name CA or name C or name O or name \ CB )) or resid 152 through 161 or (resid 162 and (name N or name CA or name C or \ name O or name CB )) or resid 163 or (resid 164 and (name N or name CA or name \ C or name O or name CB )) or resid 165 through 173 or (resid 174 and (name N or \ name CA or name C or name O or name CB )) or resid 175 or (resid 176 through 180 \ and (name N or name CA or name C or name O or name CB )) or resid 181 through 1 \ 86 or (resid 187 and (name N or name CA or name C or name O or name CB )) or res \ id 188 through 191 or (resid 192 and (name N or name CA or name C or name O or n \ ame CB )) or resid 193 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 210 or (resid 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 2 \ 17)) selection = (chain 'J' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 60 or (resid 61 through 63 and (name N or name CA or name C or name O \ or name CB )) or resid 64 through 71 or (resid 72 through 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throu \ gh 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throu \ gh 103 or (resid 104 through 106 and (name N or name CA or name C or name O or n \ ame CB )) or resid 107 through 138 or (resid 139 and (name N or name CA or name \ C or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N or \ name CA or name C or name O or name CB )) or resid 148 or (resid 149 through 151 \ and (name N or name CA or name C or name O or name CB )) or resid 152 through 1 \ 59 or (resid 160 and (name N or name CA or name C or name O or name CB )) or res \ id 161 or (resid 162 and (name N or name CA or name C or name O or name CB )) or \ resid 163 or (resid 164 and (name N or name CA or name C or name O or name CB ) \ ) or resid 165 through 166 or (resid 167 through 170 and (name N or name CA or n \ ame C or name O or name CB )) or resid 171 through 173 or (resid 174 and (name N \ or name CA or name C or name O or name CB )) or resid 175 or (resid 176 through \ 180 and (name N or name CA or name C or name O or name CB )) or resid 181 throu \ gh 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) or \ resid 188 through 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB )) or resid 193 through 195 or (resid 196 and (name N or name CA or n \ ame C or name O or name CB )) or resid 197 through 203 or (resid 204 and (name N \ or name CA or name C or name O or name CB )) or resid 205 through 206 or (resid \ 207 and (name N or name CA or name C or name O or name CB )) or resid 208 throu \ gh 210 or (resid 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.090 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.670 ------------------------------------------------------------------------------- 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 are 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 : 0.547 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7676 (tp30) REVERT: A 84 SER cc_start: 0.7246 (p) cc_final: 0.6925 (m) REVERT: C 120 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7412 (mt0) REVERT: D 33 MET cc_start: 0.7632 (ttp) cc_final: 0.7431 (ptm) REVERT: D 204 ASP cc_start: 0.6900 (m-30) cc_final: 0.6482 (m-30) REVERT: D 208 ASN cc_start: 0.7581 (t0) cc_final: 0.7303 (t0) REVERT: E 77 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7857 (m) REVERT: E 110 THR cc_start: 0.7607 (p) cc_final: 0.7245 (t) REVERT: E 218 VAL cc_start: 0.3647 (OUTLIER) cc_final: 0.3164 (m) REVERT: F 46 PHE cc_start: 0.7344 (m-10) cc_final: 0.7123 (m-10) REVERT: F 192 ASP cc_start: 0.7455 (m-30) cc_final: 0.7126 (p0) REVERT: G 33 MET cc_start: 0.6765 (ttp) cc_final: 0.6399 (tmm) REVERT: H 30 ARG cc_start: 0.7068 (ttp80) cc_final: 0.6701 (ttp-110) REVERT: H 40 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6124 (pt) REVERT: H 46 PHE cc_start: 0.7900 (m-10) cc_final: 0.7668 (m-10) REVERT: H 94 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5788 (tp30) REVERT: H 122 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7264 (tp) REVERT: H 148 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.6822 (t80) REVERT: H 192 ASP cc_start: 0.7847 (m-30) cc_final: 0.7262 (m-30) REVERT: J 49 GLU cc_start: 0.6476 (tp30) cc_final: 0.6272 (tp30) REVERT: J 130 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7202 (mmtp) outliers start: 164 outliers final: 11 residues processed: 595 average time/residue: 0.5027 time to fit residues: 336.6065 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 : 0.585 ------------------------------------------------------------------------------- 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 85 ASN J 162 ASN J 172 ASN J 200 HIS J 212 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136045 restraints weight = 19791.267| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 0.87 r_work: 0.3509 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16570 Z= 0.166 Angle : 0.604 8.090 22640 Z= 0.320 Chirality : 0.047 0.199 2585 Planarity : 0.005 0.051 2926 Dihedral : 8.412 72.918 2469 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.22 % Allowed : 17.11 % 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 are not related in a simple way. whole: -1.60 (0.16), residues: 2127 helix: -0.68 (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 0.006 0.001 ARG A 171 TYR 0.015 0.002 TYR I 159 PHE 0.022 0.002 PHE C 191 TRP 0.013 0.002 TRP B 214 HIS 0.012 0.002 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00375 (16561) covalent geometry : angle 0.60375 (22640) hydrogen bonds : bond 0.05182 ( 781) hydrogen bonds : angle 5.17633 ( 2340) Misc. bond : bond 0.00188 ( 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 343 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 294 time to evaluate : 0.507 Fit side-chains REVERT: A 61 GLU cc_start: 0.8225 (tt0) cc_final: 0.7816 (tp30) REVERT: A 94 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6584 (mm-30) REVERT: A 130 LYS cc_start: 0.8305 (tmtt) cc_final: 0.8036 (tptt) REVERT: A 174 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7626 (ttpt) REVERT: A 211 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7162 (mtt180) REVERT: D 61 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: D 204 ASP cc_start: 0.7242 (m-30) cc_final: 0.6815 (m-30) REVERT: D 208 ASN cc_start: 0.7659 (t0) cc_final: 0.7395 (t0) REVERT: E 30 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6571 (ttp-110) REVERT: E 34 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.6854 (t0) REVERT: E 164 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: E 218 VAL cc_start: 0.3263 (OUTLIER) cc_final: 0.2938 (m) REVERT: F 94 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6638 (mp0) REVERT: F 192 ASP cc_start: 0.7679 (m-30) cc_final: 0.7135 (p0) REVERT: G 33 MET cc_start: 0.7123 (ttp) cc_final: 0.6831 (tmm) REVERT: G 211 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6999 (mtp-110) REVERT: H 30 ARG cc_start: 0.7338 (ttp80) cc_final: 0.7059 (ttp-110) REVERT: H 122 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7675 (mt) REVERT: H 148 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.6947 (p90) REVERT: H 192 ASP cc_start: 0.8026 (m-30) cc_final: 0.7603 (m-30) REVERT: H 196 GLU cc_start: 0.7742 (mp0) cc_final: 0.7499 (mp0) REVERT: I 130 LYS cc_start: 0.7258 (tmtt) cc_final: 0.6890 (tttt) REVERT: I 142 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.8085 (m) REVERT: J 101 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.5933 (ttmm) REVERT: J 130 LYS cc_start: 0.7806 (tttm) cc_final: 0.6996 (tppt) REVERT: J 204 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6591 (m-30) outliers start: 49 outliers final: 15 residues processed: 325 average time/residue: 0.5847 time to fit residues: 211.1630 Evaluate side-chains 284 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR 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 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 101 LYS Chi-restraints excluded: chain J residue 146 THR 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: 10.0000 chunk 98 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 199 GLN B 34 ASN B 111 ASN B 185 HIS 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 = 0.3606 r_free = 0.3606 target = 0.139108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130405 restraints weight = 20434.884| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 0.92 r_work: 0.3440 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16570 Z= 0.267 Angle : 0.681 6.732 22640 Z= 0.369 Chirality : 0.053 0.251 2585 Planarity : 0.005 0.045 2926 Dihedral : 8.301 64.296 2436 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.01 % Allowed : 15.99 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2127 helix: 0.15 (0.13), residues: 1320 sheet: -1.23 (0.24), residues: 360 loop : -0.88 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 14 TYR 0.023 0.003 TYR I 159 PHE 0.028 0.003 PHE C 191 TRP 0.014 0.002 TRP G 20 HIS 0.011 0.003 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00629 (16561) covalent geometry : angle 0.68143 (22640) hydrogen bonds : bond 0.06312 ( 781) hydrogen bonds : angle 5.14620 ( 2340) Misc. bond : bond 0.00200 ( 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 337 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7489 (p) REVERT: A 61 GLU cc_start: 0.8237 (tt0) cc_final: 0.7799 (tp30) REVERT: A 94 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6641 (mm-30) REVERT: B 12 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 93 THR cc_start: 0.7918 (t) cc_final: 0.7606 (p) REVERT: C 122 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7912 (tt) REVERT: C 162 ASN cc_start: 0.7414 (m-40) cc_final: 0.6995 (m-40) REVERT: D 61 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: D 204 ASP cc_start: 0.7370 (m-30) cc_final: 0.7069 (m-30) REVERT: E 30 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6549 (ttp-110) REVERT: E 34 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.6939 (t0) REVERT: E 43 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7047 (mt) REVERT: E 164 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: E 171 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6315 (mmp-170) REVERT: E 218 VAL cc_start: 0.3409 (OUTLIER) cc_final: 0.2918 (m) REVERT: F 178 ASP cc_start: 0.7713 (m-30) cc_final: 0.7386 (m-30) REVERT: F 192 ASP cc_start: 0.7699 (m-30) cc_final: 0.7046 (p0) REVERT: F 196 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: G 61 GLU cc_start: 0.6661 (tt0) cc_final: 0.6401 (tt0) REVERT: G 211 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6995 (mtp-110) REVERT: H 30 ARG cc_start: 0.7122 (ttp80) cc_final: 0.6849 (ttp-110) REVERT: H 104 GLU cc_start: 0.6800 (tp30) cc_final: 0.6202 (tp30) REVERT: H 122 LEU cc_start: 0.7929 (mt) cc_final: 0.7701 (mt) REVERT: H 192 ASP cc_start: 0.8203 (m-30) cc_final: 0.7840 (m-30) REVERT: I 130 LYS cc_start: 0.7205 (tmtt) cc_final: 0.6842 (tttt) REVERT: J 130 LYS cc_start: 0.7617 (tttm) cc_final: 0.6829 (tppt) REVERT: J 204 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6641 (m-30) outliers start: 61 outliers final: 21 residues processed: 316 average time/residue: 0.5620 time to fit residues: 197.7945 Evaluate side-chains 288 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR 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 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 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 218 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain 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 136 VAL 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 103 PHE 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: 1.9990 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 34 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.141784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133012 restraints weight = 20130.297| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 0.92 r_work: 0.3462 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16570 Z= 0.154 Angle : 0.529 5.692 22640 Z= 0.287 Chirality : 0.047 0.145 2585 Planarity : 0.004 0.044 2926 Dihedral : 7.444 59.124 2432 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.29 % Allowed : 16.91 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 2127 helix: 0.87 (0.14), residues: 1320 sheet: -0.83 (0.24), residues: 378 loop : -0.61 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 14 TYR 0.014 0.002 TYR I 159 PHE 0.025 0.002 PHE C 191 TRP 0.011 0.001 TRP F 138 HIS 0.005 0.001 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00354 (16561) covalent geometry : angle 0.52944 (22640) hydrogen bonds : bond 0.04860 ( 781) hydrogen bonds : angle 4.63280 ( 2340) Misc. bond : bond 0.00114 ( 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 307 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8287 (tt0) cc_final: 0.7771 (tp30) REVERT: B 160 ASN cc_start: 0.7387 (OUTLIER) cc_final: 0.7145 (m-40) REVERT: C 49 GLU cc_start: 0.6605 (tp30) cc_final: 0.6312 (tp30) REVERT: C 122 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7918 (tt) REVERT: C 162 ASN cc_start: 0.7365 (m-40) cc_final: 0.6951 (m-40) REVERT: D 49 GLU cc_start: 0.7563 (tp30) cc_final: 0.7266 (mm-30) REVERT: D 204 ASP cc_start: 0.7327 (m-30) cc_final: 0.6991 (m-30) REVERT: E 30 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6425 (ttp-110) REVERT: E 34 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.6860 (t0) REVERT: E 43 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7120 (mt) REVERT: E 171 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6523 (mmp-170) REVERT: F 12 GLU cc_start: 0.7634 (tt0) cc_final: 0.7399 (mt-10) REVERT: F 178 ASP cc_start: 0.7696 (m-30) cc_final: 0.7410 (m-30) REVERT: F 192 ASP cc_start: 0.7563 (m-30) cc_final: 0.6733 (p0) REVERT: F 196 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: G 94 GLU cc_start: 0.7180 (tp30) cc_final: 0.6248 (tp30) REVERT: G 211 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7015 (mtp-110) REVERT: H 62 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6842 (pp) REVERT: H 122 LEU cc_start: 0.7862 (mt) cc_final: 0.7630 (mt) REVERT: H 171 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7097 (mmt90) REVERT: H 192 ASP cc_start: 0.8136 (m-30) cc_final: 0.7709 (m-30) REVERT: H 196 GLU cc_start: 0.7824 (mp0) cc_final: 0.7534 (mp0) REVERT: I 130 LYS cc_start: 0.7180 (tmtt) cc_final: 0.6852 (tttt) REVERT: J 130 LYS cc_start: 0.7560 (tttm) cc_final: 0.7045 (mmtp) REVERT: J 204 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6559 (m-30) outliers start: 50 outliers final: 20 residues processed: 294 average time/residue: 0.5606 time to fit residues: 183.7030 Evaluate side-chains 271 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 160 ASN 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 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 F residue 196 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 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 I residue 142 SER Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 204 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 62 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN F 34 ASN G 216 ASN H 200 HIS J 162 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129645 restraints weight = 20367.314| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 0.91 r_work: 0.3432 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16570 Z= 0.261 Angle : 0.654 6.264 22640 Z= 0.355 Chirality : 0.052 0.258 2585 Planarity : 0.005 0.048 2926 Dihedral : 8.231 66.493 2431 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.55 % Allowed : 16.25 % 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 are not related in a simple way. whole: -0.08 (0.17), residues: 2127 helix: 0.59 (0.14), residues: 1334 sheet: -1.00 (0.25), residues: 360 loop : -0.79 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 14 TYR 0.017 0.002 TYR G 205 PHE 0.029 0.003 PHE C 191 TRP 0.014 0.002 TRP H 214 HIS 0.007 0.002 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00618 (16561) covalent geometry : angle 0.65439 (22640) hydrogen bonds : bond 0.06165 ( 781) hydrogen bonds : angle 5.00391 ( 2340) Misc. bond : bond 0.00164 ( 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 310 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8099 (tt0) cc_final: 0.7726 (tp30) REVERT: C 49 GLU cc_start: 0.6717 (tp30) cc_final: 0.6442 (tp30) REVERT: C 122 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7866 (tt) REVERT: D 33 MET cc_start: 0.7223 (ttp) cc_final: 0.7011 (ttp) REVERT: D 49 GLU cc_start: 0.7501 (tp30) cc_final: 0.7199 (mm-30) REVERT: D 204 ASP cc_start: 0.7364 (m-30) cc_final: 0.7037 (m-30) REVERT: E 30 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6570 (ttp-110) REVERT: E 34 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.6942 (t0) REVERT: E 49 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6508 (tp30) REVERT: E 164 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: E 171 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6512 (mmp-170) REVERT: F 12 GLU cc_start: 0.7658 (tt0) cc_final: 0.7399 (mt-10) REVERT: F 49 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6511 (tm-30) REVERT: F 178 ASP cc_start: 0.7711 (m-30) cc_final: 0.7419 (m-30) REVERT: F 192 ASP cc_start: 0.7563 (m-30) cc_final: 0.6950 (p0) REVERT: F 196 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: G 61 GLU cc_start: 0.6650 (tt0) cc_final: 0.6426 (tt0) REVERT: G 94 GLU cc_start: 0.7240 (tp30) cc_final: 0.6326 (tp30) REVERT: G 211 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6893 (mtp-110) REVERT: H 62 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6881 (pp) REVERT: H 104 GLU cc_start: 0.6945 (tp30) cc_final: 0.6219 (tp30) REVERT: H 122 LEU cc_start: 0.7859 (mt) cc_final: 0.7639 (mt) REVERT: H 171 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7114 (mmt90) REVERT: H 192 ASP cc_start: 0.8157 (m-30) cc_final: 0.7774 (m-30) REVERT: I 130 LYS cc_start: 0.7195 (tmtt) cc_final: 0.6841 (tttt) REVERT: J 130 LYS cc_start: 0.7594 (tttm) cc_final: 0.7073 (mmtp) REVERT: J 139 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7477 (mtpt) REVERT: J 204 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6569 (m-30) outliers start: 54 outliers final: 28 residues processed: 297 average time/residue: 0.5821 time to fit residues: 192.0613 Evaluate side-chains 287 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 248 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 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 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 119 SER Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 197 SER 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 I residue 142 SER Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 204 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 93 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 186 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN F 63 ASN G 216 ASN H 111 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 = 0.3675 r_free = 0.3675 target = 0.144749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136335 restraints weight = 20306.540| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 0.90 r_work: 0.3508 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16570 Z= 0.102 Angle : 0.461 5.592 22640 Z= 0.249 Chirality : 0.044 0.137 2585 Planarity : 0.004 0.043 2926 Dihedral : 6.693 52.606 2431 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.30 % Allowed : 17.43 % Favored : 80.26 % 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 are not related in a simple way. whole: 1.07 (0.18), residues: 2127 helix: 1.52 (0.14), residues: 1320 sheet: -0.78 (0.25), residues: 366 loop : -0.18 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 14 TYR 0.011 0.001 TYR G 205 PHE 0.023 0.001 PHE C 191 TRP 0.013 0.001 TRP F 138 HIS 0.003 0.001 HIS I 31 Details of bonding type rmsd covalent geometry : bond 0.00219 (16561) covalent geometry : angle 0.46073 (22640) hydrogen bonds : bond 0.03873 ( 781) hydrogen bonds : angle 4.24566 ( 2340) Misc. bond : bond 0.00076 ( 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 309 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 0.610 Fit side-chains REVERT: A 61 GLU cc_start: 0.8330 (tt0) cc_final: 0.7826 (tp30) REVERT: A 174 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7615 (ttpt) REVERT: C 49 GLU cc_start: 0.6575 (tp30) cc_final: 0.6294 (tp30) REVERT: C 122 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7767 (tt) REVERT: D 204 ASP cc_start: 0.7101 (m-30) cc_final: 0.6713 (m-30) REVERT: E 30 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6344 (ttp-110) REVERT: E 34 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.6944 (t0) REVERT: E 49 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6533 (tp30) REVERT: E 150 GLN cc_start: 0.7391 (tp-100) cc_final: 0.7089 (tp-100) REVERT: E 171 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6588 (mmp-170) REVERT: E 215 ASP cc_start: 0.6418 (OUTLIER) cc_final: 0.5968 (m-30) REVERT: F 12 GLU cc_start: 0.7614 (tt0) cc_final: 0.7380 (mt-10) REVERT: F 178 ASP cc_start: 0.7714 (m-30) cc_final: 0.7422 (m-30) REVERT: G 94 GLU cc_start: 0.7123 (tp30) cc_final: 0.6163 (tp30) REVERT: G 211 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7388 (mtp180) REVERT: H 192 ASP cc_start: 0.8111 (m-30) cc_final: 0.7728 (m-30) REVERT: H 196 GLU cc_start: 0.7933 (mp0) cc_final: 0.7584 (mp0) REVERT: I 130 LYS cc_start: 0.7203 (tmtt) cc_final: 0.6923 (tttt) REVERT: J 130 LYS cc_start: 0.7589 (tttm) cc_final: 0.6894 (tppt) outliers start: 35 outliers final: 13 residues processed: 297 average time/residue: 0.5759 time to fit residues: 190.3765 Evaluate side-chains 270 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 160 ASN 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 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 208 ASN Chi-restraints excluded: chain E residue 215 ASP 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 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: 8.9990 chunk 76 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 ASN G 175 GLN G 216 ASN H 111 ASN I 185 HIS J 31 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 = 0.3617 r_free = 0.3617 target = 0.139747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131094 restraints weight = 20094.091| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 0.90 r_work: 0.3447 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16570 Z= 0.254 Angle : 0.643 7.912 22640 Z= 0.348 Chirality : 0.052 0.232 2585 Planarity : 0.005 0.046 2926 Dihedral : 7.820 63.186 2430 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.22 % Allowed : 16.91 % 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 are not related in a simple way. whole: 0.34 (0.18), residues: 2127 helix: 0.94 (0.14), residues: 1334 sheet: -0.90 (0.25), residues: 360 loop : -0.63 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 14 TYR 0.017 0.002 TYR G 205 PHE 0.033 0.003 PHE C 191 TRP 0.013 0.002 TRP H 214 HIS 0.007 0.002 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00602 (16561) covalent geometry : angle 0.64340 (22640) hydrogen bonds : bond 0.05929 ( 781) hydrogen bonds : angle 4.87352 ( 2340) Misc. bond : bond 0.00176 ( 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 300 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 0.608 Fit side-chains REVERT: A 61 GLU cc_start: 0.8092 (tt0) cc_final: 0.7721 (tp30) REVERT: C 49 GLU cc_start: 0.6698 (tp30) cc_final: 0.6421 (tp30) REVERT: C 122 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7886 (tt) REVERT: D 33 MET cc_start: 0.7243 (ttp) cc_final: 0.7041 (ttp) REVERT: D 204 ASP cc_start: 0.7348 (m-30) cc_final: 0.7008 (m-30) REVERT: E 30 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6798 (ttp-110) REVERT: E 34 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.6950 (t0) REVERT: E 49 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6562 (tp30) REVERT: E 164 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6857 (mt-10) REVERT: E 171 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6561 (mmp-170) REVERT: E 215 ASP cc_start: 0.6532 (OUTLIER) cc_final: 0.6052 (m-30) REVERT: F 12 GLU cc_start: 0.7737 (tt0) cc_final: 0.7459 (mt-10) REVERT: F 178 ASP cc_start: 0.7705 (m-30) cc_final: 0.7411 (m-30) REVERT: F 192 ASP cc_start: 0.7211 (p0) cc_final: 0.6639 (p0) REVERT: F 196 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: G 94 GLU cc_start: 0.7254 (tp30) cc_final: 0.6357 (tp30) REVERT: G 211 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6971 (mtp-110) REVERT: H 30 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6553 (ttp-110) REVERT: H 62 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6852 (pp) REVERT: H 104 GLU cc_start: 0.6775 (tp30) cc_final: 0.6129 (tp30) REVERT: H 171 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7035 (mmt90) REVERT: H 192 ASP cc_start: 0.8185 (m-30) cc_final: 0.7772 (m-30) REVERT: H 196 GLU cc_start: 0.7875 (mp0) cc_final: 0.7527 (mp0) REVERT: I 130 LYS cc_start: 0.7240 (tmtt) cc_final: 0.6865 (tttt) REVERT: J 130 LYS cc_start: 0.7578 (tttm) cc_final: 0.7068 (mmtp) outliers start: 49 outliers final: 25 residues processed: 288 average time/residue: 0.5729 time to fit residues: 183.9812 Evaluate side-chains 275 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 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 62 ILE Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN 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 = 0.3627 r_free = 0.3627 target = 0.140596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132135 restraints weight = 20430.789| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 0.90 r_work: 0.3455 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16570 Z= 0.200 Angle : 0.589 6.993 22640 Z= 0.318 Chirality : 0.049 0.198 2585 Planarity : 0.005 0.045 2926 Dihedral : 7.738 63.133 2430 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.03 % Allowed : 17.24 % Favored : 79.74 % 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 are not related in a simple way. whole: 0.42 (0.18), residues: 2127 helix: 0.99 (0.14), residues: 1334 sheet: -0.79 (0.25), residues: 378 loop : -0.65 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 14 TYR 0.014 0.002 TYR G 205 PHE 0.032 0.002 PHE C 191 TRP 0.016 0.002 TRP F 138 HIS 0.005 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00470 (16561) covalent geometry : angle 0.58859 (22640) hydrogen bonds : bond 0.05417 ( 781) hydrogen bonds : angle 4.74034 ( 2340) Misc. bond : bond 0.00177 ( 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 298 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8123 (tt0) cc_final: 0.7821 (tp30) REVERT: C 49 GLU cc_start: 0.6707 (tp30) cc_final: 0.6416 (tp30) REVERT: C 122 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7871 (tt) REVERT: D 204 ASP cc_start: 0.7356 (m-30) cc_final: 0.7019 (m-30) REVERT: E 30 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6877 (ttp-110) REVERT: E 34 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.6977 (t0) REVERT: E 49 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6570 (tp30) REVERT: E 164 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6798 (mt-10) REVERT: E 171 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6581 (mmp-170) REVERT: E 215 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.6037 (m-30) REVERT: F 12 GLU cc_start: 0.7720 (tt0) cc_final: 0.7422 (mt-10) REVERT: F 178 ASP cc_start: 0.7690 (m-30) cc_final: 0.7406 (m-30) REVERT: F 192 ASP cc_start: 0.7311 (p0) cc_final: 0.6762 (p0) REVERT: F 196 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: G 94 GLU cc_start: 0.7254 (tp30) cc_final: 0.6320 (tp30) REVERT: G 211 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6929 (mtp-110) REVERT: H 30 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6547 (ttp-110) REVERT: H 62 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6855 (pp) REVERT: H 104 GLU cc_start: 0.6798 (tp30) cc_final: 0.6126 (tp30) REVERT: H 171 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7043 (mmt90) REVERT: H 192 ASP cc_start: 0.8131 (m-30) cc_final: 0.7732 (m-30) REVERT: H 196 GLU cc_start: 0.7758 (mp0) cc_final: 0.7433 (mp0) REVERT: I 130 LYS cc_start: 0.7215 (tmtt) cc_final: 0.6862 (tttt) REVERT: J 130 LYS cc_start: 0.7559 (tttm) cc_final: 0.7040 (mmtp) outliers start: 46 outliers final: 27 residues processed: 286 average time/residue: 0.5615 time to fit residues: 178.2091 Evaluate side-chains 284 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 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 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 62 ILE Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 41 THR 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 30 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 119 SER Chi-restraints excluded: chain I residue 133 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: 4.9990 chunk 92 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 209 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 ASN ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 HIS J 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134569 restraints weight = 19901.014| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 0.89 r_work: 0.3478 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16570 Z= 0.134 Angle : 0.513 6.180 22640 Z= 0.277 Chirality : 0.046 0.166 2585 Planarity : 0.004 0.044 2926 Dihedral : 7.072 58.368 2430 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.37 % Allowed : 18.16 % Favored : 79.47 % 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 are not related in a simple way. whole: 0.91 (0.18), residues: 2127 helix: 1.40 (0.14), residues: 1327 sheet: -0.79 (0.25), residues: 366 loop : -0.37 (0.30), 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 0.027 0.002 PHE C 191 TRP 0.013 0.001 TRP C 20 HIS 0.003 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00305 (16561) covalent geometry : angle 0.51327 (22640) hydrogen bonds : bond 0.04520 ( 781) hydrogen bonds : angle 4.46242 ( 2340) Misc. bond : bond 0.00142 ( 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 286 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8275 (tt0) cc_final: 0.7784 (tp30) REVERT: A 199 GLN cc_start: 0.7700 (mt0) cc_final: 0.7028 (mm-40) REVERT: C 49 GLU cc_start: 0.6675 (tp30) cc_final: 0.6346 (tp30) REVERT: C 122 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7859 (tt) REVERT: D 204 ASP cc_start: 0.7198 (m-30) cc_final: 0.6833 (m-30) REVERT: E 30 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6944 (ttp-110) REVERT: E 34 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.6896 (t0) REVERT: E 49 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6540 (tp30) REVERT: E 171 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6454 (mmp-170) REVERT: F 12 GLU cc_start: 0.7685 (tt0) cc_final: 0.7441 (mt-10) REVERT: F 178 ASP cc_start: 0.7723 (m-30) cc_final: 0.7452 (m-30) REVERT: G 94 GLU cc_start: 0.7186 (tp30) cc_final: 0.6220 (tp30) REVERT: G 211 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7422 (mtp180) REVERT: H 30 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6553 (ttp-110) REVERT: H 62 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6844 (pp) REVERT: H 104 GLU cc_start: 0.6680 (tp30) cc_final: 0.6075 (tp30) REVERT: H 171 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7320 (mmt90) REVERT: H 192 ASP cc_start: 0.8094 (m-30) cc_final: 0.7725 (m-30) REVERT: H 196 GLU cc_start: 0.7791 (mp0) cc_final: 0.7462 (mp0) REVERT: I 6 ASP cc_start: 0.7525 (t0) cc_final: 0.7323 (t70) REVERT: I 130 LYS cc_start: 0.7228 (tmtt) cc_final: 0.6886 (tttt) REVERT: J 130 LYS cc_start: 0.7565 (tttm) cc_final: 0.6879 (tppt) outliers start: 36 outliers final: 23 residues processed: 276 average time/residue: 0.5470 time to fit residues: 167.9092 Evaluate side-chains 270 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 110 THR 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 23 ASP 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 208 ASN Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 30 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 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 84 optimal weight: 10.0000 chunk 165 optimal weight: 0.0060 chunk 13 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 140 optimal weight: 0.4980 chunk 173 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 175 GLN G 216 ASN J 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135715 restraints weight = 19828.588| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 0.89 r_work: 0.3494 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16570 Z= 0.120 Angle : 0.494 5.714 22640 Z= 0.266 Chirality : 0.045 0.154 2585 Planarity : 0.004 0.045 2926 Dihedral : 6.451 46.634 2430 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.97 % Allowed : 18.68 % 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 are not related in a simple way. whole: 1.21 (0.18), residues: 2127 helix: 1.62 (0.14), residues: 1327 sheet: -0.67 (0.26), residues: 366 loop : -0.15 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 14 TYR 0.012 0.001 TYR G 205 PHE 0.028 0.001 PHE C 191 TRP 0.013 0.001 TRP F 138 HIS 0.003 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00272 (16561) covalent geometry : angle 0.49402 (22640) hydrogen bonds : bond 0.04204 ( 781) hydrogen bonds : angle 4.31408 ( 2340) Misc. bond : bond 0.00126 ( 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 284 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8258 (tt0) cc_final: 0.7774 (tp30) REVERT: C 49 GLU cc_start: 0.6604 (tp30) cc_final: 0.6322 (tp30) REVERT: C 122 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7813 (tt) REVERT: D 204 ASP cc_start: 0.7192 (m-30) cc_final: 0.6817 (m-30) REVERT: E 30 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6884 (ttp-110) REVERT: E 34 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.6885 (t0) REVERT: E 49 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6562 (tp30) REVERT: E 171 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6514 (mmp-170) REVERT: F 12 GLU cc_start: 0.7719 (tt0) cc_final: 0.7439 (mt-10) REVERT: F 178 ASP cc_start: 0.7729 (m-30) cc_final: 0.7449 (m-30) REVERT: G 94 GLU cc_start: 0.7177 (tp30) cc_final: 0.6265 (tp30) REVERT: G 211 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7387 (mtp180) REVERT: H 30 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6576 (ttp-110) REVERT: H 62 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6825 (pp) REVERT: H 171 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7272 (mmt90) REVERT: H 192 ASP cc_start: 0.8064 (m-30) cc_final: 0.7753 (m-30) REVERT: H 196 GLU cc_start: 0.7759 (mp0) cc_final: 0.7433 (mp0) REVERT: I 6 ASP cc_start: 0.7458 (t0) cc_final: 0.7176 (t70) REVERT: I 34 ASN cc_start: 0.6700 (m-40) cc_final: 0.6386 (m110) REVERT: I 130 LYS cc_start: 0.7178 (tmtt) cc_final: 0.6863 (tttt) REVERT: J 130 LYS cc_start: 0.7543 (tttm) cc_final: 0.6887 (tppt) outliers start: 30 outliers final: 22 residues processed: 274 average time/residue: 0.5374 time to fit residues: 164.4685 Evaluate side-chains 276 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 110 THR 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 23 ASP 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 208 ASN Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 30 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 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: 4.9990 chunk 203 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 164 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN G 216 ASN I 158 ASN J 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132536 restraints weight = 19998.010| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 0.91 r_work: 0.3473 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16570 Z= 0.149 Angle : 0.531 5.896 22640 Z= 0.286 Chirality : 0.047 0.182 2585 Planarity : 0.004 0.044 2926 Dihedral : 6.720 57.180 2430 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.50 % Allowed : 18.29 % 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 are not related in a simple way. whole: 1.09 (0.18), residues: 2127 helix: 1.51 (0.14), residues: 1327 sheet: -0.67 (0.26), residues: 360 loop : -0.25 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 14 TYR 0.016 0.002 TYR C 15 PHE 0.031 0.002 PHE C 191 TRP 0.014 0.001 TRP F 138 HIS 0.005 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00344 (16561) covalent geometry : angle 0.53076 (22640) hydrogen bonds : bond 0.04706 ( 781) hydrogen bonds : angle 4.47385 ( 2340) Misc. bond : bond 0.00147 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4610.34 seconds wall clock time: 79 minutes 34.79 seconds (4774.79 seconds total)