Starting phenix.real_space_refine on Sat Sep 12 14:41:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cge_30355/09_2026/7cge_30355.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cge_30355/09_2026/7cge_30355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cge_30355/09_2026/7cge_30355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cge_30355/09_2026/7cge_30355.map" model { file = "/net/cci-nas-00/data/ceres_data/7cge_30355/09_2026/7cge_30355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cge_30355/09_2026/7cge_30355.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cge_30355/09_2026/7cge_30355.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cge_30355/09_2026/7cge_30355.cif" } resolution = 2.9 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= 0.003 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 68 5.16 5 C 10624 2.51 5 N 2654 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16406 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1996 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 18, 'TRANS': 244} Chain: "C" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "D" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1996 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 18, 'TRANS': 244} Chain: "F" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "G" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "K" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "L" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 306 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 204 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.20, per 1000 atoms: 0.26 Number of scatterers: 16406 At special positions: 0 Unit cell: (106.526, 114.135, 141.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 12 15.00 O 3048 8.00 N 2654 7.00 C 10624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 776.9 milliseconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 18 sheets defined 41.9% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 5 through 32 removed outlier: 3.740A pdb=" N LEU A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.597A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.657A pdb=" N SER A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 99 through 126 removed outlier: 3.526A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 removed outlier: 3.530A pdb=" N GLU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 143 through 175 removed outlier: 3.896A pdb=" N ARG A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.503A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.602A pdb=" N MET A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 223 removed outlier: 3.500A pdb=" N LEU A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 258 removed outlier: 3.828A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 55 removed outlier: 3.510A pdb=" N ILE B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.658A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 121 through 132 removed outlier: 3.739A pdb=" N VAL B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.587A pdb=" N LEU B 145 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 157 Processing helix chain 'B' and resid 176 through 193 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.735A pdb=" N PHE B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 51 through 68 removed outlier: 3.526A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 removed outlier: 3.586A pdb=" N LEU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 32 removed outlier: 3.741A pdb=" N LEU D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.597A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 79 removed outlier: 3.657A pdb=" N SER D 62 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 86 through 97 Processing helix chain 'D' and resid 99 through 126 removed outlier: 3.525A pdb=" N ALA D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 134 removed outlier: 3.530A pdb=" N GLU D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 143 through 175 removed outlier: 3.896A pdb=" N ARG D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Proline residue: D 156 - end of helix removed outlier: 3.503A pdb=" N VAL D 160 " --> pdb=" O PRO D 156 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.602A pdb=" N MET D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 223 removed outlier: 3.501A pdb=" N LEU D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 258 removed outlier: 3.828A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.510A pdb=" N ILE E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.659A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 107 Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.739A pdb=" N VAL E 132 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 145 removed outlier: 3.585A pdb=" N LEU E 145 " --> pdb=" O PRO E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 176 through 193 Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 237 through 246 removed outlier: 3.735A pdb=" N PHE E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 51 through 68 removed outlier: 3.525A pdb=" N GLN F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 88 removed outlier: 3.586A pdb=" N LEU F 84 " --> pdb=" O LYS F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 27 Processing helix chain 'G' and resid 143 through 152 removed outlier: 3.826A pdb=" N ILE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 28 Processing helix chain 'H' and resid 144 through 151 Processing helix chain 'I' and resid 5 through 27 removed outlier: 3.568A pdb=" N TRP I 9 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA I 17 " --> pdb=" O PHE I 13 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS I 27 " --> pdb=" O PHE I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 152 removed outlier: 3.894A pdb=" N ILE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 27 Processing helix chain 'J' and resid 143 through 152 removed outlier: 4.005A pdb=" N ILE J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 28 Processing helix chain 'K' and resid 144 through 151 Processing helix chain 'L' and resid 5 through 26 removed outlier: 3.569A pdb=" N TRP L 9 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 152 removed outlier: 3.501A pdb=" N GLY L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 32 removed outlier: 6.643A pdb=" N ILE B 23 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR B 17 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP B 25 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 15 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE B 27 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP B 13 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 9 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.609A pdb=" N HIS B 214 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 225 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 5 through 9 removed outlier: 8.753A pdb=" N ARG C 46 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 16 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N SER C 48 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N GLY C 18 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 50 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU C 20 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 32 removed outlier: 6.642A pdb=" N ILE E 23 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR E 17 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP E 25 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER E 15 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE E 27 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP E 13 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 9 " --> pdb=" O VAL E 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.610A pdb=" N HIS E 214 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 225 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 9 removed outlier: 8.753A pdb=" N ARG F 46 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU F 16 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N SER F 48 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N GLY F 18 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL F 50 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU F 20 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AA9, first strand: chain 'G' and resid 39 through 43 removed outlier: 8.417A pdb=" N VAL G 65 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL G 64 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE G 60 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY G 66 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 39 through 45 removed outlier: 3.773A pdb=" N LEU H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 63 through 66 removed outlier: 6.353A pdb=" N VAL H 58 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 73 through 74 removed outlier: 4.006A pdb=" N LEU I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N VAL I 65 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER I 59 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN I 115 " --> pdb=" O SER I 98 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER I 98 " --> pdb=" O ASN I 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 73 through 74 removed outlier: 4.006A pdb=" N LEU I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE I 134 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR I 43 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 39 through 40 removed outlier: 3.904A pdb=" N THR J 83 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA J 69 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N VAL J 65 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE J 60 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 73 through 74 removed outlier: 3.767A pdb=" N LEU J 79 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU J 42 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR J 43 " --> pdb=" O ILE J 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 73 through 74 removed outlier: 3.751A pdb=" N LEU K 79 " --> pdb=" O ASP K 74 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ILE K 134 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR K 43 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 63 through 66 removed outlier: 6.211A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 39 through 45 removed outlier: 6.793A pdb=" N ARG L 81 " --> pdb=" O ILE L 71 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE L 71 " --> pdb=" O ARG L 81 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N VAL L 65 " --> pdb=" O GLU L 87 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU L 114 " --> pdb=" O PRO L 57 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER L 59 " --> pdb=" O LEU L 114 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN L 115 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER L 98 " --> pdb=" O ASN L 115 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2091 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: 2.74 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2643 1.31 - 1.43: 4026 1.43 - 1.56: 9824 1.56 - 1.68: 51 1.68 - 1.81: 124 Bond restraints: 16668 Sorted by residual: bond pdb=" C1 PGW A 301 " pdb=" O01 PGW A 301 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 PGW D 302 " pdb=" O01 PGW D 302 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C19 PGW A 301 " pdb=" O03 PGW A 301 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C19 PGW D 302 " pdb=" O03 PGW D 302 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C1 PGW A 302 " pdb=" O01 PGW A 302 " ideal model delta sigma weight residual 1.332 1.418 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 16663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.86: 22382 6.86 - 13.73: 124 13.73 - 20.59: 0 20.59 - 27.46: 0 27.46 - 34.32: 12 Bond angle restraints: 22518 Sorted by residual: angle pdb=" C19 PGW D 304 " pdb=" C20 PGW D 304 " pdb=" C21 PGW D 304 " ideal model delta sigma weight residual 114.60 80.28 34.32 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C19 PGW A 303 " pdb=" C20 PGW A 303 " pdb=" C21 PGW A 303 " ideal model delta sigma weight residual 114.60 80.32 34.28 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C19 PGW A 304 " pdb=" C20 PGW A 304 " pdb=" C21 PGW A 304 " ideal model delta sigma weight residual 114.60 81.26 33.34 3.00e+00 1.11e-01 1.24e+02 angle pdb=" C19 PGW A 306 " pdb=" C20 PGW A 306 " pdb=" C21 PGW A 306 " ideal model delta sigma weight residual 114.60 81.29 33.31 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C19 PGW J 201 " pdb=" C20 PGW J 201 " pdb=" C21 PGW J 201 " ideal model delta sigma weight residual 114.60 81.35 33.25 3.00e+00 1.11e-01 1.23e+02 ... (remaining 22513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.63: 9476 28.63 - 57.25: 446 57.25 - 85.88: 40 85.88 - 114.50: 26 114.50 - 143.13: 26 Dihedral angle restraints: 10014 sinusoidal: 4060 harmonic: 5954 Sorted by residual: dihedral pdb=" CA ASP J 136 " pdb=" C ASP J 136 " pdb=" N THR J 137 " pdb=" CA THR J 137 " ideal model delta harmonic sigma weight residual 180.00 150.20 29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LYS J 129 " pdb=" C LYS J 129 " pdb=" N ASP J 130 " pdb=" CA ASP J 130 " ideal model delta harmonic sigma weight residual -180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA SER B 146 " pdb=" C SER B 146 " pdb=" N GLY B 147 " pdb=" CA GLY B 147 " ideal model delta harmonic sigma weight residual 180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 10011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2250 0.077 - 0.154: 379 0.154 - 0.230: 30 0.230 - 0.307: 5 0.307 - 0.384: 4 Chirality restraints: 2668 Sorted by residual: chirality pdb=" CB ILE E 223 " pdb=" CA ILE E 223 " pdb=" CG1 ILE E 223 " pdb=" CG2 ILE E 223 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB ILE B 223 " pdb=" CA ILE B 223 " pdb=" CG1 ILE B 223 " pdb=" CG2 ILE B 223 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB THR E 114 " pdb=" CA THR E 114 " pdb=" OG1 THR E 114 " pdb=" CG2 THR E 114 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 2665 not shown) Planarity restraints: 2796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 120 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO I 121 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO I 121 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 121 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 155 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO D 156 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 155 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO A 156 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.038 5.00e-02 4.00e+02 ... (remaining 2793 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1752 2.74 - 3.28: 14582 3.28 - 3.82: 24937 3.82 - 4.36: 30657 4.36 - 4.90: 53591 Nonbonded interactions: 125519 Sorted by model distance: nonbonded pdb=" O LEU E 110 " pdb=" OG1 THR E 114 " model vdw 2.198 3.040 nonbonded pdb=" O LEU B 110 " pdb=" OG1 THR B 114 " model vdw 2.199 3.040 nonbonded pdb=" CE1 PHE G 46 " pdb=" CG2 THR G 137 " model vdw 2.225 3.760 nonbonded pdb=" CD1 PHE G 46 " pdb=" CG2 THR G 137 " model vdw 2.234 3.760 nonbonded pdb=" O PRO J 94 " pdb=" OG SER J 97 " model vdw 2.284 3.040 ... (remaining 125514 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 3 through 304) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'G' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'H' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'I' selection = (chain 'J' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'K' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.700 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 : 0.011 0.090 16668 Z= 0.474 Angle : 1.494 34.319 22518 Z= 0.674 Chirality : 0.059 0.384 2668 Planarity : 0.007 0.075 2796 Dihedral : 18.718 143.126 6190 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.19 % Favored : 88.23 % Rotamer: Outliers : 0.95 % Allowed : 6.06 % Favored : 92.99 % 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: -5.74 (0.13), residues: 2056 helix: -4.53 (0.06), residues: 878 sheet: -2.34 (0.29), residues: 290 loop : -3.39 (0.16), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 111 TYR 0.035 0.003 TYR B 261 PHE 0.028 0.003 PHE G 118 TRP 0.011 0.002 TRP K 9 HIS 0.009 0.002 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.01061 / 0.47 (16668) covalent geometry : angle 1.49417 / 0.67 (22518) hydrogen bonds : bond 0.30308 / 19.68 ( 714) hydrogen bonds : angle 10.17861 / 7.05 ( 2091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 332 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7862 (mtm-85) REVERT: A 134 MET cc_start: 0.9257 (mmt) cc_final: 0.9048 (mmm) REVERT: A 197 MET cc_start: 0.8645 (mmm) cc_final: 0.8414 (tpt) REVERT: B 13 ASP cc_start: 0.7032 (t70) cc_final: 0.6504 (t0) REVERT: B 130 GLU cc_start: 0.8159 (tp30) cc_final: 0.7923 (tp30) REVERT: C 21 ASP cc_start: 0.8047 (t70) cc_final: 0.7569 (t70) REVERT: C 22 GLN cc_start: 0.8718 (pp30) cc_final: 0.8405 (pp30) REVERT: C 23 ASP cc_start: 0.8515 (p0) cc_final: 0.8052 (p0) REVERT: D 18 ARG cc_start: 0.8115 (ptm160) cc_final: 0.7862 (mtm-85) REVERT: D 39 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8789 (tppt) REVERT: D 134 MET cc_start: 0.9271 (mmt) cc_final: 0.9034 (mmm) REVERT: D 197 MET cc_start: 0.8660 (mmm) cc_final: 0.8430 (tpt) REVERT: E 13 ASP cc_start: 0.7137 (t70) cc_final: 0.6517 (t0) REVERT: E 40 MET cc_start: 0.8519 (mtm) cc_final: 0.8314 (mtm) REVERT: E 130 GLU cc_start: 0.8272 (tp30) cc_final: 0.8030 (tp30) REVERT: E 180 MET cc_start: 0.8935 (mtt) cc_final: 0.8722 (mtm) REVERT: F 14 LEU cc_start: 0.8457 (tp) cc_final: 0.8255 (tm) REVERT: F 21 ASP cc_start: 0.8002 (t70) cc_final: 0.7559 (t70) REVERT: F 22 GLN cc_start: 0.8728 (pp30) cc_final: 0.8421 (pp30) REVERT: F 23 ASP cc_start: 0.8647 (p0) cc_final: 0.8156 (p0) REVERT: G 5 LYS cc_start: 0.8496 (tppt) cc_final: 0.8278 (tmmm) REVERT: G 88 GLN cc_start: 0.7923 (tp40) cc_final: 0.7174 (pm20) REVERT: G 92 HIS cc_start: 0.7626 (t70) cc_final: 0.7313 (t-170) REVERT: I 85 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7730 (mm-30) REVERT: J 5 LYS cc_start: 0.8506 (tppt) cc_final: 0.8273 (tmmm) REVERT: J 67 ARG cc_start: 0.6422 (mmt180) cc_final: 0.5813 (mmm-85) REVERT: J 89 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7860 (mpp-170) REVERT: J 92 HIS cc_start: 0.7846 (t70) cc_final: 0.7394 (t70) REVERT: L 85 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7787 (mm-30) outliers start: 16 outliers final: 3 residues processed: 342 average time/residue: 0.7365 time to fit residues: 274.2864 Evaluate side-chains 272 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 269 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 83 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.0170 chunk 194 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 50 ASN A 190 GLN B 7 ASN B 57 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 175 GLN B 226 HIS C 89 ASN D 29 ASN D 50 ASN D 190 GLN E 7 ASN E 57 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN E 175 GLN E 226 HIS F 89 ASN G 88 GLN G 110 GLN J 110 GLN L 110 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.140266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100795 restraints weight = 22092.493| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.93 r_work: 0.3042 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16668 Z= 0.131 Angle : 0.701 8.420 22518 Z= 0.358 Chirality : 0.042 0.201 2668 Planarity : 0.006 0.057 2796 Dihedral : 18.328 135.214 2640 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.24 % Favored : 90.52 % Rotamer: Outliers : 2.08 % Allowed : 15.26 % Favored : 82.66 % 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: -3.10 (0.16), residues: 2056 helix: -1.23 (0.15), residues: 856 sheet: -1.77 (0.33), residues: 248 loop : -2.94 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 97 TYR 0.015 0.001 TYR E 261 PHE 0.015 0.001 PHE G 118 TRP 0.010 0.001 TRP G 9 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16668) covalent geometry : angle 0.70127 / 0.36 (22518) hydrogen bonds : bond 0.05039 / 3.26 ( 714) hydrogen bonds : angle 5.15751 / 3.55 ( 2091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 311 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 PHE cc_start: 0.9135 (m-80) cc_final: 0.8896 (m-80) REVERT: A 38 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8599 (ttm170) REVERT: A 197 MET cc_start: 0.9099 (mmm) cc_final: 0.8861 (tpt) REVERT: B 139 LYS cc_start: 0.9089 (mtpp) cc_final: 0.8882 (mmmt) REVERT: C 22 GLN cc_start: 0.8813 (pp30) cc_final: 0.8605 (pp30) REVERT: C 31 MET cc_start: 0.7305 (mmm) cc_final: 0.7105 (mmm) REVERT: C 75 GLN cc_start: 0.7278 (pt0) cc_final: 0.6588 (mt0) REVERT: D 20 PHE cc_start: 0.9126 (m-80) cc_final: 0.8896 (m-80) REVERT: D 39 LYS cc_start: 0.9013 (mtpp) cc_final: 0.8786 (tppt) REVERT: D 197 MET cc_start: 0.9128 (mmm) cc_final: 0.8847 (tpt) REVERT: E 222 LYS cc_start: 0.8751 (mmtp) cc_final: 0.8509 (mmmm) REVERT: F 21 ASP cc_start: 0.8506 (t70) cc_final: 0.7795 (t70) REVERT: F 22 GLN cc_start: 0.8781 (pp30) cc_final: 0.8234 (pp30) REVERT: F 23 ASP cc_start: 0.8570 (p0) cc_final: 0.8011 (p0) REVERT: F 31 MET cc_start: 0.7525 (mmm) cc_final: 0.7303 (mmm) REVERT: F 49 ARG cc_start: 0.8413 (pmt170) cc_final: 0.8142 (pmt170) REVERT: G 89 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7693 (mmp80) REVERT: G 92 HIS cc_start: 0.7900 (t70) cc_final: 0.7467 (t70) REVERT: G 93 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.6962 (mp) REVERT: H 27 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8228 (tttm) REVERT: H 144 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7257 (mp0) REVERT: I 73 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7728 (tp) REVERT: I 85 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8120 (mm-30) REVERT: J 55 ARG cc_start: 0.7841 (mtp-110) cc_final: 0.7508 (mtm180) REVERT: J 83 THR cc_start: 0.6308 (OUTLIER) cc_final: 0.6016 (t) REVERT: J 89 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7580 (mmp80) REVERT: J 92 HIS cc_start: 0.8005 (t70) cc_final: 0.7490 (t70) REVERT: K 27 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8196 (tttm) REVERT: L 76 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6398 (tptp) REVERT: L 85 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8103 (mm-30) outliers start: 35 outliers final: 7 residues processed: 330 average time/residue: 0.7698 time to fit residues: 276.7063 Evaluate side-chains 281 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain L residue 76 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 GLN B 175 GLN E 57 GLN E 175 GLN H 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.141368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102258 restraints weight = 22408.238| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.90 r_work: 0.3040 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16668 Z= 0.122 Angle : 0.644 7.920 22518 Z= 0.325 Chirality : 0.042 0.185 2668 Planarity : 0.005 0.058 2796 Dihedral : 16.591 140.422 2639 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.39 % Favored : 90.47 % Rotamer: Outliers : 3.50 % Allowed : 16.75 % Favored : 79.75 % 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: -1.74 (0.18), residues: 2056 helix: 0.53 (0.18), residues: 856 sheet: -1.59 (0.33), residues: 248 loop : -2.71 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 67 TYR 0.018 0.001 TYR E 261 PHE 0.011 0.001 PHE G 13 TRP 0.006 0.001 TRP D 186 HIS 0.003 0.001 HIS H 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16668) covalent geometry : angle 0.64399 / 0.33 (22518) hydrogen bonds : bond 0.04392 / 2.86 ( 714) hydrogen bonds : angle 4.50020 / 3.10 ( 2091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9087 (mmm) cc_final: 0.8831 (tpt) REVERT: B 175 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8877 (mm110) REVERT: C 14 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8356 (tm) REVERT: C 31 MET cc_start: 0.7423 (mmm) cc_final: 0.7103 (mmm) REVERT: C 49 ARG cc_start: 0.8571 (pmt170) cc_final: 0.8120 (pmt170) REVERT: C 75 GLN cc_start: 0.7309 (pt0) cc_final: 0.6776 (mt0) REVERT: D 197 MET cc_start: 0.9115 (mmm) cc_final: 0.8859 (tpt) REVERT: E 58 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.6936 (pt) REVERT: E 98 THR cc_start: 0.8842 (m) cc_final: 0.8376 (p) REVERT: F 21 ASP cc_start: 0.8498 (t70) cc_final: 0.7803 (t70) REVERT: F 22 GLN cc_start: 0.8759 (pp30) cc_final: 0.8456 (pp30) REVERT: F 23 ASP cc_start: 0.8528 (p0) cc_final: 0.7938 (p0) REVERT: F 31 MET cc_start: 0.7389 (mmm) cc_final: 0.7088 (mmm) REVERT: G 88 GLN cc_start: 0.7641 (tp-100) cc_final: 0.6855 (pm20) REVERT: G 92 HIS cc_start: 0.7870 (t70) cc_final: 0.7385 (t70) REVERT: G 93 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7044 (mp) REVERT: G 139 SER cc_start: 0.7962 (p) cc_final: 0.7500 (m) REVERT: H 27 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8206 (tttm) REVERT: H 144 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7330 (mp0) REVERT: I 109 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7686 (tp30) REVERT: J 83 THR cc_start: 0.6182 (OUTLIER) cc_final: 0.5940 (t) REVERT: J 89 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7543 (mmp80) REVERT: J 92 HIS cc_start: 0.8047 (t70) cc_final: 0.7552 (t70) REVERT: K 27 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8254 (tttm) REVERT: L 76 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6411 (tptp) outliers start: 59 outliers final: 16 residues processed: 311 average time/residue: 0.7786 time to fit residues: 263.4167 Evaluate side-chains 284 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 141 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 34 optimal weight: 0.0970 chunk 164 optimal weight: 0.0170 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 0.0050 chunk 114 optimal weight: 0.0060 chunk 183 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 188 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.9508 > 50:) chunk 181 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 overall best weight: 0.1646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 HIS D 241 HIS E 175 GLN J 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105556 restraints weight = 22316.450| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.90 r_work: 0.3107 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16668 Z= 0.103 Angle : 0.587 7.527 22518 Z= 0.296 Chirality : 0.040 0.213 2668 Planarity : 0.004 0.059 2796 Dihedral : 15.204 159.932 2637 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.10 % Favored : 90.81 % Rotamer: Outliers : 2.79 % Allowed : 18.47 % Favored : 78.74 % 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: -1.06 (0.19), residues: 2056 helix: 1.28 (0.19), residues: 862 sheet: -1.51 (0.31), residues: 268 loop : -2.49 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 233 TYR 0.009 0.001 TYR K 111 PHE 0.010 0.001 PHE D 219 TRP 0.006 0.001 TRP E 216 HIS 0.002 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (16668) covalent geometry : angle 0.58723 / 0.30 (22518) hydrogen bonds : bond 0.03048 / 2.01 ( 714) hydrogen bonds : angle 4.15004 / 2.85 ( 2091) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 291 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9024 (mmm) cc_final: 0.8789 (tpt) REVERT: B 48 THR cc_start: 0.8860 (t) cc_final: 0.8560 (m) REVERT: B 58 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.6701 (pt) REVERT: C 22 GLN cc_start: 0.8853 (pp30) cc_final: 0.8651 (pp30) REVERT: C 31 MET cc_start: 0.7383 (mmm) cc_final: 0.7069 (mmm) REVERT: D 39 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8724 (ttpt) REVERT: D 197 MET cc_start: 0.9076 (mmm) cc_final: 0.8835 (tpt) REVERT: E 48 THR cc_start: 0.8800 (t) cc_final: 0.8462 (m) REVERT: E 58 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.6711 (pt) REVERT: G 5 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7691 (tttt) REVERT: G 67 ARG cc_start: 0.5860 (mmt180) cc_final: 0.5532 (mmm160) REVERT: G 88 GLN cc_start: 0.7507 (tp-100) cc_final: 0.6767 (pm20) REVERT: G 92 HIS cc_start: 0.7741 (t70) cc_final: 0.7276 (t70) REVERT: G 93 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6901 (mp) REVERT: G 139 SER cc_start: 0.7987 (p) cc_final: 0.7476 (m) REVERT: H 27 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8170 (tttm) REVERT: H 144 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7293 (mp0) REVERT: J 5 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7683 (tttt) REVERT: J 55 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.7553 (mtm180) REVERT: J 89 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7509 (mmp80) REVERT: J 92 HIS cc_start: 0.8018 (t70) cc_final: 0.7517 (t70) REVERT: K 27 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8239 (tttm) REVERT: L 143 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7559 (mt) outliers start: 47 outliers final: 7 residues processed: 323 average time/residue: 0.7304 time to fit residues: 258.1097 Evaluate side-chains 276 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 263 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 105 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 198 optimal weight: 0.0670 chunk 176 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 90 optimal weight: 0.0000 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS B 115 GLN B 175 GLN E 62 HIS E 175 GLN E 230 GLN F 89 ASN H 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106391 restraints weight = 22259.587| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.90 r_work: 0.3123 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16668 Z= 0.100 Angle : 0.583 9.264 22518 Z= 0.292 Chirality : 0.041 0.251 2668 Planarity : 0.004 0.058 2796 Dihedral : 14.151 158.716 2637 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.75 % Favored : 91.10 % Rotamer: Outliers : 2.38 % Allowed : 20.07 % Favored : 77.55 % 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: -0.79 (0.19), residues: 2056 helix: 1.61 (0.19), residues: 870 sheet: -1.35 (0.32), residues: 276 loop : -2.52 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 67 TYR 0.009 0.001 TYR K 111 PHE 0.010 0.001 PHE A 219 TRP 0.007 0.001 TRP D 186 HIS 0.004 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (16668) covalent geometry : angle 0.58303 / 0.29 (22518) hydrogen bonds : bond 0.03088 / 2.03 ( 714) hydrogen bonds : angle 4.01797 / 2.76 ( 2091) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 272 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9059 (mmm) cc_final: 0.8792 (tpt) REVERT: B 48 THR cc_start: 0.8795 (t) cc_final: 0.8525 (m) REVERT: B 58 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.6557 (pt) REVERT: B 230 GLN cc_start: 0.8365 (mp-120) cc_final: 0.8102 (mp10) REVERT: C 22 GLN cc_start: 0.8894 (pp30) cc_final: 0.8686 (pp30) REVERT: D 39 LYS cc_start: 0.8993 (mtpp) cc_final: 0.8709 (ttpt) REVERT: D 197 MET cc_start: 0.9067 (mmm) cc_final: 0.8797 (tpt) REVERT: E 48 THR cc_start: 0.8770 (t) cc_final: 0.8446 (m) REVERT: E 58 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6480 (pt) REVERT: F 21 ASP cc_start: 0.8170 (t70) cc_final: 0.7831 (t70) REVERT: F 22 GLN cc_start: 0.8689 (pp30) cc_final: 0.8426 (pp30) REVERT: F 31 MET cc_start: 0.7436 (mmm) cc_final: 0.7171 (mmm) REVERT: G 5 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7685 (tttt) REVERT: G 85 GLU cc_start: 0.6678 (tt0) cc_final: 0.6024 (tm-30) REVERT: G 88 GLN cc_start: 0.7529 (tp-100) cc_final: 0.6725 (pm20) REVERT: G 92 HIS cc_start: 0.7798 (t70) cc_final: 0.7342 (t70) REVERT: G 93 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6923 (mp) REVERT: G 139 SER cc_start: 0.8026 (p) cc_final: 0.7510 (m) REVERT: G 151 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7161 (pp) REVERT: H 27 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8250 (tttm) REVERT: H 132 ASP cc_start: 0.7968 (m-30) cc_final: 0.7164 (t0) REVERT: I 109 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: J 5 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7678 (tttt) REVERT: J 89 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7461 (mmp80) REVERT: J 92 HIS cc_start: 0.8003 (t70) cc_final: 0.7484 (t70) REVERT: K 27 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8231 (tttm) REVERT: L 143 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7618 (mt) outliers start: 40 outliers final: 13 residues processed: 299 average time/residue: 0.7621 time to fit residues: 247.9685 Evaluate side-chains 283 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 262 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 89 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 HIS B 62 HIS B 115 GLN B 175 GLN D 241 HIS E 62 HIS E 115 GLN E 175 GLN H 110 GLN K 110 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101389 restraints weight = 22195.338| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.92 r_work: 0.3046 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16668 Z= 0.130 Angle : 0.614 8.160 22518 Z= 0.308 Chirality : 0.042 0.274 2668 Planarity : 0.004 0.058 2796 Dihedral : 13.523 112.567 2637 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.24 % Favored : 90.56 % Rotamer: Outliers : 3.15 % Allowed : 19.77 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.68 (0.19), residues: 2056 helix: 1.76 (0.19), residues: 862 sheet: -1.30 (0.33), residues: 256 loop : -2.46 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 67 TYR 0.017 0.001 TYR E 261 PHE 0.013 0.001 PHE G 13 TRP 0.007 0.001 TRP C 29 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (16668) covalent geometry : angle 0.61361 / 0.31 (22518) hydrogen bonds : bond 0.03965 / 2.58 ( 714) hydrogen bonds : angle 4.07330 / 2.80 ( 2091) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 265 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8336 (mmm160) REVERT: A 197 MET cc_start: 0.9111 (mmm) cc_final: 0.8785 (tpt) REVERT: B 25 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: B 48 THR cc_start: 0.8864 (t) cc_final: 0.8594 (m) REVERT: B 58 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.6716 (pp) REVERT: B 62 HIS cc_start: 0.8018 (t-90) cc_final: 0.7751 (t70) REVERT: B 230 GLN cc_start: 0.8322 (mp-120) cc_final: 0.8024 (mp10) REVERT: C 22 GLN cc_start: 0.8971 (pp30) cc_final: 0.8750 (pp30) REVERT: C 49 ARG cc_start: 0.8615 (pmt170) cc_final: 0.8212 (pmt170) REVERT: D 18 ARG cc_start: 0.8758 (mtp85) cc_final: 0.8314 (mmm-85) REVERT: D 39 LYS cc_start: 0.9008 (mtpp) cc_final: 0.8716 (ttpt) REVERT: D 197 MET cc_start: 0.9126 (mmm) cc_final: 0.8799 (tpt) REVERT: E 48 THR cc_start: 0.8834 (t) cc_final: 0.8498 (m) REVERT: E 58 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.6726 (pt) REVERT: G 88 GLN cc_start: 0.7523 (tp-100) cc_final: 0.6643 (pm20) REVERT: G 92 HIS cc_start: 0.7885 (t70) cc_final: 0.7398 (t70) REVERT: G 93 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7040 (mp) REVERT: G 139 SER cc_start: 0.8072 (p) cc_final: 0.7560 (m) REVERT: H 27 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8274 (tmtt) REVERT: J 89 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7431 (mmp80) REVERT: J 92 HIS cc_start: 0.8191 (t70) cc_final: 0.7683 (t70) REVERT: K 27 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8220 (tmtt) REVERT: L 143 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7625 (mt) outliers start: 53 outliers final: 21 residues processed: 306 average time/residue: 0.7541 time to fit residues: 251.2064 Evaluate side-chains 288 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 136 optimal weight: 0.4980 chunk 111 optimal weight: 0.0000 chunk 158 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN C 60 HIS E 62 HIS E 115 GLN E 230 GLN H 110 GLN K 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102532 restraints weight = 22189.937| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.88 r_work: 0.3042 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16668 Z= 0.124 Angle : 0.618 9.904 22518 Z= 0.310 Chirality : 0.042 0.282 2668 Planarity : 0.004 0.058 2796 Dihedral : 13.000 93.191 2637 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.34 % Favored : 90.61 % Rotamer: Outliers : 3.03 % Allowed : 20.07 % Favored : 76.90 % 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: -0.56 (0.19), residues: 2056 helix: 1.84 (0.19), residues: 862 sheet: -1.23 (0.33), residues: 256 loop : -2.38 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 67 TYR 0.017 0.001 TYR E 261 PHE 0.011 0.001 PHE G 13 TRP 0.006 0.001 TRP A 186 HIS 0.004 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (16668) covalent geometry : angle 0.61761 / 0.31 (22518) hydrogen bonds : bond 0.03813 / 2.49 ( 714) hydrogen bonds : angle 4.04599 / 2.78 ( 2091) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8727 (mtp85) cc_final: 0.8380 (mmm160) REVERT: A 197 MET cc_start: 0.9118 (mmm) cc_final: 0.8831 (tpt) REVERT: B 48 THR cc_start: 0.8848 (t) cc_final: 0.8564 (m) REVERT: B 58 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6615 (pp) REVERT: B 62 HIS cc_start: 0.7899 (t-90) cc_final: 0.7673 (t70) REVERT: B 230 GLN cc_start: 0.8371 (mp-120) cc_final: 0.8090 (mp10) REVERT: C 49 ARG cc_start: 0.8581 (pmt170) cc_final: 0.8241 (pmt170) REVERT: D 18 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8396 (mmm-85) REVERT: D 39 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8745 (ttpt) REVERT: D 197 MET cc_start: 0.9121 (mmm) cc_final: 0.8830 (tpt) REVERT: E 48 THR cc_start: 0.8831 (t) cc_final: 0.8527 (m) REVERT: E 58 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6498 (pt) REVERT: E 62 HIS cc_start: 0.7839 (t-90) cc_final: 0.7585 (t-90) REVERT: F 21 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7871 (t70) REVERT: G 89 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7583 (mmp80) REVERT: G 92 HIS cc_start: 0.8037 (t70) cc_final: 0.7549 (t70) REVERT: G 93 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7169 (mp) REVERT: G 139 SER cc_start: 0.8057 (p) cc_final: 0.7554 (m) REVERT: G 151 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7186 (pp) REVERT: H 27 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8322 (tmtt) REVERT: H 132 ASP cc_start: 0.7732 (m-30) cc_final: 0.6923 (t0) REVERT: I 109 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: J 87 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7122 (mm-30) REVERT: J 89 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7488 (mmp80) REVERT: J 92 HIS cc_start: 0.8160 (t70) cc_final: 0.7595 (t70) REVERT: K 27 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8278 (tmtt) REVERT: L 143 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7667 (mt) outliers start: 51 outliers final: 17 residues processed: 306 average time/residue: 0.7710 time to fit residues: 256.9420 Evaluate side-chains 288 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 140 optimal weight: 0.0970 chunk 64 optimal weight: 0.6980 chunk 189 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN B 175 GLN E 115 GLN E 175 GLN F 89 ASN H 110 GLN K 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.142993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.102706 restraints weight = 22306.529| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.95 r_work: 0.3057 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16668 Z= 0.114 Angle : 0.612 8.720 22518 Z= 0.308 Chirality : 0.042 0.280 2668 Planarity : 0.004 0.059 2796 Dihedral : 12.498 89.678 2637 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.14 % Favored : 90.71 % Rotamer: Outliers : 2.67 % Allowed : 20.84 % Favored : 76.48 % 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: -0.39 (0.19), residues: 2056 helix: 1.99 (0.19), residues: 862 sheet: -0.98 (0.34), residues: 242 loop : -2.35 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 67 TYR 0.012 0.001 TYR E 261 PHE 0.010 0.001 PHE G 13 TRP 0.007 0.001 TRP A 186 HIS 0.003 0.001 HIS E 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (16668) covalent geometry : angle 0.61245 / 0.31 (22518) hydrogen bonds : bond 0.03553 / 2.32 ( 714) hydrogen bonds : angle 3.97654 / 2.73 ( 2091) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 0.630 Fit side-chains REVERT: A 18 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8396 (mmm160) REVERT: A 197 MET cc_start: 0.9147 (mmm) cc_final: 0.8840 (tpt) REVERT: B 48 THR cc_start: 0.8836 (t) cc_final: 0.8559 (m) REVERT: B 58 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.6485 (pp) REVERT: B 62 HIS cc_start: 0.7943 (t-90) cc_final: 0.7742 (t70) REVERT: B 230 GLN cc_start: 0.8342 (mp-120) cc_final: 0.8078 (mp10) REVERT: C 49 ARG cc_start: 0.8586 (pmt170) cc_final: 0.8281 (pmt170) REVERT: C 82 TYR cc_start: 0.8130 (m-80) cc_final: 0.7892 (m-80) REVERT: D 18 ARG cc_start: 0.8722 (mtp85) cc_final: 0.8373 (mmm-85) REVERT: D 197 MET cc_start: 0.9127 (mmm) cc_final: 0.8817 (tpt) REVERT: E 48 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8503 (m) REVERT: E 58 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6595 (pp) REVERT: E 62 HIS cc_start: 0.7861 (t-90) cc_final: 0.7635 (t70) REVERT: F 21 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7946 (t70) REVERT: G 87 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7040 (mm-30) REVERT: G 88 GLN cc_start: 0.7300 (tp-100) cc_final: 0.6592 (pm20) REVERT: G 92 HIS cc_start: 0.8076 (t70) cc_final: 0.7623 (t70) REVERT: G 93 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7048 (mp) REVERT: G 139 SER cc_start: 0.8175 (p) cc_final: 0.7665 (m) REVERT: G 151 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7112 (pp) REVERT: H 27 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8357 (tmtt) REVERT: H 132 ASP cc_start: 0.7810 (m-30) cc_final: 0.6973 (t0) REVERT: I 109 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7886 (tp30) REVERT: J 87 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6905 (mm-30) REVERT: J 89 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7586 (mpp-170) REVERT: K 27 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8295 (tmtt) REVERT: L 143 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7578 (mt) outliers start: 45 outliers final: 21 residues processed: 299 average time/residue: 0.7793 time to fit residues: 253.4626 Evaluate side-chains 288 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 259 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 105 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 196 optimal weight: 0.0670 chunk 115 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 188 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN B 214 HIS E 115 GLN H 110 GLN K 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102077 restraints weight = 22323.163| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.86 r_work: 0.3043 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16668 Z= 0.117 Angle : 0.625 8.568 22518 Z= 0.313 Chirality : 0.042 0.264 2668 Planarity : 0.004 0.058 2796 Dihedral : 12.101 88.964 2637 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.48 % Favored : 90.42 % Rotamer: Outliers : 2.26 % Allowed : 21.73 % Favored : 76.01 % 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: -0.31 (0.19), residues: 2056 helix: 2.05 (0.19), residues: 864 sheet: -0.97 (0.34), residues: 246 loop : -2.29 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 12 TYR 0.012 0.001 TYR B 261 PHE 0.010 0.001 PHE G 13 TRP 0.007 0.001 TRP A 186 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (16668) covalent geometry : angle 0.62506 / 0.31 (22518) hydrogen bonds : bond 0.03568 / 2.33 ( 714) hydrogen bonds : angle 3.96140 / 2.72 ( 2091) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.582 Fit side-chains REVERT: A 18 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8412 (mmm160) REVERT: A 197 MET cc_start: 0.9081 (mmm) cc_final: 0.8782 (tpt) REVERT: B 48 THR cc_start: 0.8834 (t) cc_final: 0.8561 (m) REVERT: B 58 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6435 (pp) REVERT: B 230 GLN cc_start: 0.8361 (mp-120) cc_final: 0.8093 (mp10) REVERT: C 49 ARG cc_start: 0.8570 (pmt170) cc_final: 0.8253 (pmt170) REVERT: D 18 ARG cc_start: 0.8786 (mtp85) cc_final: 0.8465 (mmm160) REVERT: D 197 MET cc_start: 0.9076 (mmm) cc_final: 0.8776 (tpt) REVERT: E 48 THR cc_start: 0.8820 (t) cc_final: 0.8517 (m) REVERT: E 58 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6546 (pp) REVERT: E 62 HIS cc_start: 0.7931 (t-90) cc_final: 0.7723 (t70) REVERT: F 89 ASN cc_start: 0.9102 (t0) cc_final: 0.8635 (t0) REVERT: G 87 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6922 (tp30) REVERT: G 88 GLN cc_start: 0.7320 (tp-100) cc_final: 0.6692 (pm20) REVERT: G 92 HIS cc_start: 0.8129 (t70) cc_final: 0.7641 (t70) REVERT: G 93 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7061 (mp) REVERT: G 139 SER cc_start: 0.8164 (p) cc_final: 0.7641 (m) REVERT: H 27 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8376 (tmtt) REVERT: I 109 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7834 (tp30) REVERT: J 87 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6906 (mm-30) REVERT: J 89 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7549 (mpp-170) REVERT: K 27 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8347 (tmtt) REVERT: L 143 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7569 (mt) outliers start: 38 outliers final: 24 residues processed: 298 average time/residue: 0.7402 time to fit residues: 240.1025 Evaluate side-chains 291 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 96 optimal weight: 0.0060 chunk 87 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 117 optimal weight: 0.2980 chunk 180 optimal weight: 0.4980 chunk 159 optimal weight: 0.0270 chunk 82 optimal weight: 0.0170 chunk 31 optimal weight: 0.6980 overall best weight: 0.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN B 175 GLN C 89 ASN D 241 HIS E 115 GLN E 175 GLN H 110 GLN J 110 GLN K 110 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106433 restraints weight = 22185.819| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.94 r_work: 0.3124 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16668 Z= 0.102 Angle : 0.601 8.434 22518 Z= 0.301 Chirality : 0.041 0.231 2668 Planarity : 0.004 0.059 2796 Dihedral : 10.964 82.975 2637 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.61 % Favored : 91.34 % Rotamer: Outliers : 1.72 % Allowed : 22.15 % Favored : 76.13 % 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: -0.07 (0.20), residues: 2056 helix: 2.24 (0.19), residues: 874 sheet: -0.88 (0.33), residues: 266 loop : -2.21 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 67 TYR 0.009 0.001 TYR K 111 PHE 0.009 0.001 PHE A 219 TRP 0.008 0.001 TRP A 168 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (16668) covalent geometry : angle 0.60125 / 0.30 (22518) hydrogen bonds : bond 0.02694 / 1.77 ( 714) hydrogen bonds : angle 3.82873 / 2.62 ( 2091) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 0.543 Fit side-chains REVERT: A 18 ARG cc_start: 0.8633 (mtp85) cc_final: 0.8300 (mmm160) REVERT: A 197 MET cc_start: 0.9084 (mmm) cc_final: 0.8765 (tpt) REVERT: B 48 THR cc_start: 0.8781 (t) cc_final: 0.8512 (m) REVERT: B 58 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6155 (pp) REVERT: B 230 GLN cc_start: 0.8345 (mp-120) cc_final: 0.8038 (mp10) REVERT: C 21 ASP cc_start: 0.8405 (t70) cc_final: 0.8089 (t70) REVERT: C 49 ARG cc_start: 0.8580 (pmt170) cc_final: 0.8269 (pmt170) REVERT: C 82 TYR cc_start: 0.7938 (m-80) cc_final: 0.7698 (m-80) REVERT: D 18 ARG cc_start: 0.8728 (mtp85) cc_final: 0.8444 (mmm160) REVERT: D 197 MET cc_start: 0.9064 (mmm) cc_final: 0.8740 (tpt) REVERT: E 48 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8467 (m) REVERT: E 58 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6204 (pp) REVERT: F 21 ASP cc_start: 0.8380 (t70) cc_final: 0.8042 (t70) REVERT: F 89 ASN cc_start: 0.9095 (t0) cc_final: 0.8637 (t0) REVERT: G 5 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7660 (ttpt) REVERT: G 67 ARG cc_start: 0.5832 (mmt180) cc_final: 0.5415 (mmm160) REVERT: G 87 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6732 (tp30) REVERT: G 88 GLN cc_start: 0.7243 (tp-100) cc_final: 0.6626 (pm20) REVERT: G 92 HIS cc_start: 0.8032 (t70) cc_final: 0.7564 (t70) REVERT: G 93 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7028 (mp) REVERT: G 139 SER cc_start: 0.8157 (p) cc_final: 0.7620 (m) REVERT: H 27 LYS cc_start: 0.8807 (ttmm) cc_final: 0.8368 (tmtt) REVERT: H 132 ASP cc_start: 0.7464 (m-30) cc_final: 0.6869 (t0) REVERT: I 109 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7853 (tp30) REVERT: J 5 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7649 (ttpt) REVERT: J 83 THR cc_start: 0.6464 (OUTLIER) cc_final: 0.6074 (p) REVERT: J 87 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6675 (mm-30) REVERT: J 89 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7466 (mpp-170) REVERT: K 27 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8294 (tmtt) REVERT: L 143 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7523 (mt) outliers start: 29 outliers final: 11 residues processed: 293 average time/residue: 0.7469 time to fit residues: 237.7698 Evaluate side-chains 281 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 261 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 182 optimal weight: 0.0570 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 220 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN C 89 ASN D 241 HIS E 115 GLN H 110 GLN K 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.101854 restraints weight = 22176.159| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.93 r_work: 0.2923 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16668 Z= 0.135 Angle : 0.637 8.389 22518 Z= 0.320 Chirality : 0.043 0.270 2668 Planarity : 0.004 0.058 2796 Dihedral : 11.168 86.505 2637 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.19 % Favored : 90.76 % Rotamer: Outliers : 1.19 % Allowed : 23.16 % Favored : 75.65 % 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: -0.14 (0.19), residues: 2056 helix: 2.17 (0.19), residues: 868 sheet: -0.94 (0.34), residues: 246 loop : -2.18 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 67 TYR 0.017 0.001 TYR E 261 PHE 0.013 0.001 PHE G 13 TRP 0.007 0.001 TRP D 186 HIS 0.007 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (16668) covalent geometry : angle 0.63700 / 0.32 (22518) hydrogen bonds : bond 0.03982 / 2.60 ( 714) hydrogen bonds : angle 3.96930 / 2.73 ( 2091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6792.35 seconds wall clock time: 116 minutes 5.48 seconds (6965.48 seconds total)