Starting phenix.real_space_refine on Sat Mar 7 03:15:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z17_14443/03_2026/7z17_14443_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z17_14443/03_2026/7z17_14443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z17_14443/03_2026/7z17_14443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z17_14443/03_2026/7z17_14443.map" model { file = "/net/cci-nas-00/data/ceres_data/7z17_14443/03_2026/7z17_14443_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z17_14443/03_2026/7z17_14443_neut_trim.cif" } resolution = 2.57 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= 0.001 sd= 0.023 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 2 5.49 5 S 86 5.16 5 C 11872 2.51 5 N 3355 2.21 5 O 3604 1.98 5 H 18669 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 37592 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2217 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "B" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2955 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "C" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5395 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "D" Number of atoms: 4377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4377 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 20, 'TRANS': 258} Chain: "E" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2210 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "F" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2955 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "G" Number of atoms: 5394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5394 Classifications: {'peptide': 353} Modifications used: {'NH2NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "H" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4324 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 20, 'TRANS': 255} Chain: "I" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3872 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3872 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'I9X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14354 SG CYS D 241 89.774 40.640 48.741 1.00 9.58 S ATOM 14393 SG CYS D 244 89.821 39.823 45.064 1.00 15.56 S ATOM 14713 SG CYS D 266 87.007 41.976 46.593 1.00 7.80 S ATOM 14793 SG CYS D 272 87.308 38.160 47.275 1.00 17.11 S ATOM 29290 SG CYS H 241 19.061 63.889 106.354 1.00 77.35 S ATOM 29329 SG CYS H 244 18.821 63.092 110.096 1.00 78.83 S ATOM 29649 SG CYS H 266 21.937 64.638 108.663 1.00 67.99 S ATOM 29729 SG CYS H 272 20.968 60.973 107.802 1.00 65.98 S Time building chain proxies: 6.47, per 1000 atoms: 0.17 Number of scatterers: 37592 At special positions: 0 Unit cell: (106.017, 133.674, 151.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 86 16.00 P 2 15.00 O 3604 8.00 N 3355 7.00 C 11872 6.00 H 18669 1.00 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: 3.48 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 333 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 328 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 241 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 272 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 244 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 266 " pdb=" ZN G1000 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS C 219 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 333 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 328 " pdb=" ZN H1000 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 241 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 244 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 266 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 272 " Number of angles added : 12 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4514 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 22 sheets defined 45.7% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 88 through 103 Processing helix chain 'A' and resid 104 through 115 removed outlier: 4.304A pdb=" N GLN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASN A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'B' and resid 9 through 27 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 70 through 81 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.826A pdb=" N GLY B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'C' and resid 8 through 25 removed outlier: 3.587A pdb=" N ALA C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 41 through 53 Processing helix chain 'C' and resid 56 through 67 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.787A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.556A pdb=" N LEU C 158 " --> pdb=" O HIS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 198 Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.555A pdb=" N GLN C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.634A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 333 through 352 Processing helix chain 'D' and resid 8 through 12 removed outlier: 3.977A pdb=" N LEU D 12 " --> pdb=" O PHE D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 30 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 137 through 148 removed outlier: 4.328A pdb=" N THR D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.557A pdb=" N GLN D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 197 Proline residue: D 194 - end of helix Processing helix chain 'D' and resid 268 through 278 Processing helix chain 'E' and resid 4 through 18 Processing helix chain 'E' and resid 19 through 31 removed outlier: 3.564A pdb=" N ASN E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.648A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 115 through 136 Processing helix chain 'F' and resid 9 through 27 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 70 through 81 Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.567A pdb=" N GLN F 91 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 116 through 120 removed outlier: 4.203A pdb=" N GLY F 120 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 163 Processing helix chain 'G' and resid 8 through 25 Processing helix chain 'G' and resid 33 through 41 removed outlier: 3.515A pdb=" N ILE G 37 " --> pdb=" O SER G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 53 Processing helix chain 'G' and resid 56 through 67 Processing helix chain 'G' and resid 70 through 82 Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 188 through 198 Processing helix chain 'G' and resid 200 through 214 removed outlier: 3.679A pdb=" N ALA G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 295 removed outlier: 4.148A pdb=" N ALA G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 305 through 308 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.871A pdb=" N HIS G 316 " --> pdb=" O PHE G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 331 removed outlier: 3.524A pdb=" N LEU G 329 " --> pdb=" O PHE G 325 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS G 330 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU G 331 " --> pdb=" O SER G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 352 Processing helix chain 'H' and resid 8 through 12 removed outlier: 3.982A pdb=" N LEU H 12 " --> pdb=" O PHE H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 30 Processing helix chain 'H' and resid 51 through 60 Processing helix chain 'H' and resid 76 through 90 Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.639A pdb=" N PHE H 133 " --> pdb=" O PRO H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 148 removed outlier: 4.111A pdb=" N THR H 141 " --> pdb=" O ARG H 137 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS H 145 " --> pdb=" O THR H 141 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA H 146 " --> pdb=" O ARG H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 165 removed outlier: 3.983A pdb=" N LEU H 157 " --> pdb=" O MET H 153 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA H 162 " --> pdb=" O TYR H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 Processing helix chain 'H' and resid 268 through 278 Processing helix chain 'I' and resid 40 through 42 No H-bonds generated for 'chain 'I' and resid 40 through 42' Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 73 through 84 removed outlier: 3.524A pdb=" N ARG I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 3.792A pdb=" N GLY I 95 " --> pdb=" O HIS I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 4.764A pdb=" N ARG I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 135 through 139 removed outlier: 3.705A pdb=" N ARG I 138 " --> pdb=" O PRO I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 Processing helix chain 'I' and resid 147 through 161 Processing helix chain 'I' and resid 177 through 195 Processing helix chain 'I' and resid 205 through 212 removed outlier: 4.187A pdb=" N ALA I 209 " --> pdb=" O ASP I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 250 Processing helix chain 'J' and resid 40 through 42 No H-bonds generated for 'chain 'J' and resid 40 through 42' Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 73 through 84 removed outlier: 3.528A pdb=" N ARG J 82 " --> pdb=" O ARG J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 removed outlier: 3.788A pdb=" N GLY J 95 " --> pdb=" O HIS J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 114 removed outlier: 4.476A pdb=" N ARG J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 132 Processing helix chain 'J' and resid 142 through 146 Processing helix chain 'J' and resid 147 through 161 Processing helix chain 'J' and resid 177 through 195 Processing helix chain 'J' and resid 205 through 212 removed outlier: 4.067A pdb=" N ALA J 209 " --> pdb=" O ASP J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 250 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 85 removed outlier: 4.357A pdb=" N ARG A 59 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 51 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 61 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 49 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY A 63 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL A 47 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 65 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY A 45 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 67 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU A 43 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 69 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA A 41 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 71 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU C 88 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU A 46 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL C 90 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN A 48 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.525A pdb=" N VAL A 139 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN C 116 " --> pdb=" O VAL A 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA4, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.597A pdb=" N LEU B 123 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR B 177 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 125 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA B 95 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLN B 126 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR B 97 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP B 63 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ASP B 98 " --> pdb=" O TRP B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 147 through 149 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.548A pdb=" N THR E 143 " --> pdb=" O VAL C 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 105 removed outlier: 5.788A pdb=" N LEU C 101 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR C 229 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLU C 254 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C 225 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU C 252 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER C 227 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET C 250 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR C 229 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU C 248 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP C 231 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY C 246 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER C 233 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 244 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLU C 252 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU C 254 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLY C 274 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL C 256 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY C 272 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY C 258 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.415A pdb=" N ILE D 104 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLN D 124 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR D 106 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL D 65 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLN D 105 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS D 67 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ARG D 107 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE D 69 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'D' and resid 251 through 253 Processing sheet with id=AB2, first strand: chain 'E' and resid 79 through 85 removed outlier: 3.522A pdb=" N ALA E 70 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG E 59 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA E 51 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE E 61 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE E 49 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY E 63 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL E 47 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA E 65 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY E 45 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU E 67 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU E 43 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG E 69 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ALA E 41 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA E 71 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU G 88 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU E 46 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL G 90 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN E 48 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 138 through 139 removed outlier: 4.284A pdb=" N GLN G 116 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.321A pdb=" N ALA F 95 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLN F 126 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR F 97 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TRP F 63 " --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 147 through 149 Processing sheet with id=AB6, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.527A pdb=" N SER G 227 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG G 104 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE G 225 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU G 254 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE G 225 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU G 252 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER G 227 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET G 250 " --> pdb=" O SER G 227 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR G 229 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU G 248 " --> pdb=" O TYR G 229 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP G 231 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY G 246 " --> pdb=" O ASP G 231 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER G 233 " --> pdb=" O ASN G 244 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN G 244 " --> pdb=" O SER G 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR G 270 " --> pdb=" O ASN G 257 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE G 259 " --> pdb=" O HIS G 268 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N HIS G 268 " --> pdb=" O PHE G 259 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 35 through 36 removed outlier: 6.181A pdb=" N ILE H 121 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLY H 206 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE H 123 " --> pdb=" O GLY H 206 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'H' and resid 251 through 255 Processing sheet with id=AC1, first strand: chain 'I' and resid 21 through 28 removed outlier: 3.618A pdb=" N ASP I 23 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU I 11 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER I 25 " --> pdb=" O ASN I 9 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN I 9 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP I 27 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER I 7 " --> pdb=" O ASP I 27 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL I 8 " --> pdb=" O HIS I 63 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N HIS I 63 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASN I 10 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU I 61 " --> pdb=" O ASN I 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 86 through 88 removed outlier: 6.569A pdb=" N GLY I 86 " --> pdb=" O PHE I 168 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ASP I 170 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL I 88 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL I 167 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL I 202 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET I 169 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY I 38 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL I 33 " --> pdb=" O ARG I 215 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU I 217 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY I 35 " --> pdb=" O LEU I 217 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N MET I 219 " --> pdb=" O GLY I 35 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL I 37 " --> pdb=" O MET I 219 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL I 218 " --> pdb=" O GLU I 226 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU I 226 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS I 220 " --> pdb=" O VAL I 224 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL I 224 " --> pdb=" O LYS I 220 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 21 through 28 removed outlier: 3.644A pdb=" N ASP J 23 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU J 11 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER J 25 " --> pdb=" O ASN J 9 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN J 9 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP J 27 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER J 7 " --> pdb=" O ASP J 27 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU J 11 " --> pdb=" O GLN J 59 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN J 59 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 85 through 88 removed outlier: 6.343A pdb=" N GLY J 86 " --> pdb=" O PHE J 168 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASP J 170 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL J 88 " --> pdb=" O ASP J 170 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL J 167 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL J 202 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N MET J 169 " --> pdb=" O VAL J 202 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY J 38 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL J 33 " --> pdb=" O ARG J 215 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU J 217 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY J 35 " --> pdb=" O LEU J 217 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N MET J 219 " --> pdb=" O GLY J 35 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL J 37 " --> pdb=" O MET J 219 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL J 218 " --> pdb=" O GLU J 226 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU J 226 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYS J 220 " --> pdb=" O VAL J 224 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL J 224 " --> pdb=" O LYS J 220 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2319 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: 9.44 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.14: 18657 1.14 - 1.44: 8118 1.44 - 1.74: 11030 1.74 - 2.04: 152 2.04 - 2.34: 2 Bond restraints: 37959 Sorted by residual: bond pdb=" C03 I9X D1001 " pdb=" C04 I9X D1001 " ideal model delta sigma weight residual 1.545 1.214 0.331 2.00e-02 2.50e+03 2.73e+02 bond pdb=" C05 I9X D1001 " pdb=" O07 I9X D1001 " ideal model delta sigma weight residual 1.471 1.214 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" O10 I9X D1001 " pdb=" P08 I9X D1001 " ideal model delta sigma weight residual 1.559 1.332 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C04 I9X D1001 " pdb=" P08 I9X D1001 " ideal model delta sigma weight residual 2.463 2.239 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C05 I9X D1001 " pdb=" P08 I9X D1001 " ideal model delta sigma weight residual 2.519 2.339 0.180 2.00e-02 2.50e+03 8.09e+01 ... (remaining 37954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 68574 3.96 - 7.92: 25 7.92 - 11.88: 4 11.88 - 15.84: 2 15.84 - 19.80: 2 Bond angle restraints: 68607 Sorted by residual: angle pdb=" C03 I9X D1001 " pdb=" C04 I9X D1001 " pdb=" P08 I9X D1001 " ideal model delta sigma weight residual 140.66 120.86 19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" C02 I9X D1001 " pdb=" O06 I9X D1001 " pdb=" C05 I9X D1001 " ideal model delta sigma weight residual 122.18 105.21 16.97 3.00e+00 1.11e-01 3.20e+01 angle pdb=" O16 I9X D1001 " pdb=" P14 I9X D1001 " pdb=" O17 I9X D1001 " ideal model delta sigma weight residual 95.28 109.67 -14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C05 I9X D1001 " pdb=" P08 I9X D1001 " pdb=" O10 I9X D1001 " ideal model delta sigma weight residual 68.28 82.33 -14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" O15 I9X D1001 " pdb=" P14 I9X D1001 " pdb=" O16 I9X D1001 " ideal model delta sigma weight residual 120.11 109.27 10.84 3.00e+00 1.11e-01 1.31e+01 ... (remaining 68602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 16689 17.80 - 35.59: 813 35.59 - 53.39: 296 53.39 - 71.18: 80 71.18 - 88.98: 15 Dihedral angle restraints: 17893 sinusoidal: 9935 harmonic: 7958 Sorted by residual: dihedral pdb=" CA LEU C 101 " pdb=" C LEU C 101 " pdb=" N GLU C 102 " pdb=" CA GLU C 102 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG C 100 " pdb=" C ARG C 100 " pdb=" N LEU C 101 " pdb=" CA LEU C 101 " ideal model delta harmonic sigma weight residual -180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ARG D 180 " pdb=" C ARG D 180 " pdb=" N TYR D 181 " pdb=" CA TYR D 181 " ideal model delta harmonic sigma weight residual -180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 17890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2840 0.096 - 0.192: 140 0.192 - 0.289: 0 0.289 - 0.385: 0 0.385 - 0.481: 1 Chirality restraints: 2981 Sorted by residual: chirality pdb=" C04 I9X D1001 " pdb=" C03 I9X D1001 " pdb=" O10 I9X D1001 " pdb=" P08 I9X D1001 " both_signs ideal model delta sigma weight residual True 1.45 -1.93 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CA ILE D 110 " pdb=" N ILE D 110 " pdb=" C ILE D 110 " pdb=" CB ILE D 110 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE D 30 " pdb=" N ILE D 30 " pdb=" C ILE D 30 " pdb=" CB ILE D 30 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 2978 not shown) Planarity restraints: 5750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 186 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO D 187 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 187 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 187 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 186 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO H 187 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 187 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 187 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 150 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO G 151 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 151 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 151 " 0.021 5.00e-02 4.00e+02 ... (remaining 5747 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1664 2.17 - 2.78: 76820 2.78 - 3.39: 111742 3.39 - 3.99: 147548 3.99 - 4.60: 230018 Nonbonded interactions: 567792 Sorted by model distance: nonbonded pdb=" OD1 ASP C 130 " pdb=" HG1 THR C 132 " model vdw 1.564 2.450 nonbonded pdb=" O PHE H 86 " pdb=" HG1 THR H 90 " model vdw 1.583 2.450 nonbonded pdb="HD22 ASN C 218 " pdb=" OE2 GLU G 340 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP G 177 " pdb=" HG1 THR G 179 " model vdw 1.608 2.450 nonbonded pdb=" HG1 THR H 106 " pdb=" O ARG H 109 " model vdw 1.613 2.450 ... (remaining 567787 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 146) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name SD or name CE or name H2 or name H3 or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)) or resid \ 2 through 1000)) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 3 through 278) selection = (chain 'H' and resid 3 through 278) } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.00 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: 5.630 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: 0.190 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 45.190 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.006 0.331 19303 Z= 0.267 Angle : 0.534 19.802 26229 Z= 0.253 Chirality : 0.040 0.481 2981 Planarity : 0.003 0.046 3462 Dihedral : 10.982 88.978 7205 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.84 % Allowed : 2.97 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.01 (0.18), residues: 2412 helix: 1.90 (0.18), residues: 942 sheet: -0.53 (0.27), residues: 391 loop : 0.15 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.012 0.001 TYR G 209 PHE 0.010 0.001 PHE D 191 TRP 0.017 0.001 TRP A 11 HIS 0.003 0.001 HIS J 63 Details of bonding type rmsd covalent geometry : bond 0.00493 (19290) covalent geometry : angle 0.53184 (26217) hydrogen bonds : bond 0.14556 ( 837) hydrogen bonds : angle 6.50021 ( 2319) metal coordination : bond 0.13076 ( 13) metal coordination : angle 2.13868 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 350 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 333 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 156 ILE cc_start: 0.7309 (mp) cc_final: 0.7023 (tp) outliers start: 17 outliers final: 8 residues processed: 346 average time/residue: 1.5438 time to fit residues: 593.5642 Evaluate side-chains 227 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain I residue 142 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN H 78 ASN I 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.164654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113539 restraints weight = 77973.989| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.52 r_work: 0.3391 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19303 Z= 0.187 Angle : 0.547 6.634 26229 Z= 0.283 Chirality : 0.041 0.152 2981 Planarity : 0.005 0.053 3462 Dihedral : 5.104 55.644 2706 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.78 % Allowed : 8.81 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 0.83 (0.18), residues: 2412 helix: 1.74 (0.17), residues: 941 sheet: -0.65 (0.27), residues: 393 loop : 0.06 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 22 TYR 0.013 0.001 TYR G 203 PHE 0.015 0.001 PHE G 337 TRP 0.016 0.001 TRP A 11 HIS 0.006 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00424 (19290) covalent geometry : angle 0.54464 (26217) hydrogen bonds : bond 0.04600 ( 837) hydrogen bonds : angle 5.39797 ( 2319) metal coordination : bond 0.01122 ( 13) metal coordination : angle 2.22275 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 260 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8671 (m-30) cc_final: 0.8290 (m-30) REVERT: B 57 ASP cc_start: 0.8349 (p0) cc_final: 0.8012 (p0) REVERT: B 135 MET cc_start: 0.8524 (tpp) cc_final: 0.8267 (tpp) REVERT: G 326 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8456 (t) REVERT: G 338 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6940 (mt0) REVERT: H 149 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7919 (tm-30) REVERT: I 156 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7183 (tp) REVERT: J 69 LEU cc_start: 0.3186 (tt) cc_final: 0.2813 (mm) outliers start: 36 outliers final: 16 residues processed: 249 average time/residue: 1.3587 time to fit residues: 383.9939 Evaluate side-chains 227 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 338 GLN Chi-restraints excluded: chain G residue 352 ASN Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 169 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.165618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115623 restraints weight = 78043.438| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.30 r_work: 0.3435 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19303 Z= 0.118 Angle : 0.505 6.403 26229 Z= 0.256 Chirality : 0.040 0.147 2981 Planarity : 0.004 0.063 3462 Dihedral : 4.857 54.958 2703 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.53 % Allowed : 10.59 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 0.89 (0.18), residues: 2412 helix: 1.81 (0.17), residues: 950 sheet: -0.70 (0.26), residues: 395 loop : 0.10 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 22 TYR 0.012 0.001 TYR D 214 PHE 0.011 0.001 PHE G 337 TRP 0.015 0.001 TRP A 11 HIS 0.005 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00265 (19290) covalent geometry : angle 0.50334 (26217) hydrogen bonds : bond 0.03978 ( 837) hydrogen bonds : angle 5.07802 ( 2319) metal coordination : bond 0.00527 ( 13) metal coordination : angle 1.91770 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8690 (m-30) cc_final: 0.8338 (t0) REVERT: B 57 ASP cc_start: 0.8362 (p0) cc_final: 0.8014 (p0) REVERT: B 135 MET cc_start: 0.8529 (tpp) cc_final: 0.8231 (tpp) REVERT: B 145 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6523 (tm-30) REVERT: G 326 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8441 (t) REVERT: G 349 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6327 (mp-120) REVERT: H 225 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5867 (mp) REVERT: I 156 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7220 (tp) REVERT: J 69 LEU cc_start: 0.3125 (tt) cc_final: 0.2828 (mm) outliers start: 31 outliers final: 13 residues processed: 245 average time/residue: 1.3802 time to fit residues: 383.6453 Evaluate side-chains 226 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain G residue 352 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 169 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 144 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS C 136 ASN H 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.163908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113444 restraints weight = 78177.057| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.47 r_work: 0.3398 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19303 Z= 0.177 Angle : 0.527 5.623 26229 Z= 0.269 Chirality : 0.041 0.146 2981 Planarity : 0.004 0.070 3462 Dihedral : 4.847 55.389 2701 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.48 % Allowed : 11.88 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 0.76 (0.18), residues: 2412 helix: 1.70 (0.17), residues: 947 sheet: -0.84 (0.26), residues: 397 loop : 0.06 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 22 TYR 0.012 0.001 TYR G 203 PHE 0.014 0.001 PHE D 191 TRP 0.016 0.001 TRP A 11 HIS 0.005 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00406 (19290) covalent geometry : angle 0.52613 (26217) hydrogen bonds : bond 0.04010 ( 837) hydrogen bonds : angle 5.00430 ( 2319) metal coordination : bond 0.00654 ( 13) metal coordination : angle 1.85020 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8690 (m-30) cc_final: 0.8333 (t0) REVERT: B 57 ASP cc_start: 0.8415 (p0) cc_final: 0.8159 (p0) REVERT: B 135 MET cc_start: 0.8506 (tpp) cc_final: 0.8213 (tpp) REVERT: B 145 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6710 (tm-30) REVERT: G 326 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8460 (t) REVERT: G 349 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6408 (mp-120) REVERT: H 149 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7747 (tm-30) REVERT: H 171 TYR cc_start: 0.7256 (m-80) cc_final: 0.6971 (m-10) REVERT: H 225 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5813 (mp) REVERT: I 156 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7253 (tp) REVERT: J 69 LEU cc_start: 0.3165 (tt) cc_final: 0.2783 (mm) outliers start: 30 outliers final: 16 residues processed: 235 average time/residue: 1.3538 time to fit residues: 361.7020 Evaluate side-chains 225 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain G residue 352 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 185 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN C 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.162604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112067 restraints weight = 78497.653| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.42 r_work: 0.3381 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19303 Z= 0.211 Angle : 0.549 6.523 26229 Z= 0.281 Chirality : 0.042 0.146 2981 Planarity : 0.005 0.080 3462 Dihedral : 5.005 55.931 2701 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.98 % Allowed : 11.63 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 0.59 (0.17), residues: 2412 helix: 1.62 (0.17), residues: 940 sheet: -1.04 (0.25), residues: 399 loop : -0.01 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 22 TYR 0.013 0.001 TYR G 203 PHE 0.019 0.002 PHE I 21 TRP 0.016 0.001 TRP A 11 HIS 0.022 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00484 (19290) covalent geometry : angle 0.54706 (26217) hydrogen bonds : bond 0.04161 ( 837) hydrogen bonds : angle 4.96796 ( 2319) metal coordination : bond 0.00722 ( 13) metal coordination : angle 1.97624 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8736 (m-30) cc_final: 0.8331 (t0) REVERT: B 145 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: C 340 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: G 326 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8494 (t) REVERT: G 338 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.7022 (mt0) REVERT: G 342 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: H 149 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7887 (tm-30) REVERT: H 171 TYR cc_start: 0.7330 (m-80) cc_final: 0.7013 (m-10) REVERT: H 225 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5802 (mp) REVERT: I 6 LEU cc_start: 0.6444 (tp) cc_final: 0.6194 (tt) REVERT: I 156 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7312 (tp) REVERT: J 138 ARG cc_start: 0.0157 (ptm160) cc_final: -0.0168 (mtp-110) outliers start: 40 outliers final: 20 residues processed: 245 average time/residue: 1.4237 time to fit residues: 394.1404 Evaluate side-chains 228 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 302 HIS Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 338 GLN Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain G residue 352 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain J residue 201 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 63 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 92 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 195 GLN H 78 ASN H 261 ASN I 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.163582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113591 restraints weight = 78400.612| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.40 r_work: 0.3417 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19303 Z= 0.140 Angle : 0.509 5.724 26229 Z= 0.259 Chirality : 0.040 0.144 2981 Planarity : 0.004 0.088 3462 Dihedral : 4.863 55.703 2701 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.63 % Allowed : 12.47 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 0.74 (0.18), residues: 2412 helix: 1.76 (0.17), residues: 940 sheet: -1.04 (0.26), residues: 397 loop : 0.07 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 22 TYR 0.012 0.001 TYR G 203 PHE 0.022 0.001 PHE I 21 TRP 0.015 0.001 TRP A 11 HIS 0.010 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00321 (19290) covalent geometry : angle 0.50794 (26217) hydrogen bonds : bond 0.03742 ( 837) hydrogen bonds : angle 4.80741 ( 2319) metal coordination : bond 0.00484 ( 13) metal coordination : angle 1.76585 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8631 (m-30) cc_final: 0.8284 (t0) REVERT: B 39 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7789 (tmm-80) REVERT: B 145 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: C 340 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: C 350 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7015 (mt-10) REVERT: E 58 GLU cc_start: 0.7944 (mp0) cc_final: 0.7512 (mp0) REVERT: G 326 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8439 (t) REVERT: G 338 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: G 349 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6457 (mp-120) REVERT: H 149 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7947 (tm-30) REVERT: H 171 TYR cc_start: 0.7340 (m-80) cc_final: 0.6996 (m-10) REVERT: H 225 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5816 (mp) REVERT: H 271 TYR cc_start: 0.4179 (t80) cc_final: 0.3698 (t80) REVERT: I 6 LEU cc_start: 0.6417 (tp) cc_final: 0.6163 (tt) REVERT: I 47 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.5905 (tp) REVERT: I 156 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7317 (tp) REVERT: J 138 ARG cc_start: 0.0142 (ptm160) cc_final: -0.0180 (mtp-110) outliers start: 33 outliers final: 14 residues processed: 241 average time/residue: 1.3626 time to fit residues: 373.5772 Evaluate side-chains 231 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 338 GLN Chi-restraints excluded: chain G residue 346 ARG Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain G residue 352 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 187 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.161263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111423 restraints weight = 78463.910| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.36 r_work: 0.3382 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 19303 Z= 0.249 Angle : 0.571 5.842 26229 Z= 0.294 Chirality : 0.043 0.147 2981 Planarity : 0.005 0.097 3462 Dihedral : 5.085 56.479 2701 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.98 % Allowed : 12.72 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 0.50 (0.17), residues: 2412 helix: 1.54 (0.17), residues: 938 sheet: -1.17 (0.25), residues: 401 loop : -0.01 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 22 TYR 0.013 0.002 TYR C 334 PHE 0.026 0.002 PHE I 21 TRP 0.016 0.001 TRP A 11 HIS 0.010 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00576 (19290) covalent geometry : angle 0.56921 (26217) hydrogen bonds : bond 0.04272 ( 837) hydrogen bonds : angle 4.94658 ( 2319) metal coordination : bond 0.00789 ( 13) metal coordination : angle 1.96876 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8653 (m-30) cc_final: 0.8358 (t0) REVERT: B 39 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7863 (tmt90) REVERT: C 340 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: C 350 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7026 (mt-10) REVERT: E 58 GLU cc_start: 0.7929 (mp0) cc_final: 0.7544 (mp0) REVERT: G 326 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8503 (t) REVERT: G 349 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6443 (mp-120) REVERT: H 41 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: H 149 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7825 (tm-30) REVERT: H 171 TYR cc_start: 0.7305 (m-80) cc_final: 0.6963 (m-10) REVERT: H 230 HIS cc_start: 0.7118 (m-70) cc_final: 0.6716 (m170) REVERT: I 6 LEU cc_start: 0.6479 (tp) cc_final: 0.6220 (tt) REVERT: I 130 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5772 (mp0) REVERT: I 156 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7396 (tp) REVERT: I 173 THR cc_start: 0.5591 (p) cc_final: 0.5358 (p) REVERT: J 138 ARG cc_start: -0.0109 (ptm160) cc_final: -0.0363 (mtp-110) outliers start: 40 outliers final: 27 residues processed: 227 average time/residue: 1.4365 time to fit residues: 369.1012 Evaluate side-chains 235 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 302 HIS Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 346 ARG Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain G residue 352 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 59 GLN Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain J residue 201 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 62 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 218 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 78 ASN H 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.163493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113866 restraints weight = 77818.199| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.33 r_work: 0.3419 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19303 Z= 0.122 Angle : 0.510 5.913 26229 Z= 0.260 Chirality : 0.040 0.147 2981 Planarity : 0.004 0.095 3462 Dihedral : 4.878 56.270 2701 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.63 % Allowed : 13.41 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 0.73 (0.18), residues: 2412 helix: 1.76 (0.17), residues: 938 sheet: -1.08 (0.26), residues: 399 loop : 0.09 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 22 TYR 0.012 0.001 TYR D 214 PHE 0.024 0.001 PHE I 21 TRP 0.016 0.001 TRP A 11 HIS 0.007 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00276 (19290) covalent geometry : angle 0.50832 (26217) hydrogen bonds : bond 0.03641 ( 837) hydrogen bonds : angle 4.74530 ( 2319) metal coordination : bond 0.00385 ( 13) metal coordination : angle 1.80249 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8609 (m-30) cc_final: 0.8302 (t0) REVERT: B 30 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8096 (t) REVERT: B 39 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7849 (tmt90) REVERT: C 340 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: C 350 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6977 (mt-10) REVERT: E 58 GLU cc_start: 0.7935 (mp0) cc_final: 0.7538 (mp0) REVERT: G 326 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8426 (t) REVERT: G 349 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6361 (mp-120) REVERT: H 149 GLU cc_start: 0.8238 (tm-30) cc_final: 0.8007 (tm-30) REVERT: H 171 TYR cc_start: 0.7349 (m-80) cc_final: 0.6998 (m-10) REVERT: H 225 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5940 (mp) REVERT: H 230 HIS cc_start: 0.7092 (m-70) cc_final: 0.6685 (m170) REVERT: I 6 LEU cc_start: 0.6487 (tp) cc_final: 0.6202 (tt) REVERT: I 47 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6047 (tp) REVERT: I 156 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7364 (tp) REVERT: I 173 THR cc_start: 0.5568 (p) cc_final: 0.5346 (p) REVERT: J 138 ARG cc_start: -0.0057 (ptm160) cc_final: -0.0314 (mtp-110) REVERT: J 158 ARG cc_start: 0.1850 (ttt90) cc_final: 0.1532 (ptm160) outliers start: 33 outliers final: 16 residues processed: 240 average time/residue: 1.4823 time to fit residues: 401.8431 Evaluate side-chains 232 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 346 ARG Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain G residue 352 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 201 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 4 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN H 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.160131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108647 restraints weight = 76325.279| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.42 r_work: 0.3308 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 19303 Z= 0.267 Angle : 0.590 11.553 26229 Z= 0.303 Chirality : 0.043 0.143 2981 Planarity : 0.005 0.096 3462 Dihedral : 5.131 56.674 2701 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.98 % Allowed : 13.26 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 0.44 (0.17), residues: 2412 helix: 1.46 (0.17), residues: 940 sheet: -1.22 (0.25), residues: 399 loop : -0.02 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 22 TYR 0.013 0.002 TYR C 334 PHE 0.028 0.002 PHE I 21 TRP 0.016 0.002 TRP A 11 HIS 0.015 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00622 (19290) covalent geometry : angle 0.58826 (26217) hydrogen bonds : bond 0.04337 ( 837) hydrogen bonds : angle 4.92520 ( 2319) metal coordination : bond 0.00838 ( 13) metal coordination : angle 2.14103 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8649 (m-30) cc_final: 0.8331 (t0) REVERT: B 30 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8110 (t) REVERT: B 39 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7955 (tmt90) REVERT: C 340 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: C 350 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: E 58 GLU cc_start: 0.7947 (mp0) cc_final: 0.7553 (mp0) REVERT: G 326 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8486 (t) REVERT: G 349 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6394 (mp-120) REVERT: H 149 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7978 (tm-30) REVERT: H 230 HIS cc_start: 0.7130 (m-70) cc_final: 0.6713 (m170) REVERT: H 271 TYR cc_start: 0.4180 (t80) cc_final: 0.3450 (t80) REVERT: I 6 LEU cc_start: 0.6519 (tp) cc_final: 0.6281 (tt) REVERT: I 156 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7313 (tp) REVERT: I 173 THR cc_start: 0.5734 (p) cc_final: 0.5507 (p) REVERT: J 138 ARG cc_start: 0.0166 (ptm160) cc_final: -0.0211 (mtp-110) outliers start: 40 outliers final: 18 residues processed: 225 average time/residue: 1.4064 time to fit residues: 357.7890 Evaluate side-chains 225 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 302 HIS Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 346 ARG Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain G residue 352 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain J residue 201 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.160947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109664 restraints weight = 75777.563| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.41 r_work: 0.3321 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19303 Z= 0.192 Angle : 0.557 12.251 26229 Z= 0.283 Chirality : 0.041 0.144 2981 Planarity : 0.005 0.095 3462 Dihedral : 5.067 56.666 2701 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.39 % Allowed : 13.81 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 0.49 (0.17), residues: 2412 helix: 1.49 (0.17), residues: 946 sheet: -1.19 (0.25), residues: 397 loop : 0.02 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 22 TYR 0.012 0.001 TYR G 203 PHE 0.030 0.002 PHE I 21 TRP 0.016 0.001 TRP A 11 HIS 0.015 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00442 (19290) covalent geometry : angle 0.55529 (26217) hydrogen bonds : bond 0.04017 ( 837) hydrogen bonds : angle 4.84552 ( 2319) metal coordination : bond 0.00611 ( 13) metal coordination : angle 2.07655 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8675 (m-30) cc_final: 0.8356 (t0) REVERT: B 13 ASP cc_start: 0.8541 (m-30) cc_final: 0.8245 (m-30) REVERT: B 30 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8086 (t) REVERT: B 39 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7958 (tmt90) REVERT: B 145 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: C 340 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: C 350 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7027 (mt-10) REVERT: E 58 GLU cc_start: 0.7969 (mp0) cc_final: 0.7571 (mp0) REVERT: G 326 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8450 (t) REVERT: G 349 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: H 149 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7942 (tm-30) REVERT: H 225 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5913 (mp) REVERT: H 230 HIS cc_start: 0.7127 (m-70) cc_final: 0.6721 (m170) REVERT: H 271 TYR cc_start: 0.4169 (t80) cc_final: 0.3455 (t80) REVERT: I 6 LEU cc_start: 0.6538 (tp) cc_final: 0.6279 (tt) REVERT: I 156 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7397 (tp) REVERT: I 173 THR cc_start: 0.5667 (p) cc_final: 0.5438 (p) REVERT: I 187 LEU cc_start: 0.5473 (OUTLIER) cc_final: 0.5196 (tp) REVERT: J 138 ARG cc_start: 0.0225 (ptm160) cc_final: -0.0168 (mtp-110) outliers start: 28 outliers final: 16 residues processed: 229 average time/residue: 1.3237 time to fit residues: 344.9697 Evaluate side-chains 231 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 346 ARG Chi-restraints excluded: chain G residue 349 GLN Chi-restraints excluded: chain G residue 352 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain J residue 201 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 196 optimal weight: 9.9990 chunk 237 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 195 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 78 ASN I 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.162118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110913 restraints weight = 75797.794| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.45 r_work: 0.3341 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19303 Z= 0.139 Angle : 0.523 10.420 26229 Z= 0.265 Chirality : 0.040 0.145 2981 Planarity : 0.005 0.090 3462 Dihedral : 4.916 56.190 2701 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.24 % Allowed : 14.35 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 0.67 (0.18), residues: 2412 helix: 1.67 (0.17), residues: 946 sheet: -1.11 (0.26), residues: 397 loop : 0.08 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 22 TYR 0.014 0.001 TYR I 64 PHE 0.029 0.001 PHE I 21 TRP 0.016 0.001 TRP A 11 HIS 0.012 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00318 (19290) covalent geometry : angle 0.52163 (26217) hydrogen bonds : bond 0.03690 ( 837) hydrogen bonds : angle 4.70998 ( 2319) metal coordination : bond 0.00444 ( 13) metal coordination : angle 1.96955 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16096.30 seconds wall clock time: 272 minutes 24.25 seconds (16344.25 seconds total)