Starting phenix.real_space_refine on Wed Mar 4 19:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zy3_11548/03_2026/6zy3_11548.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy3_11548/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zy3_11548/03_2026/6zy3_11548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy3_11548/03_2026/6zy3_11548.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy3_11548/03_2026/6zy3_11548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy3_11548/03_2026/6zy3_11548.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.86, per 1000 atoms: 0.24 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: 1.17 Conformation dependent library (CDL) restraints added in 776.0 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: 0.54 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: 2.31 Time building geometry restraints manager: 1.60 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: 9166 24.36 - 48.72: 392 48.72 - 73.09: 21 73.09 - 97.45: 10 97.45 - 121.81: 5 Dihedral angle restraints: 9594 sinusoidal: 3694 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 9591 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.140 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 : 13.134 121.812 5798 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 covalent geometry : bond 0.00313 (16040) covalent geometry : angle 0.70193 (21783) hydrogen bonds : bond 0.32802 ( 479) hydrogen bonds : angle 10.57802 ( 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 : 0.641 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: 0.1510 time to fit residues: 83.2491 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 : 0.599 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 E 201 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.200799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.160056 restraints weight = 18980.224| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.96 r_work: 0.3340 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2324 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= 0.123 Angle : 0.556 11.821 21783 Z= 0.276 Chirality : 0.041 0.171 2649 Planarity : 0.004 0.038 2718 Dihedral : 6.355 90.840 2248 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.83 % Allowed : 12.35 % Favored : 85.82 % 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: -2.55 (0.14), residues: 756 sheet: -2.23 (0.32), residues: 229 loop : -3.05 (0.15), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 239 TYR 0.017 0.001 TYR L 40 PHE 0.028 0.001 PHE F 254 TRP 0.012 0.001 TRP G 216 HIS 0.003 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00288 (16040) covalent geometry : angle 0.55643 (21783) hydrogen bonds : bond 0.04132 ( 479) hydrogen bonds : angle 4.63101 ( 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 331 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: D 85 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7364 (mp0) REVERT: I 6 ASN cc_start: 0.8803 (t0) cc_final: 0.8564 (t0) REVERT: B 37 LYS cc_start: 0.6260 (pttm) cc_final: 0.5966 (mttt) REVERT: G 207 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7247 (mt-10) REVERT: E 46 ARG cc_start: 0.8617 (tpt90) cc_final: 0.7891 (ttm-80) REVERT: H 89 MET cc_start: 0.7526 (mmm) cc_final: 0.7223 (tpt) outliers start: 31 outliers final: 21 residues processed: 317 average time/residue: 0.1379 time to fit residues: 64.0832 Evaluate side-chains 291 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 270 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU 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 F residue 100 MET 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 E residue 201 ASN 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: 0.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 149 GLN B 70 ASN F 175 GLN E 201 ASN H 190 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.192660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144920 restraints weight = 18990.302| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.60 r_work: 0.3327 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16040 Z= 0.133 Angle : 0.556 11.084 21783 Z= 0.275 Chirality : 0.041 0.173 2649 Planarity : 0.004 0.040 2718 Dihedral : 5.985 82.561 2248 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.48 % Allowed : 15.60 % Favored : 81.91 % 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: -2.86 (0.17), residues: 2027 helix: -0.97 (0.18), residues: 778 sheet: -1.96 (0.35), residues: 218 loop : -2.68 (0.16), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 81 TYR 0.016 0.001 TYR L 40 PHE 0.018 0.001 PHE G 172 TRP 0.014 0.001 TRP B 7 HIS 0.003 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00321 (16040) covalent geometry : angle 0.55577 (21783) hydrogen bonds : bond 0.03828 ( 479) hydrogen bonds : angle 3.93864 ( 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 324 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 ARG cc_start: 0.6893 (mmt180) cc_final: 0.6666 (mmt180) REVERT: B 19 GLU cc_start: 0.6925 (tp30) cc_final: 0.6530 (tp30) REVERT: C 82 TYR cc_start: 0.7946 (m-10) cc_final: 0.7386 (m-80) REVERT: F 11 MET cc_start: 0.7183 (pmm) cc_final: 0.6761 (pmm) REVERT: G 207 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7654 (mt-10) REVERT: E 46 ARG cc_start: 0.8655 (tpt90) cc_final: 0.7813 (ttm-80) REVERT: E 122 LEU cc_start: 0.8908 (tp) cc_final: 0.8613 (mt) REVERT: E 196 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8139 (tpp-160) REVERT: H 47 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: H 233 ARG cc_start: 0.8746 (ttm170) cc_final: 0.8161 (mtt180) outliers start: 42 outliers final: 28 residues processed: 304 average time/residue: 0.1427 time to fit residues: 61.9977 Evaluate side-chains 296 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain I residue 3 THR 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 I residue 141 MET 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 47 VAL Chi-restraints excluded: chain B residue 64 LEU 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 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 130 SER Chi-restraints excluded: chain H residue 204 ILE 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: 1.9990 chunk 2 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 60 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 149 GLN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4100 r_free = 0.4100 target = 0.192464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146015 restraints weight = 18779.583| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.76 r_work: 0.3238 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3593 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= 0.098 Angle : 0.503 14.710 21783 Z= 0.246 Chirality : 0.040 0.173 2649 Planarity : 0.003 0.035 2718 Dihedral : 5.811 79.744 2248 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.84 % Allowed : 17.38 % Favored : 79.79 % 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: -2.12 (0.18), residues: 2027 helix: -0.10 (0.19), residues: 764 sheet: -1.76 (0.36), residues: 218 loop : -2.41 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 102 TYR 0.015 0.001 TYR L 40 PHE 0.014 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 covalent geometry : bond 0.00232 (16040) covalent geometry : angle 0.50262 (21783) hydrogen bonds : bond 0.02947 ( 479) hydrogen bonds : angle 3.65846 ( 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 331 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 0.642 Fit side-chains REVERT: D 85 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7787 (mp0) REVERT: L 88 GLN cc_start: 0.5940 (mm110) cc_final: 0.5591 (tp40) REVERT: B 19 GLU cc_start: 0.6959 (tp30) cc_final: 0.6693 (tp30) REVERT: C 82 TYR cc_start: 0.8015 (m-10) cc_final: 0.7540 (m-80) REVERT: F 12 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7981 (ttm-80) REVERT: G 180 MET cc_start: 0.8937 (ttp) cc_final: 0.8606 (ttp) REVERT: G 207 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7495 (mt-10) REVERT: E 46 ARG cc_start: 0.8601 (tpt90) cc_final: 0.7732 (ttm-80) REVERT: E 122 LEU cc_start: 0.8905 (tp) cc_final: 0.8612 (mt) REVERT: H 46 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.7870 (tpt170) REVERT: H 47 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.7944 (mp-120) REVERT: H 190 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6673 (tm-30) REVERT: H 233 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8112 (mtt180) outliers start: 48 outliers final: 31 residues processed: 310 average time/residue: 0.1408 time to fit residues: 63.4030 Evaluate side-chains 303 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 64 VAL 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 64 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 THR 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 143 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 190 GLN 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: 1.9990 chunk 153 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 193 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 88 GLN L 149 GLN F 175 GLN F 262 HIS H 47 GLN H 190 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.190551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141901 restraints weight = 18718.903| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.66 r_work: 0.3200 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3785 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 : 0.504 13.028 21783 Z= 0.246 Chirality : 0.040 0.186 2649 Planarity : 0.003 0.035 2718 Dihedral : 5.663 77.917 2248 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.43 % Allowed : 18.03 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.19), residues: 2027 helix: 0.29 (0.20), residues: 772 sheet: -1.60 (0.35), residues: 231 loop : -2.29 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 102 TYR 0.015 0.001 TYR L 40 PHE 0.012 0.001 PHE F 172 TRP 0.007 0.001 TRP G 216 HIS 0.002 0.000 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00239 (16040) covalent geometry : angle 0.50433 (21783) hydrogen bonds : bond 0.02884 ( 479) hydrogen bonds : angle 3.55137 ( 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 334 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 276 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7479 (mmt180) cc_final: 0.7265 (mmt180) REVERT: D 85 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7806 (mp0) REVERT: B 19 GLU cc_start: 0.6942 (tp30) cc_final: 0.6605 (tp30) REVERT: F 12 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7988 (ttm-80) REVERT: G 180 MET cc_start: 0.8975 (ttp) cc_final: 0.8747 (ttp) REVERT: E 46 ARG cc_start: 0.8599 (tpt90) cc_final: 0.7736 (ttm-80) REVERT: E 122 LEU cc_start: 0.8921 (tp) cc_final: 0.8598 (mt) REVERT: H 46 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7905 (tpt170) REVERT: H 190 GLN cc_start: 0.7011 (tp-100) cc_final: 0.6590 (tm-30) REVERT: H 233 ARG cc_start: 0.8656 (ttm170) cc_final: 0.8072 (mtt180) outliers start: 58 outliers final: 39 residues processed: 307 average time/residue: 0.1338 time to fit residues: 60.2996 Evaluate side-chains 304 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 79 LEU 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 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 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 184 VAL 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 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: 2.9990 chunk 192 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 chunk 182 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 187 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 262 HIS H 47 GLN H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.187150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139150 restraints weight = 18661.427| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.66 r_work: 0.3140 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16040 Z= 0.130 Angle : 0.544 15.414 21783 Z= 0.266 Chirality : 0.041 0.199 2649 Planarity : 0.003 0.039 2718 Dihedral : 5.805 80.721 2248 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.43 % Allowed : 18.20 % Favored : 78.37 % 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: -1.54 (0.19), residues: 2027 helix: 0.39 (0.20), residues: 790 sheet: -1.52 (0.36), residues: 213 loop : -2.11 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 81 TYR 0.016 0.001 TYR L 40 PHE 0.017 0.001 PHE K 150 TRP 0.010 0.001 TRP G 216 HIS 0.002 0.001 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00318 (16040) covalent geometry : angle 0.54369 (21783) hydrogen bonds : bond 0.03167 ( 479) hydrogen bonds : angle 3.55939 ( 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 333 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 275 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7455 (mmt180) cc_final: 0.7208 (mmt180) REVERT: D 67 ARG cc_start: 0.7115 (mmt180) cc_final: 0.6824 (mmt180) REVERT: K 47 ASP cc_start: 0.7732 (m-30) cc_final: 0.7503 (m-30) REVERT: K 67 ARG cc_start: 0.8597 (mmm160) cc_final: 0.8334 (mmt180) REVERT: K 85 GLU cc_start: 0.8286 (tp30) cc_final: 0.7841 (mm-30) REVERT: B 19 GLU cc_start: 0.7035 (tp30) cc_final: 0.6529 (tp30) REVERT: F 12 ARG cc_start: 0.8237 (ttm170) cc_final: 0.8030 (ttm-80) REVERT: F 35 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8622 (mttt) REVERT: G 180 MET cc_start: 0.8943 (ttp) cc_final: 0.8605 (ttp) REVERT: G 207 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7385 (mt-10) REVERT: E 46 ARG cc_start: 0.8594 (tpt90) cc_final: 0.7713 (ttm-80) REVERT: E 76 LEU cc_start: 0.8616 (pt) cc_final: 0.8329 (mt) REVERT: E 122 LEU cc_start: 0.8892 (tp) cc_final: 0.8585 (mt) REVERT: E 196 ARG cc_start: 0.8589 (mmm160) cc_final: 0.7987 (tpp-160) REVERT: H 47 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8091 (mp-120) REVERT: H 190 GLN cc_start: 0.7055 (tp-100) cc_final: 0.6717 (tm-30) REVERT: H 233 ARG cc_start: 0.8647 (ttm170) cc_final: 0.8057 (mtt180) outliers start: 58 outliers final: 47 residues processed: 313 average time/residue: 0.1321 time to fit residues: 60.7716 Evaluate side-chains 313 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 265 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 60 ILE 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 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 59 SER Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 88 GLN 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 36 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 14 VAL 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 184 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 262 HIS Chi-restraints excluded: chain E residue 81 TYR 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 64 VAL 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: 0.9980 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 187 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4064 r_free = 0.4064 target = 0.188946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.139651 restraints weight = 18525.438| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.65 r_work: 0.3158 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16040 Z= 0.102 Angle : 0.520 16.205 21783 Z= 0.252 Chirality : 0.040 0.192 2649 Planarity : 0.003 0.034 2718 Dihedral : 5.686 80.415 2248 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.96 % Allowed : 19.09 % Favored : 77.96 % 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: -1.29 (0.19), residues: 2027 helix: 0.73 (0.20), residues: 780 sheet: -1.40 (0.37), residues: 213 loop : -2.06 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 81 TYR 0.015 0.001 TYR L 40 PHE 0.014 0.001 PHE F 172 TRP 0.007 0.001 TRP I 9 HIS 0.001 0.000 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00245 (16040) covalent geometry : angle 0.52002 (21783) hydrogen bonds : bond 0.02773 ( 479) hydrogen bonds : angle 3.44245 ( 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 312 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7459 (mmt180) cc_final: 0.7214 (mmt180) REVERT: D 67 ARG cc_start: 0.7065 (mmt180) cc_final: 0.6128 (ptp-170) REVERT: D 85 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7773 (mp0) REVERT: K 22 LEU cc_start: 0.1706 (OUTLIER) cc_final: 0.1397 (pp) REVERT: K 47 ASP cc_start: 0.7753 (m-30) cc_final: 0.7513 (m-30) REVERT: K 85 GLU cc_start: 0.8236 (tp30) cc_final: 0.7777 (mm-30) REVERT: B 19 GLU cc_start: 0.7031 (tp30) cc_final: 0.6504 (tp30) REVERT: F 35 LYS cc_start: 0.8869 (mmtp) cc_final: 0.8650 (mttt) REVERT: G 180 MET cc_start: 0.8933 (ttp) cc_final: 0.8562 (ttp) REVERT: G 207 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7326 (mt-10) REVERT: E 46 ARG cc_start: 0.8582 (tpt90) cc_final: 0.7702 (ttm-80) REVERT: E 76 LEU cc_start: 0.8557 (pt) cc_final: 0.8202 (mt) REVERT: E 122 LEU cc_start: 0.8871 (tp) cc_final: 0.8598 (mt) REVERT: E 172 LEU cc_start: 0.8988 (tp) cc_final: 0.8597 (tt) REVERT: H 47 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8849 (mm-40) REVERT: H 190 GLN cc_start: 0.6889 (tp-100) cc_final: 0.6677 (tm-30) REVERT: H 233 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8073 (mtt180) outliers start: 50 outliers final: 43 residues processed: 291 average time/residue: 0.1260 time to fit residues: 54.2569 Evaluate side-chains 301 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 3 THR 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 59 SER Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 88 GLN 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 36 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 14 VAL 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 184 VAL 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 189 MET 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: 5.9990 chunk 159 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 147 optimal weight: 0.1980 chunk 173 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 88 GLN K 6 ASN F 113 HIS ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 HIS H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.186778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 145)---------------| | r_work = 0.3509 r_free = 0.3509 target = 0.135183 restraints weight = 18607.847| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.45 r_work: 0.3263 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16040 Z= 0.115 Angle : 0.529 15.936 21783 Z= 0.258 Chirality : 0.041 0.177 2649 Planarity : 0.003 0.032 2718 Dihedral : 5.732 80.418 2248 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.37 % Allowed : 18.97 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.19), residues: 2027 helix: 0.75 (0.20), residues: 788 sheet: -1.37 (0.35), residues: 231 loop : -1.97 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 81 TYR 0.019 0.001 TYR K 43 PHE 0.014 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 covalent geometry : bond 0.00281 (16040) covalent geometry : angle 0.52886 (21783) hydrogen bonds : bond 0.02923 ( 479) hydrogen bonds : angle 3.44001 ( 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 322 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 265 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7506 (mmt180) cc_final: 0.7245 (mmt180) REVERT: A 89 ARG cc_start: 0.5390 (ttp-110) cc_final: 0.4953 (ttp80) REVERT: D 67 ARG cc_start: 0.7203 (mmt180) cc_final: 0.6296 (ptp-170) REVERT: D 85 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7387 (mp0) REVERT: D 143 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6481 (pp) REVERT: K 47 ASP cc_start: 0.7822 (m-30) cc_final: 0.7613 (m-30) REVERT: K 67 ARG cc_start: 0.8537 (mmm160) cc_final: 0.8333 (mmt180) REVERT: B 19 GLU cc_start: 0.7080 (tp30) cc_final: 0.6561 (tp30) REVERT: F 35 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8664 (mttt) REVERT: F 218 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8678 (tt) REVERT: G 180 MET cc_start: 0.8918 (ttp) cc_final: 0.8541 (ttp) REVERT: G 207 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7414 (mt-10) REVERT: E 46 ARG cc_start: 0.8478 (tpt90) cc_final: 0.7620 (ttm-80) REVERT: E 76 LEU cc_start: 0.8567 (pt) cc_final: 0.8342 (mt) REVERT: E 122 LEU cc_start: 0.8877 (tp) cc_final: 0.8590 (mt) REVERT: E 172 LEU cc_start: 0.9108 (tp) cc_final: 0.8761 (tt) REVERT: H 47 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8157 (mp-120) REVERT: H 233 ARG cc_start: 0.8570 (ttm170) cc_final: 0.8001 (mtt180) outliers start: 57 outliers final: 44 residues processed: 301 average time/residue: 0.1338 time to fit residues: 58.9410 Evaluate side-chains 313 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER 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 D residue 143 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 3 THR 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 82 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 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 180 MET Chi-restraints excluded: chain F residue 218 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 147 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 199 optimal weight: 0.0980 chunk 114 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 ASN K 48 ASN F 262 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.188073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140308 restraints weight = 18630.517| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.70 r_work: 0.3150 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4599 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= 0.094 Angle : 0.521 15.651 21783 Z= 0.252 Chirality : 0.040 0.167 2649 Planarity : 0.003 0.031 2718 Dihedral : 5.652 79.804 2248 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.01 % Allowed : 19.44 % Favored : 77.54 % 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: -1.02 (0.19), residues: 2027 helix: 0.95 (0.20), residues: 783 sheet: -1.35 (0.35), residues: 231 loop : -1.89 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 12 TYR 0.014 0.001 TYR K 43 PHE 0.019 0.001 PHE K 150 TRP 0.015 0.001 TRP E 195 HIS 0.001 0.000 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00224 (16040) covalent geometry : angle 0.52120 (21783) hydrogen bonds : bond 0.02681 ( 479) hydrogen bonds : angle 3.39759 ( 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 323 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7452 (mmt180) cc_final: 0.7176 (mmt180) REVERT: A 89 ARG cc_start: 0.5493 (ttp-110) cc_final: 0.5027 (ttp80) REVERT: D 67 ARG cc_start: 0.7207 (mmt180) cc_final: 0.6194 (ptp-170) REVERT: D 85 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7401 (mp0) REVERT: D 143 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6322 (pp) REVERT: K 22 LEU cc_start: 0.1821 (OUTLIER) cc_final: 0.1524 (pp) REVERT: K 47 ASP cc_start: 0.7804 (m-30) cc_final: 0.7601 (m-30) REVERT: K 67 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8317 (mmt180) REVERT: B 49 ARG cc_start: 0.8194 (ptm160) cc_final: 0.7775 (ptm160) REVERT: C 34 GLU cc_start: 0.8361 (mp0) cc_final: 0.8155 (mp0) REVERT: F 218 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8659 (tt) REVERT: G 84 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7721 (ttp-170) REVERT: G 180 MET cc_start: 0.8909 (ttp) cc_final: 0.8493 (ttp) REVERT: G 207 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7339 (mt-10) REVERT: E 46 ARG cc_start: 0.8645 (tpt90) cc_final: 0.7753 (ttm-80) REVERT: E 76 LEU cc_start: 0.8565 (pt) cc_final: 0.8329 (mt) REVERT: E 122 LEU cc_start: 0.8883 (tp) cc_final: 0.8594 (mt) REVERT: E 132 MET cc_start: 0.9044 (ttm) cc_final: 0.8742 (ttm) REVERT: E 172 LEU cc_start: 0.9108 (tp) cc_final: 0.8763 (tt) REVERT: H 190 GLN cc_start: 0.6389 (tm-30) cc_final: 0.5914 (tm-30) REVERT: H 233 ARG cc_start: 0.8663 (ttm170) cc_final: 0.8093 (mtt180) outliers start: 51 outliers final: 43 residues processed: 301 average time/residue: 0.1264 time to fit residues: 56.0023 Evaluate side-chains 312 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER 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 D residue 143 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 3 THR 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 82 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 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 218 LEU 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 171 SER Chi-restraints excluded: chain E residue 189 MET 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 257 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 100 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 168 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 94 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 ASN F 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.188742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147079 restraints weight = 18557.046| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.87 r_work: 0.3071 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4637 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= 0.091 Angle : 0.514 15.624 21783 Z= 0.249 Chirality : 0.040 0.153 2649 Planarity : 0.003 0.030 2718 Dihedral : 5.570 78.464 2248 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.72 % Allowed : 19.62 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.19), residues: 2027 helix: 1.08 (0.20), residues: 784 sheet: -1.33 (0.35), residues: 231 loop : -1.85 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 12 TYR 0.018 0.001 TYR K 43 PHE 0.019 0.001 PHE K 150 TRP 0.013 0.001 TRP E 195 HIS 0.001 0.000 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00215 (16040) covalent geometry : angle 0.51447 (21783) hydrogen bonds : bond 0.02584 ( 479) hydrogen bonds : angle 3.33254 ( 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 316 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7331 (mmt180) cc_final: 0.7018 (mmt180) REVERT: A 89 ARG cc_start: 0.5519 (ttp-110) cc_final: 0.5001 (ttp80) REVERT: D 85 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7400 (mp0) REVERT: D 143 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6173 (pp) REVERT: K 47 ASP cc_start: 0.7870 (m-30) cc_final: 0.7664 (m-30) REVERT: K 67 ARG cc_start: 0.8500 (mmm160) cc_final: 0.8287 (mmt180) REVERT: F 218 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8632 (tt) REVERT: G 84 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7664 (ttp-170) REVERT: G 180 MET cc_start: 0.8905 (ttp) cc_final: 0.8626 (ttp) REVERT: G 207 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7418 (mt-10) REVERT: E 46 ARG cc_start: 0.8587 (tpt90) cc_final: 0.7705 (ttm-80) REVERT: E 76 LEU cc_start: 0.8518 (pt) cc_final: 0.8285 (mt) REVERT: E 122 LEU cc_start: 0.8872 (tp) cc_final: 0.8576 (mt) REVERT: E 132 MET cc_start: 0.8991 (ttm) cc_final: 0.8695 (ttm) REVERT: E 172 LEU cc_start: 0.9118 (tp) cc_final: 0.8753 (tt) REVERT: H 123 MET cc_start: 0.8928 (mtp) cc_final: 0.8650 (mtp) REVERT: H 233 ARG cc_start: 0.8619 (ttm170) cc_final: 0.8044 (mtt180) outliers start: 46 outliers final: 41 residues processed: 297 average time/residue: 0.1309 time to fit residues: 57.0671 Evaluate side-chains 309 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 143 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 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 3 THR 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 82 VAL Chi-restraints excluded: chain L residue 88 GLN Chi-restraints excluded: chain L residue 93 ILE 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 218 LEU 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 189 MET 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 257 MET 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: 0.5980 chunk 143 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 ASN F 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.187325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138653 restraints weight = 18596.921| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.75 r_work: 0.3124 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4797 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= 0.110 Angle : 0.541 15.508 21783 Z= 0.260 Chirality : 0.041 0.141 2649 Planarity : 0.003 0.033 2718 Dihedral : 5.675 79.773 2248 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.90 % Allowed : 19.92 % Favored : 77.19 % 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: -0.93 (0.19), residues: 2027 helix: 0.99 (0.20), residues: 795 sheet: -1.31 (0.36), residues: 222 loop : -1.83 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 12 TYR 0.019 0.001 TYR K 43 PHE 0.019 0.001 PHE K 150 TRP 0.010 0.001 TRP E 195 HIS 0.002 0.000 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00268 (16040) covalent geometry : angle 0.54074 (21783) hydrogen bonds : bond 0.02850 ( 479) hydrogen bonds : angle 3.37793 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4694.59 seconds wall clock time: 80 minutes 39.13 seconds (4839.13 seconds total)