Starting phenix.real_space_refine on Fri Jul 3 19:11:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zy3_11548/07_2026/6zy3_11548.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy3_11548/07_2026/6zy3_11548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6zy3_11548/07_2026/6zy3_11548.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zy3_11548/07_2026/6zy3_11548.cif" model { file = "/net/cci-nas-00/data/ceres_data/6zy3_11548/07_2026/6zy3_11548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy3_11548/07_2026/6zy3_11548.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zy3_11548/07_2026/6zy3_11548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy3_11548/07_2026/6zy3_11548.map" } resolution = 3.3 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= 0.004 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 1 5.49 5 S 71 5.16 5 C 10175 2.51 5 N 2639 2.21 5 O 2884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15770 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1081 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1017 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1093 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1111 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1078 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 2 Chain: "B" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 757 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 733 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1984 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 18, 'TRANS': 242} Chain: "G" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1989 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 18, 'TRANS': 243} Chain: "E" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1946 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "H" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1942 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.68, per 1000 atoms: 0.23 Number of scatterers: 15770 At special positions: 0 Unit cell: (99.372, 125.736, 145.002, 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 71 16.00 P 1 15.00 O 2884 8.00 N 2639 7.00 C 10175 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: 0.86 Conformation dependent library (CDL) restraints added in 533.3 milliseconds 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 20 sheets defined 38.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 3 through 27 removed outlier: 3.883A pdb=" N GLU A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 152 removed outlier: 4.227A pdb=" N ILE A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 10 removed outlier: 3.608A pdb=" N ILE D 8 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4 through 10' Processing helix chain 'D' and resid 10 through 27 removed outlier: 3.734A pdb=" N ALA D 17 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS D 27 " --> pdb=" O PHE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 152 removed outlier: 4.781A pdb=" N GLY D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 25 removed outlier: 3.985A pdb=" N TRP I 9 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 142 through 152 removed outlier: 4.191A pdb=" N ILE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 26 removed outlier: 3.703A pdb=" N TRP J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL J 10 " --> pdb=" O ASN J 6 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 151 removed outlier: 3.838A pdb=" N LEU J 146 " --> pdb=" O VAL J 142 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 20 removed outlier: 3.658A pdb=" N LEU K 14 " --> pdb=" O VAL K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 152 removed outlier: 3.680A pdb=" N GLY K 148 " --> pdb=" O GLU K 144 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE K 150 " --> pdb=" O LEU K 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 26 removed outlier: 3.579A pdb=" N PHE L 13 " --> pdb=" O TRP L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 149 removed outlier: 4.230A pdb=" N ILE L 147 " --> pdb=" O LEU L 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.624A pdb=" N GLU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.537A pdb=" N ALA B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 4.243A pdb=" N TYR B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.654A pdb=" N GLU C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 68 removed outlier: 3.632A pdb=" N ALA C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 86 removed outlier: 4.089A pdb=" N TYR C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 86 " --> pdb=" O TYR C 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 56 removed outlier: 4.294A pdb=" N LEU F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU F 53 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.510A pdb=" N TYR F 81 " --> pdb=" O ARG F 77 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 101 through 107 removed outlier: 3.600A pdb=" N ALA F 107 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 133 removed outlier: 3.505A pdb=" N HIS F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 130 " --> pdb=" O MET F 126 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 131 " --> pdb=" O MET F 127 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 159 removed outlier: 3.937A pdb=" N ARG F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.767A pdb=" N GLY F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 244 removed outlier: 3.804A pdb=" N PHE F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 56 removed outlier: 3.757A pdb=" N LEU G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 84 Processing helix chain 'G' and resid 85 through 87 No H-bonds generated for 'chain 'G' and resid 85 through 87' Processing helix chain 'G' and resid 101 through 107 Processing helix chain 'G' and resid 108 through 113 removed outlier: 4.078A pdb=" N GLU G 112 " --> pdb=" O TYR G 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 108 through 113' Processing helix chain 'G' and resid 117 through 133 removed outlier: 3.974A pdb=" N MET G 126 " --> pdb=" O HIS G 122 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N MET G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 140 removed outlier: 4.473A pdb=" N LYS G 139 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 159 removed outlier: 4.015A pdb=" N ARG G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 191 removed outlier: 3.602A pdb=" N VAL G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL G 184 " --> pdb=" O MET G 180 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS G 185 " --> pdb=" O GLY G 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 removed outlier: 3.546A pdb=" N VAL G 208 " --> pdb=" O ASP G 204 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU G 209 " --> pdb=" O VAL G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 204 through 209' Processing helix chain 'G' and resid 237 through 242 Processing helix chain 'G' and resid 260 through 265 removed outlier: 3.586A pdb=" N ASP G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 29 removed outlier: 3.821A pdb=" N LEU E 6 " --> pdb=" O LEU E 2 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 47 removed outlier: 3.868A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 74 removed outlier: 3.950A pdb=" N VAL E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 126 removed outlier: 3.702A pdb=" N GLY E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 134 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 150 through 171 removed outlier: 3.560A pdb=" N LEU E 155 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Proline residue: E 156 - end of helix removed outlier: 3.897A pdb=" N VAL E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 220 removed outlier: 3.535A pdb=" N LEU E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 258 removed outlier: 3.839A pdb=" N ILE E 231 " --> pdb=" O THR E 227 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL E 252 " --> pdb=" O GLY E 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 32 removed outlier: 3.601A pdb=" N ALA H 30 " --> pdb=" O MET H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 47 removed outlier: 3.770A pdb=" N VAL H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 56 through 73 removed outlier: 3.822A pdb=" N VAL H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER H 62 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL H 64 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 removed outlier: 3.996A pdb=" N THR H 79 " --> pdb=" O LEU H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 98 removed outlier: 3.774A pdb=" N VAL H 91 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU H 93 " --> pdb=" O MET H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.533A pdb=" N THR H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 135 removed outlier: 3.829A pdb=" N MET H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 175 removed outlier: 3.735A pdb=" N VAL H 143 " --> pdb=" O PRO H 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER H 145 " --> pdb=" O ARG H 141 " (cutoff:3.500A) Proline residue: H 146 - end of helix removed outlier: 3.969A pdb=" N LEU H 155 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Proline residue: H 156 - end of helix removed outlier: 3.585A pdb=" N VAL H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 173 " --> pdb=" O GLY H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 187 removed outlier: 3.665A pdb=" N SER H 187 " --> pdb=" O GLY H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 221 removed outlier: 3.504A pdb=" N LEU H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER H 206 " --> pdb=" O CYS H 202 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 207 " --> pdb=" O LEU H 203 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL H 208 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 254 removed outlier: 3.898A pdb=" N VAL H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE H 251 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 252 " --> pdb=" O GLY H 248 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 254 " --> pdb=" O ASP H 250 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.108A pdb=" N TYR A 40 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 86 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.108A pdb=" N TYR A 40 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 86 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 83 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP A 70 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLU A 85 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 68 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 4.220A pdb=" N VAL A 63 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 58 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 115 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 98 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 41 removed outlier: 3.825A pdb=" N ILE D 86 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 43 through 44 removed outlier: 7.512A pdb=" N TYR D 43 " --> pdb=" O ILE D 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 100 through 103 Processing sheet with id=AA7, first strand: chain 'I' and resid 39 through 40 removed outlier: 3.752A pdb=" N ILE I 86 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 43 through 45 Processing sheet with id=AA9, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.913A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE I 60 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 44 through 45 removed outlier: 3.653A pdb=" N LEU J 79 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASP J 70 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL J 68 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 63 through 64 removed outlier: 3.910A pdb=" N VAL J 63 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE J 60 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER J 59 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 68 through 73 removed outlier: 6.546A pdb=" N VAL K 68 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU K 85 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP K 70 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA K 44 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU K 42 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE K 86 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ILE K 134 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR K 43 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 63 through 66 removed outlier: 4.185A pdb=" N VAL K 63 " --> pdb=" O ILE K 60 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE K 60 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 44 through 45 removed outlier: 4.683A pdb=" N ASP L 70 " --> pdb=" O THR L 83 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL L 68 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL L 63 " --> pdb=" O ILE L 60 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG L 67 " --> pdb=" O SER L 56 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER L 56 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU L 112 " --> pdb=" O PRO L 57 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU L 114 " --> pdb=" O SER L 59 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU L 99 " --> pdb=" O LYS L 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 8 through 9 removed outlier: 4.136A pdb=" N MET B 8 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B 15 " --> pdb=" O MET B 8 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER B 45 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE B 42 " --> pdb=" O GLN B 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 7 through 8 removed outlier: 3.917A pdb=" N ALA C 15 " --> pdb=" O MET C 8 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER C 45 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 75 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 44 " --> pdb=" O GLN C 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 165 through 169 removed outlier: 6.605A pdb=" N ILE F 166 " --> pdb=" O VAL F 199 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL F 201 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE F 168 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER F 202 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA F 215 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N HIS F 226 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE F 217 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AC1, first strand: chain 'G' and resid 165 through 168 removed outlier: 6.721A pdb=" N ILE G 36 " --> pdb=" O HIS G 214 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TRP G 216 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA G 38 " --> pdb=" O TRP G 216 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU G 218 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET G 40 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE G 217 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA G 225 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA G 219 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 66 through 67 479 hydrogen bonds defined for protein. 1398 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: 1.96 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4967 1.34 - 1.46: 2257 1.46 - 1.58: 8686 1.58 - 1.69: 2 1.69 - 1.81: 128 Bond restraints: 16040 Sorted by residual: bond pdb=" C30 PEE H 301 " pdb=" O3 PEE H 301 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C10 PEE H 301 " pdb=" O2 PEE H 301 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C TYR G 108 " pdb=" N PRO G 109 " ideal model delta sigma weight residual 1.336 1.384 -0.049 1.23e-02 6.61e+03 1.56e+01 bond pdb=" O4P PEE H 301 " pdb=" P PEE H 301 " ideal model delta sigma weight residual 1.653 1.610 0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C ILE G 72 " pdb=" N PRO G 73 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.54e+00 ... (remaining 16035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 21618 3.31 - 6.62: 145 6.62 - 9.92: 17 9.92 - 13.23: 2 13.23 - 16.54: 1 Bond angle restraints: 21783 Sorted by residual: angle pdb=" O3P PEE H 301 " pdb=" P PEE H 301 " pdb=" O4P PEE H 301 " ideal model delta sigma weight residual 92.91 109.45 -16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb=" C VAL G 9 " pdb=" N ASP G 10 " pdb=" CA ASP G 10 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C ARG J 35 " pdb=" N THR J 36 " pdb=" CA THR J 36 " ideal model delta sigma weight residual 122.08 127.64 -5.56 1.47e+00 4.63e-01 1.43e+01 angle pdb=" C PRO F 171 " pdb=" N PHE F 172 " pdb=" CA PHE F 172 " ideal model delta sigma weight residual 122.46 127.66 -5.20 1.41e+00 5.03e-01 1.36e+01 angle pdb=" C GLU E 84 " pdb=" N THR E 85 " pdb=" CA THR E 85 " ideal model delta sigma weight residual 122.08 127.42 -5.34 1.47e+00 4.63e-01 1.32e+01 ... (remaining 21778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.36: 9162 24.36 - 48.72: 389 48.72 - 73.09: 20 73.09 - 97.45: 10 97.45 - 121.81: 3 Dihedral angle restraints: 9584 sinusoidal: 3684 harmonic: 5900 Sorted by residual: dihedral pdb=" CA TYR L 40 " pdb=" C TYR L 40 " pdb=" N THR L 41 " pdb=" CA THR L 41 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C21 PEE H 301 " pdb=" C22 PEE H 301 " pdb=" C23 PEE H 301 " pdb=" C24 PEE H 301 " ideal model delta sinusoidal sigma weight residual 180.10 58.29 121.81 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C23 PEE H 301 " pdb=" C24 PEE H 301 " pdb=" C25 PEE H 301 " pdb=" C26 PEE H 301 " ideal model delta sinusoidal sigma weight residual -179.89 -61.68 -118.21 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 9581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2112 0.052 - 0.104: 432 0.104 - 0.157: 96 0.157 - 0.209: 7 0.209 - 0.261: 2 Chirality restraints: 2649 Sorted by residual: chirality pdb=" C2 PEE H 301 " pdb=" C1 PEE H 301 " pdb=" C3 PEE H 301 " pdb=" O2 PEE H 301 " both_signs ideal model delta sigma weight residual False -2.33 -2.59 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB THR I 96 " pdb=" CA THR I 96 " pdb=" OG1 THR I 96 " pdb=" CG2 THR I 96 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE D 60 " pdb=" CA ILE D 60 " pdb=" CG1 ILE D 60 " pdb=" CG2 ILE D 60 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 2646 not shown) Planarity restraints: 2718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 26 " -0.038 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO B 27 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 155 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO E 156 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 156 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 156 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 155 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO H 156 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 156 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 156 " 0.026 5.00e-02 4.00e+02 ... (remaining 2715 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 5049 2.85 - 3.36: 13005 3.36 - 3.87: 24568 3.87 - 4.39: 27286 4.39 - 4.90: 48091 Nonbonded interactions: 117999 Sorted by model distance: nonbonded pdb=" O SER H 82 " pdb=" OG SER H 82 " model vdw 2.332 3.040 nonbonded pdb=" O LEU F 110 " pdb=" OG1 THR F 114 " model vdw 2.339 3.040 nonbonded pdb=" OH TYR K 40 " pdb=" O TYR K 90 " model vdw 2.340 3.040 nonbonded pdb=" O ILE H 231 " pdb=" OG1 THR H 235 " model vdw 2.342 3.040 nonbonded pdb=" O ALA E 83 " pdb=" OG SER E 86 " model vdw 2.345 3.040 ... (remaining 117994 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 29 or resid 38 through 89 or (resid 90 and (name \ N or name CA or name C or name O or name CB )) or resid 91 through 94 or (resid \ 95 through 96 and (name N or name CA or name C or name O or name CB )) or resid \ 97 through 108 or (resid 109 and (name N or name CA or name C or name O or name \ CB )) or resid 110 through 113 or resid 128 or (resid 129 and (name N or name C \ A or name C or name O or name CB )) or resid 130 through 131 or (resid 132 and ( \ name N or name CA or name C or name O or name CB )) or resid 133 through 135 or \ (resid 136 and (name N or name CA or name C or name O or name CB )) or resid 137 \ through 140 or (resid 141 and (name N or name CA or name C or name O or name CB \ )) or resid 142 through 144 or (resid 145 and (name N or name CA or name C or n \ ame O or name CB )) or resid 146 through 148 or (resid 149 and (name N or name C \ A or name C or name O or name CB )) or resid 150 through 152)) selection = (chain 'D' and (resid 3 through 26 or (resid 27 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 52 or (resid 53 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) or resi \ d 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or re \ sid 93 through 94 or (resid 95 through 96 and (name N or name CA or name C or na \ me O or name CB )) or resid 97 through 108 or (resid 109 and (name N or name CA \ or name C or name O or name CB )) or resid 110 through 113 or resid 128 through \ 144 or (resid 145 and (name N or name CA or name C or name O or name CB )) or re \ sid 146 through 148 or (resid 149 and (name N or name CA or name C or name O or \ name CB )) or resid 150 through 152)) selection = (chain 'I' and (resid 3 through 26 or (resid 27 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 52 or (resid 53 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or resi \ d 93 through 95 or (resid 96 and (name N or name CA or name C or name O or name \ CB )) or resid 97 through 113 or resid 128 or (resid 129 and (name N or name CA \ or name C or name O or name CB )) or resid 130 through 131 or (resid 132 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 140 or (r \ esid 141 and (name N or name CA or name C or name O or name CB )) or resid 142 t \ hrough 152)) selection = (chain 'J' and (resid 3 through 26 or (resid 27 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 52 or (resid 53 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) or resi \ d 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or re \ sid 93 through 113 or resid 128 through 131 or (resid 132 and (name N or name CA \ or name C or name O or name CB )) or resid 133 through 135 or (resid 136 and (n \ ame N or name CA or name C or name O or name CB )) or resid 137 through 140 or ( \ resid 141 and (name N or name CA or name C or name O or name CB )) or resid 142 \ through 144 or (resid 145 and (name N or name CA or name C or name O or name CB \ )) or resid 146 through 148 or (resid 149 and (name N or name CA or name C or na \ me O or name CB )) or resid 150 through 152)) selection = (chain 'K' and (resid 3 through 29 or resid 38 through 52 or (resid 53 through 5 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 56 through 8 \ 9 or (resid 90 and (name N or name CA or name C or name O or name CB )) or resid \ 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or res \ id 93 through 94 or (resid 95 through 96 and (name N or name CA or name C or nam \ e O or name CB )) or resid 97 through 108 or (resid 109 and (name N or name CA o \ r name C or name O or name CB )) or resid 110 through 113 or resid 128 or (resid \ 129 and (name N or name CA or name C or name O or name CB )) or resid 130 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB )) or resid 137 through 140 or (resid 141 and (name N or name CA or n \ ame C or name O or name CB )) or resid 142 through 144 or (resid 145 and (name N \ or name CA or name C or name O or name CB )) or resid 146 through 148 or (resid \ 149 and (name N or name CA or name C or name O or name CB )) or resid 150 throu \ gh 152)) selection = (chain 'L' and (resid 3 through 26 or (resid 27 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 52 or (resid 53 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) or resi \ d 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or re \ sid 93 through 94 or (resid 95 through 96 and (name N or name CA or name C or na \ me O or name CB )) or resid 97 through 108 or (resid 109 and (name N or name CA \ or name C or name O or name CB )) or resid 110 through 113 or resid 128 or (resi \ d 129 and (name N or name CA or name C or name O or name CB )) or resid 130 thro \ ugh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) o \ r resid 133 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB )) or resid 137 through 140 or (resid 141 and (name N or name CA or \ name C or name O or name CB )) or resid 142 through 144 or (resid 145 and (name \ N or name CA or name C or name O or name CB )) or resid 146 through 148 or (resi \ d 149 and (name N or name CA or name C or name O or name CB )) or resid 150 thro \ ugh 152)) } ncs_group { reference = (chain 'B' and resid 3 through 97) selection = chain 'C' } ncs_group { reference = (chain 'E' and resid 2 through 258) selection = (chain 'H' and resid 2 through 258) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 7 through 267) } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.060 Find NCS groups from input model: 0.270 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 : 0.003 0.128 16040 Z= 0.164 Angle : 0.702 16.538 21783 Z= 0.369 Chirality : 0.045 0.261 2649 Planarity : 0.005 0.056 2718 Dihedral : 12.966 121.812 5788 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.18 % Allowed : 6.09 % Favored : 93.74 % 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: -5.92 (0.12), residues: 2027 helix: -4.99 (0.04), residues: 727 sheet: -2.45 (0.33), residues: 206 loop : -3.52 (0.14), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 55 TYR 0.017 0.001 TYR L 40 PHE 0.008 0.001 PHE G 172 TRP 0.006 0.000 TRP H 177 HIS 0.002 0.000 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (16040) covalent geometry : angle 0.70193 / 0.37 (21783) hydrogen bonds : bond 0.32802 / 21.56 ( 479) hydrogen bonds : angle 10.57802 / 7.17 ( 1398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 386 time to evaluate : 0.456 Fit side-chains REVERT: F 141 MET cc_start: 0.8267 (mmt) cc_final: 0.8028 (mmt) REVERT: E 46 ARG cc_start: 0.7898 (tpt90) cc_final: 0.7471 (ttm-80) REVERT: H 124 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7845 (mtm180) outliers start: 3 outliers final: 0 residues processed: 389 average time/residue: 0.1195 time to fit residues: 66.3517 Evaluate side-chains 278 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 88 GLN K 48 ASN K 135 GLN L 48 ASN L 88 GLN L 91 ASN L 149 GLN F 57 GLN F 262 HIS G 175 GLN E 47 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.200177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.158480 restraints weight = 18959.884| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.75 r_work: 0.3288 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16040 Z= 0.122 Angle : 0.556 11.531 21783 Z= 0.274 Chirality : 0.041 0.173 2649 Planarity : 0.004 0.036 2718 Dihedral : 5.675 87.743 2238 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.07 % Allowed : 12.35 % Favored : 85.58 % 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: -4.13 (0.14), residues: 2027 helix: -2.59 (0.14), residues: 750 sheet: -2.20 (0.32), residues: 227 loop : -3.01 (0.15), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 239 TYR 0.017 0.001 TYR L 40 PHE 0.031 0.001 PHE F 254 TRP 0.013 0.001 TRP G 216 HIS 0.003 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (16040) covalent geometry : angle 0.55622 / 0.27 (21783) hydrogen bonds : bond 0.03712 / 2.50 ( 479) hydrogen bonds : angle 4.64501 / 3.10 ( 1398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7566 (mmt180) cc_final: 0.7353 (mmt180) REVERT: D 85 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7393 (mp0) REVERT: I 6 ASN cc_start: 0.8817 (t0) cc_final: 0.8583 (t0) REVERT: B 37 LYS cc_start: 0.6225 (pttm) cc_final: 0.5956 (mttt) REVERT: C 34 GLU cc_start: 0.7806 (mp0) cc_final: 0.7590 (mp0) REVERT: G 207 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7136 (mt-10) REVERT: E 46 ARG cc_start: 0.8609 (tpt90) cc_final: 0.7851 (ttm-80) REVERT: H 233 ARG cc_start: 0.8590 (ttm170) cc_final: 0.8228 (mtm-85) outliers start: 35 outliers final: 21 residues processed: 316 average time/residue: 0.1105 time to fit residues: 51.3397 Evaluate side-chains 292 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 271 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 262 HIS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain H residue 257 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 157 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 197 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 149 GLN B 70 ASN F 175 GLN H 47 GLN H 190 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.194918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.151503 restraints weight = 18997.329| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.62 r_work: 0.3175 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16040 Z= 0.114 Angle : 0.527 11.136 21783 Z= 0.258 Chirality : 0.040 0.170 2649 Planarity : 0.003 0.039 2718 Dihedral : 5.240 81.775 2238 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.95 % Allowed : 15.96 % Favored : 82.09 % 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: -2.84 (0.17), residues: 2027 helix: -0.95 (0.18), residues: 776 sheet: -1.91 (0.34), residues: 234 loop : -2.68 (0.16), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 67 TYR 0.015 0.001 TYR L 40 PHE 0.017 0.001 PHE I 13 TRP 0.010 0.001 TRP G 216 HIS 0.002 0.001 HIS H 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (16040) covalent geometry : angle 0.52736 / 0.26 (21783) hydrogen bonds : bond 0.03517 / 2.34 ( 479) hydrogen bonds : angle 3.88815 / 2.59 ( 1398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: D 85 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7534 (mp0) REVERT: K 3 THR cc_start: 0.7564 (m) cc_final: 0.7337 (t) REVERT: L 88 GLN cc_start: 0.5980 (mm110) cc_final: 0.5610 (tp40) REVERT: B 19 GLU cc_start: 0.6838 (tp30) cc_final: 0.6548 (tp30) REVERT: G 115 GLN cc_start: 0.8166 (mp10) cc_final: 0.7955 (mm-40) REVERT: G 180 MET cc_start: 0.8921 (ttp) cc_final: 0.8579 (ttp) REVERT: E 46 ARG cc_start: 0.8691 (tpt90) cc_final: 0.7823 (ttm-80) REVERT: E 122 LEU cc_start: 0.8887 (tp) cc_final: 0.8567 (mt) REVERT: H 46 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7720 (tpm170) REVERT: H 47 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.7779 (mp-120) outliers start: 33 outliers final: 24 residues processed: 297 average time/residue: 0.1167 time to fit residues: 50.9333 Evaluate side-chains 290 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 262 HIS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 112 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 181 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 149 GLN F 262 HIS H 47 GLN H 190 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.193351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.146248 restraints weight = 18774.591| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.71 r_work: 0.3247 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16040 Z= 0.101 Angle : 0.501 11.040 21783 Z= 0.245 Chirality : 0.040 0.172 2649 Planarity : 0.003 0.036 2718 Dihedral : 5.169 79.010 2238 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.78 % Allowed : 16.90 % Favored : 80.32 % 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: -2.14 (0.18), residues: 2027 helix: -0.10 (0.19), residues: 763 sheet: -1.73 (0.34), residues: 234 loop : -2.44 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 81 TYR 0.015 0.001 TYR L 40 PHE 0.016 0.001 PHE F 172 TRP 0.009 0.001 TRP G 216 HIS 0.002 0.000 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (16040) covalent geometry : angle 0.50117 / 0.24 (21783) hydrogen bonds : bond 0.02906 / 1.94 ( 479) hydrogen bonds : angle 3.65090 / 2.44 ( 1398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 0.551 Fit side-chains REVERT: A 67 ARG cc_start: 0.7503 (mmt180) cc_final: 0.7096 (mmt90) REVERT: D 85 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7694 (mp0) REVERT: L 88 GLN cc_start: 0.5954 (mm110) cc_final: 0.5613 (tp40) REVERT: B 19 GLU cc_start: 0.6969 (tp30) cc_final: 0.6716 (tp30) REVERT: C 82 TYR cc_start: 0.7993 (m-10) cc_final: 0.7674 (m-80) REVERT: F 12 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7948 (ttm-80) REVERT: G 180 MET cc_start: 0.9003 (ttp) cc_final: 0.8672 (ttp) REVERT: G 207 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7335 (mt-10) REVERT: E 46 ARG cc_start: 0.8607 (tpt90) cc_final: 0.7742 (ttm-80) REVERT: E 122 LEU cc_start: 0.8904 (tp) cc_final: 0.8568 (mt) REVERT: H 46 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7821 (tpm170) REVERT: H 190 GLN cc_start: 0.6582 (tp-100) cc_final: 0.6315 (tm-30) REVERT: H 233 ARG cc_start: 0.8695 (ttm170) cc_final: 0.8095 (mtt180) outliers start: 47 outliers final: 32 residues processed: 309 average time/residue: 0.1250 time to fit residues: 56.2711 Evaluate side-chains 306 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 274 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 262 HIS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 60 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 193 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 197 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 88 GLN L 149 GLN F 175 GLN F 262 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.191682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143320 restraints weight = 18716.859| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.59 r_work: 0.3210 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16040 Z= 0.101 Angle : 0.507 15.453 21783 Z= 0.246 Chirality : 0.040 0.188 2649 Planarity : 0.003 0.033 2718 Dihedral : 4.930 79.030 2238 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.19 % Allowed : 18.03 % Favored : 78.78 % 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: 2027 helix: 0.24 (0.20), residues: 786 sheet: -1.51 (0.35), residues: 228 loop : -2.27 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 81 TYR 0.014 0.001 TYR L 40 PHE 0.011 0.001 PHE F 172 TRP 0.008 0.001 TRP G 216 HIS 0.002 0.000 HIS H 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (16040) covalent geometry : angle 0.50658 / 0.25 (21783) hydrogen bonds : bond 0.02840 / 1.90 ( 479) hydrogen bonds : angle 3.50777 / 2.35 ( 1398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 57 PRO cc_start: 0.7554 (Cg_endo) cc_final: 0.7226 (Cg_exo) REVERT: A 67 ARG cc_start: 0.7311 (mmt180) cc_final: 0.6930 (mmt90) REVERT: B 19 GLU cc_start: 0.6949 (tp30) cc_final: 0.6637 (tp30) REVERT: B 31 MET cc_start: 0.7979 (mmm) cc_final: 0.7640 (mmm) REVERT: C 33 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7907 (mp0) REVERT: F 7 ASN cc_start: 0.7574 (m110) cc_final: 0.7373 (m-40) REVERT: F 12 ARG cc_start: 0.8229 (ttm170) cc_final: 0.7982 (ttm-80) REVERT: F 207 GLU cc_start: 0.8683 (mp0) cc_final: 0.8392 (mp0) REVERT: E 46 ARG cc_start: 0.8594 (tpt90) cc_final: 0.7751 (ttm-80) REVERT: E 122 LEU cc_start: 0.8877 (tp) cc_final: 0.8549 (mt) REVERT: H 46 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7956 (tpt170) REVERT: H 190 GLN cc_start: 0.6555 (tp-100) cc_final: 0.6229 (tm-30) REVERT: H 233 ARG cc_start: 0.8651 (ttm170) cc_final: 0.8068 (mtt180) outliers start: 54 outliers final: 40 residues processed: 308 average time/residue: 0.1235 time to fit residues: 55.8303 Evaluate side-chains 310 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 262 HIS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 88 GLN F 175 GLN F 262 HIS H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.186597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136983 restraints weight = 18697.686| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.64 r_work: 0.3118 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16040 Z= 0.161 Angle : 0.576 13.433 21783 Z= 0.282 Chirality : 0.042 0.198 2649 Planarity : 0.003 0.050 2718 Dihedral : 5.435 85.531 2238 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.31 % Allowed : 18.44 % Favored : 78.25 % 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: -1.58 (0.19), residues: 2027 helix: 0.33 (0.20), residues: 782 sheet: -1.51 (0.36), residues: 225 loop : -2.10 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 81 TYR 0.018 0.001 TYR L 40 PHE 0.020 0.002 PHE G 172 TRP 0.011 0.001 TRP G 216 HIS 0.003 0.001 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (16040) covalent geometry : angle 0.57578 / 0.28 (21783) hydrogen bonds : bond 0.03448 / 2.30 ( 479) hydrogen bonds : angle 3.65894 / 2.45 ( 1398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7378 (mmt180) cc_final: 0.6596 (mmm-85) REVERT: A 89 ARG cc_start: 0.5404 (ttp-110) cc_final: 0.4953 (ttp80) REVERT: D 67 ARG cc_start: 0.7151 (mmt180) cc_final: 0.6887 (mmt180) REVERT: D 85 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7785 (mp0) REVERT: K 85 GLU cc_start: 0.8337 (tp30) cc_final: 0.7869 (mm-30) REVERT: B 19 GLU cc_start: 0.7110 (tp30) cc_final: 0.6452 (tp30) REVERT: B 31 MET cc_start: 0.8137 (mmm) cc_final: 0.7829 (mmm) REVERT: C 33 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7916 (mp0) REVERT: F 12 ARG cc_start: 0.8287 (ttm170) cc_final: 0.8067 (ttm-80) REVERT: G 180 MET cc_start: 0.9020 (ttp) cc_final: 0.8566 (ttp) REVERT: G 207 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7599 (mt-10) REVERT: E 46 ARG cc_start: 0.8593 (tpt90) cc_final: 0.7706 (ttm-80) REVERT: E 76 LEU cc_start: 0.8671 (pt) cc_final: 0.8382 (mt) REVERT: E 122 LEU cc_start: 0.8883 (tp) cc_final: 0.8527 (mt) REVERT: E 196 ARG cc_start: 0.8641 (mmm160) cc_final: 0.8061 (tpp-160) REVERT: H 46 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7899 (tpt170) REVERT: H 47 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8102 (mp-120) REVERT: H 190 GLN cc_start: 0.6798 (tp-100) cc_final: 0.6563 (tm-30) REVERT: H 233 ARG cc_start: 0.8643 (ttm170) cc_final: 0.8054 (mtt180) outliers start: 56 outliers final: 42 residues processed: 318 average time/residue: 0.1171 time to fit residues: 55.1587 Evaluate side-chains 305 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 262 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain L residue 88 GLN Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 262 HIS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 1 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN F 262 HIS H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.186874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137285 restraints weight = 18568.064| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.56 r_work: 0.3276 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16040 Z= 0.126 Angle : 0.532 12.372 21783 Z= 0.262 Chirality : 0.041 0.191 2649 Planarity : 0.003 0.039 2718 Dihedral : 5.339 85.470 2238 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.37 % Allowed : 19.27 % Favored : 77.36 % 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: -1.40 (0.19), residues: 2027 helix: 0.50 (0.20), residues: 789 sheet: -1.45 (0.36), residues: 216 loop : -2.03 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 49 TYR 0.018 0.001 TYR K 43 PHE 0.015 0.001 PHE G 172 TRP 0.009 0.001 TRP I 9 HIS 0.002 0.000 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (16040) covalent geometry : angle 0.53194 / 0.26 (21783) hydrogen bonds : bond 0.03026 / 2.03 ( 479) hydrogen bonds : angle 3.55524 / 2.39 ( 1398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 57 PRO cc_start: 0.7718 (Cg_endo) cc_final: 0.7464 (Cg_exo) REVERT: A 67 ARG cc_start: 0.7545 (mmt180) cc_final: 0.6831 (mmm-85) REVERT: A 89 ARG cc_start: 0.5226 (ttp-110) cc_final: 0.4864 (ttp80) REVERT: D 67 ARG cc_start: 0.7144 (mmt180) cc_final: 0.6451 (ptp-170) REVERT: D 85 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7740 (mp0) REVERT: K 22 LEU cc_start: 0.1477 (OUTLIER) cc_final: 0.1107 (pp) REVERT: B 31 MET cc_start: 0.8043 (mmm) cc_final: 0.7739 (mmm) REVERT: B 49 ARG cc_start: 0.8165 (ptm160) cc_final: 0.7842 (ptm160) REVERT: C 33 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7869 (mp0) REVERT: C 34 GLU cc_start: 0.8359 (mp0) cc_final: 0.7868 (mp0) REVERT: F 35 LYS cc_start: 0.8883 (mmtp) cc_final: 0.8650 (mttt) REVERT: E 46 ARG cc_start: 0.8489 (tpt90) cc_final: 0.7638 (ttm-80) REVERT: E 76 LEU cc_start: 0.8630 (pt) cc_final: 0.8377 (mt) REVERT: E 122 LEU cc_start: 0.8882 (tp) cc_final: 0.8588 (mt) REVERT: H 47 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8204 (mp-120) REVERT: H 233 ARG cc_start: 0.8660 (ttm170) cc_final: 0.8101 (mtt180) outliers start: 57 outliers final: 46 residues processed: 296 average time/residue: 0.1218 time to fit residues: 53.7265 Evaluate side-chains 306 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 88 GLN Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 262 HIS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 34 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 193 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 173 optimal weight: 0.3980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN F 262 HIS H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.185240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136118 restraints weight = 18668.550| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.66 r_work: 0.3215 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16040 Z= 0.145 Angle : 0.560 11.606 21783 Z= 0.274 Chirality : 0.042 0.173 2649 Planarity : 0.003 0.032 2718 Dihedral : 5.510 86.454 2238 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.31 % Allowed : 19.56 % Favored : 77.13 % 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: -1.32 (0.19), residues: 2027 helix: 0.59 (0.20), residues: 781 sheet: -1.48 (0.35), residues: 225 loop : -1.96 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 12 TYR 0.017 0.001 TYR L 40 PHE 0.018 0.001 PHE G 172 TRP 0.010 0.001 TRP I 9 HIS 0.002 0.001 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.14 (16040) covalent geometry : angle 0.56030 / 0.27 (21783) hydrogen bonds : bond 0.03205 / 2.15 ( 479) hydrogen bonds : angle 3.60051 / 2.42 ( 1398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 57 PRO cc_start: 0.7703 (Cg_endo) cc_final: 0.7476 (Cg_exo) REVERT: A 67 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7066 (mmm-85) REVERT: A 89 ARG cc_start: 0.5393 (ttp-110) cc_final: 0.4974 (ttp80) REVERT: D 67 ARG cc_start: 0.7282 (mmt180) cc_final: 0.6525 (ptp-170) REVERT: D 85 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7815 (mp0) REVERT: K 85 GLU cc_start: 0.8338 (tp30) cc_final: 0.7926 (mm-30) REVERT: B 31 MET cc_start: 0.8126 (mmm) cc_final: 0.7825 (mmm) REVERT: B 49 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7886 (ptm160) REVERT: C 33 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7904 (mp0) REVERT: F 35 LYS cc_start: 0.8926 (mmtp) cc_final: 0.8704 (mttt) REVERT: G 84 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7810 (ttp-170) REVERT: E 46 ARG cc_start: 0.8534 (tpt90) cc_final: 0.7657 (ttm-80) REVERT: E 122 LEU cc_start: 0.8847 (tp) cc_final: 0.8517 (mt) REVERT: E 196 ARG cc_start: 0.8727 (mmm160) cc_final: 0.8225 (tpp-160) REVERT: H 46 ARG cc_start: 0.8300 (ttm110) cc_final: 0.8089 (tpt170) REVERT: H 47 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8277 (mp-120) REVERT: H 233 ARG cc_start: 0.8717 (ttm170) cc_final: 0.8147 (mtt180) outliers start: 56 outliers final: 48 residues processed: 298 average time/residue: 0.1237 time to fit residues: 54.1075 Evaluate side-chains 308 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 88 GLN Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 262 HIS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 147 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 40 optimal weight: 0.0570 chunk 39 optimal weight: 9.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN F 262 HIS H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.186739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 151)---------------| | r_work = 0.3526 r_free = 0.3526 target = 0.136947 restraints weight = 18655.469| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.48 r_work: 0.3278 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16040 Z= 0.100 Angle : 0.525 11.337 21783 Z= 0.258 Chirality : 0.041 0.163 2649 Planarity : 0.003 0.031 2718 Dihedral : 5.343 85.801 2238 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.01 % Allowed : 20.09 % Favored : 76.89 % 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: -1.14 (0.19), residues: 2027 helix: 0.80 (0.20), residues: 785 sheet: -1.44 (0.35), residues: 225 loop : -1.90 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 81 TYR 0.014 0.001 TYR L 40 PHE 0.019 0.001 PHE K 150 TRP 0.009 0.001 TRP I 9 HIS 0.001 0.000 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (16040) covalent geometry : angle 0.52506 / 0.26 (21783) hydrogen bonds : bond 0.02770 / 1.86 ( 479) hydrogen bonds : angle 3.48625 / 2.36 ( 1398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 57 PRO cc_start: 0.7481 (Cg_endo) cc_final: 0.7204 (Cg_exo) REVERT: A 67 ARG cc_start: 0.7505 (mmt180) cc_final: 0.6758 (mmm-85) REVERT: A 89 ARG cc_start: 0.5493 (ttp-110) cc_final: 0.5052 (ttp80) REVERT: D 67 ARG cc_start: 0.7192 (mmt180) cc_final: 0.6274 (ptp-170) REVERT: D 85 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7429 (mp0) REVERT: K 22 LEU cc_start: 0.1428 (OUTLIER) cc_final: 0.1072 (pp) REVERT: B 31 MET cc_start: 0.7987 (mmm) cc_final: 0.7707 (mmm) REVERT: B 49 ARG cc_start: 0.8145 (ptm160) cc_final: 0.7863 (ptm160) REVERT: C 33 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7918 (mp0) REVERT: F 35 LYS cc_start: 0.8887 (mmtp) cc_final: 0.8681 (mttt) REVERT: G 84 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7717 (ttp-170) REVERT: E 46 ARG cc_start: 0.8488 (tpt90) cc_final: 0.7617 (ttm-80) REVERT: E 122 LEU cc_start: 0.8834 (tp) cc_final: 0.8532 (mt) REVERT: E 132 MET cc_start: 0.8969 (ttm) cc_final: 0.8705 (ttm) REVERT: H 47 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8113 (mp-120) REVERT: H 190 GLN cc_start: 0.6585 (tm-30) cc_final: 0.5933 (tm-30) REVERT: H 233 ARG cc_start: 0.8548 (ttm170) cc_final: 0.7990 (mtt180) outliers start: 51 outliers final: 45 residues processed: 290 average time/residue: 0.1234 time to fit residues: 52.5217 Evaluate side-chains 306 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 88 GLN Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 262 HIS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 100 optimal weight: 0.3980 chunk 118 optimal weight: 0.9990 chunk 113 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 HIS H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.186947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138564 restraints weight = 18579.186| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.61 r_work: 0.3148 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16040 Z= 0.095 Angle : 0.517 11.136 21783 Z= 0.253 Chirality : 0.040 0.147 2649 Planarity : 0.003 0.031 2718 Dihedral : 5.273 85.816 2238 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.72 % Allowed : 20.74 % Favored : 76.54 % 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: -1.00 (0.19), residues: 2027 helix: 0.94 (0.20), residues: 783 sheet: -1.37 (0.35), residues: 231 loop : -1.84 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 81 TYR 0.023 0.001 TYR K 43 PHE 0.019 0.001 PHE K 150 TRP 0.008 0.001 TRP I 9 HIS 0.001 0.000 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (16040) covalent geometry : angle 0.51688 / 0.25 (21783) hydrogen bonds : bond 0.02657 / 1.78 ( 479) hydrogen bonds : angle 3.40988 / 2.30 ( 1398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 57 PRO cc_start: 0.7424 (Cg_endo) cc_final: 0.7174 (Cg_exo) REVERT: A 67 ARG cc_start: 0.7461 (mmt180) cc_final: 0.6868 (mmm-85) REVERT: A 89 ARG cc_start: 0.5546 (ttp-110) cc_final: 0.5055 (ttp80) REVERT: D 67 ARG cc_start: 0.7213 (mmt180) cc_final: 0.6220 (ptp-170) REVERT: D 85 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7414 (mp0) REVERT: K 22 LEU cc_start: 0.1805 (OUTLIER) cc_final: 0.1493 (pp) REVERT: B 31 MET cc_start: 0.7985 (mmm) cc_final: 0.7663 (mmm) REVERT: B 49 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7890 (ptm160) REVERT: C 33 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7916 (mp0) REVERT: G 84 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7689 (ttp-170) REVERT: E 46 ARG cc_start: 0.8589 (tpt90) cc_final: 0.7693 (ttm-80) REVERT: E 122 LEU cc_start: 0.8840 (tp) cc_final: 0.8512 (mt) REVERT: E 132 MET cc_start: 0.9059 (ttm) cc_final: 0.8790 (ttm) REVERT: E 172 LEU cc_start: 0.9010 (tp) cc_final: 0.8637 (tt) REVERT: H 46 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7921 (tpt170) REVERT: H 47 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8099 (mp-120) REVERT: H 233 ARG cc_start: 0.8640 (ttm170) cc_final: 0.8065 (mtt180) outliers start: 46 outliers final: 42 residues processed: 287 average time/residue: 0.1254 time to fit residues: 52.9463 Evaluate side-chains 299 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 262 HIS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 0.0570 chunk 143 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN F 262 HIS H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.188273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 126)---------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128499 restraints weight = 18602.122| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.98 r_work: 0.3084 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16040 Z= 0.095 Angle : 0.515 10.969 21783 Z= 0.252 Chirality : 0.040 0.140 2649 Planarity : 0.003 0.031 2718 Dihedral : 5.235 85.978 2238 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.90 % Allowed : 20.63 % 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: -0.92 (0.19), residues: 2027 helix: 1.02 (0.20), residues: 786 sheet: -1.33 (0.35), residues: 231 loop : -1.81 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 12 TYR 0.020 0.001 TYR K 43 PHE 0.018 0.001 PHE K 150 TRP 0.007 0.001 TRP I 9 HIS 0.001 0.000 HIS G 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (16040) covalent geometry : angle 0.51527 / 0.25 (21783) hydrogen bonds : bond 0.02634 / 1.76 ( 479) hydrogen bonds : angle 3.40497 / 2.31 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4373.08 seconds wall clock time: 75 minutes 19.95 seconds (4519.95 seconds total)