Starting phenix.real_space_refine on Thu Feb 15 18:16:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj6_25917/02_2024/7tj6_25917_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj6_25917/02_2024/7tj6_25917.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj6_25917/02_2024/7tj6_25917_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj6_25917/02_2024/7tj6_25917_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj6_25917/02_2024/7tj6_25917_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj6_25917/02_2024/7tj6_25917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj6_25917/02_2024/7tj6_25917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj6_25917/02_2024/7tj6_25917_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj6_25917/02_2024/7tj6_25917_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 28 5.16 5 C 8616 2.51 5 N 2108 2.21 5 O 2252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 417": "NH1" <-> "NH2" Residue "B ARG 417": "NH1" <-> "NH2" Residue "C ARG 417": "NH1" <-> "NH2" Residue "D ARG 417": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13008 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "C" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "D" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 101 Unusual residues: {'D21': 5} Classifications: {'RNA': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-3': 5, 'D21:plan-2': 4, 'D21:plan-1': 4} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 135 Unusual residues: {'D21': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-3': 5, 'D21:plan-2': 4, 'D21:plan-1': 4} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 135 Unusual residues: {'D21': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-3': 5, 'D21:plan-2': 4, 'D21:plan-1': 4} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 169 Unusual residues: {'D21': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-3': 5, 'D21:plan-2': 4, 'D21:plan-1': 4} Unresolved non-hydrogen planarities: 47 Time building chain proxies: 7.02, per 1000 atoms: 0.54 Number of scatterers: 13008 At special positions: 0 Unit cell: (104.796, 104.796, 116.298, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 4 15.00 O 2252 8.00 N 2108 7.00 C 8616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.46 Conformation dependent library (CDL) restraints added in 2.4 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 62.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 12 through 35 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 49 through 57 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 102 through 128 removed outlier: 5.091A pdb=" N LEU A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.772A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 Processing helix chain 'A' and resid 194 through 245 removed outlier: 4.033A pdb=" N ALA A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 No H-bonds generated for 'chain 'A' and resid 250 through 253' Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.274A pdb=" N GLU A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 298 removed outlier: 3.702A pdb=" N ALA A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 4.319A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 405 through 417 removed outlier: 3.644A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 35 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 102 through 128 removed outlier: 5.091A pdb=" N LEU B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ARG B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.772A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 194 through 245 removed outlier: 4.033A pdb=" N ALA B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.273A pdb=" N GLU B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.702A pdb=" N ALA B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 315 removed outlier: 4.319A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 394 through 403 Processing helix chain 'B' and resid 405 through 417 removed outlier: 3.644A pdb=" N GLN B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 35 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 49 through 57 Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 102 through 128 removed outlier: 5.091A pdb=" N LEU C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ARG C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 127 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 158 removed outlier: 3.772A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 181 Processing helix chain 'C' and resid 194 through 245 removed outlier: 4.033A pdb=" N ALA C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 No H-bonds generated for 'chain 'C' and resid 250 through 253' Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 272 through 278 removed outlier: 4.273A pdb=" N GLU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 298 removed outlier: 3.702A pdb=" N ALA C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 315 removed outlier: 4.319A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 394 through 403 Processing helix chain 'C' and resid 405 through 417 removed outlier: 3.645A pdb=" N GLN C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 35 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 91 through 98 Processing helix chain 'D' and resid 102 through 128 removed outlier: 5.090A pdb=" N LEU D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 158 removed outlier: 3.772A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'D' and resid 194 through 245 removed outlier: 4.033A pdb=" N ALA D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP D 226 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 253 No H-bonds generated for 'chain 'D' and resid 250 through 253' Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 272 through 278 removed outlier: 4.274A pdb=" N GLU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 298 removed outlier: 3.703A pdb=" N ALA D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 315 removed outlier: 4.319A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.644A pdb=" N GLN D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.180A pdb=" N TYR A 390 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A 341 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 392 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR A 339 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 346 through 349 Processing sheet with id= C, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.181A pdb=" N TYR B 390 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE B 341 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 392 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 339 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 346 through 349 Processing sheet with id= E, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.181A pdb=" N TYR C 390 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE C 341 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 392 " --> pdb=" O TYR C 339 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR C 339 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 346 through 349 Processing sheet with id= G, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.181A pdb=" N TYR D 390 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE D 341 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU D 392 " --> pdb=" O TYR D 339 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR D 339 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 346 through 349 656 hydrogen bonds defined for protein. 1944 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: 3.63 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1944 1.30 - 1.43: 3365 1.43 - 1.56: 7871 1.56 - 1.68: 48 1.68 - 1.81: 48 Bond restraints: 13276 Sorted by residual: bond pdb=" C09 D21 B 504 " pdb=" C10 D21 B 504 " ideal model delta sigma weight residual 1.543 1.306 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C09 D21 A 503 " pdb=" C10 D21 A 503 " ideal model delta sigma weight residual 1.543 1.307 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C09 D21 C 504 " pdb=" C10 D21 C 504 " ideal model delta sigma weight residual 1.543 1.307 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C09 D21 D 505 " pdb=" C10 D21 D 505 " ideal model delta sigma weight residual 1.543 1.307 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C08 D21 D 508 " pdb=" C09 D21 D 508 " ideal model delta sigma weight residual 1.532 1.304 0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 13271 not shown) Histogram of bond angle deviations from ideal: 98.20 - 109.98: 2372 109.98 - 121.76: 13164 121.76 - 133.55: 2352 133.55 - 145.33: 28 145.33 - 157.12: 32 Bond angle restraints: 17948 Sorted by residual: angle pdb=" C07 D21 B 507 " pdb=" C08 D21 B 507 " pdb=" C09 D21 B 507 " ideal model delta sigma weight residual 109.44 157.12 -47.68 3.00e+00 1.11e-01 2.53e+02 angle pdb=" C07 D21 D 508 " pdb=" C08 D21 D 508 " pdb=" C09 D21 D 508 " ideal model delta sigma weight residual 109.44 157.10 -47.66 3.00e+00 1.11e-01 2.52e+02 angle pdb=" C07 D21 C 507 " pdb=" C08 D21 C 507 " pdb=" C09 D21 C 507 " ideal model delta sigma weight residual 109.44 157.06 -47.62 3.00e+00 1.11e-01 2.52e+02 angle pdb=" C07 D21 A 506 " pdb=" C08 D21 A 506 " pdb=" C09 D21 A 506 " ideal model delta sigma weight residual 109.44 157.04 -47.60 3.00e+00 1.11e-01 2.52e+02 angle pdb=" C08 D21 A 506 " pdb=" C09 D21 A 506 " pdb=" C10 D21 A 506 " ideal model delta sigma weight residual 109.52 155.27 -45.75 3.00e+00 1.11e-01 2.33e+02 ... (remaining 17943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 7664 31.61 - 63.22: 352 63.22 - 94.83: 32 94.83 - 126.44: 8 126.44 - 158.05: 16 Dihedral angle restraints: 8072 sinusoidal: 3472 harmonic: 4600 Sorted by residual: dihedral pdb=" C5' CMP D 502 " pdb=" O5' CMP D 502 " pdb=" P CMP D 502 " pdb=" O1P CMP D 502 " ideal model delta sinusoidal sigma weight residual 60.00 172.83 -112.83 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' CMP C 502 " pdb=" O5' CMP C 502 " pdb=" P CMP C 502 " pdb=" O1P CMP C 502 " ideal model delta sinusoidal sigma weight residual 60.00 172.83 -112.83 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 172.83 -112.83 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 8069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1477 0.062 - 0.125: 461 0.125 - 0.187: 95 0.187 - 0.250: 51 0.250 - 0.312: 8 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CA LEU B 373 " pdb=" N LEU B 373 " pdb=" C LEU B 373 " pdb=" CB LEU B 373 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA LEU C 373 " pdb=" N LEU C 373 " pdb=" C LEU C 373 " pdb=" CB LEU C 373 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA LEU A 373 " pdb=" N LEU A 373 " pdb=" C LEU A 373 " pdb=" CB LEU A 373 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 2089 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 269 " 0.022 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY C 269 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY C 269 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR C 270 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 269 " 0.022 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY D 269 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY D 269 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR D 270 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 269 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C GLY A 269 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY A 269 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR A 270 " 0.025 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1139 2.74 - 3.28: 13174 3.28 - 3.82: 21077 3.82 - 4.36: 25853 4.36 - 4.90: 42199 Nonbonded interactions: 103442 Sorted by model distance: nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.198 2.440 nonbonded pdb=" O SER A 220 " pdb=" OG SER A 223 " model vdw 2.302 2.440 nonbonded pdb=" O SER C 220 " pdb=" OG SER C 223 " model vdw 2.302 2.440 nonbonded pdb=" O SER B 220 " pdb=" OG SER B 223 " model vdw 2.302 2.440 nonbonded pdb=" O SER D 220 " pdb=" OG SER D 223 " model vdw 2.303 2.440 ... (remaining 103437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 418 or resid 503 through 504 or (resid 506 and \ (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) selection = (chain 'B' and (resid 10 through 418 or (resid 503 and (name C02 or name C03 or \ name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13 or name C14 or name C15)) or (resid 504 and \ (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C \ 08 or name C09 or name C10 or name C11 or name C12 or name C13)) or (resid 506 a \ nd (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) selection = (chain 'C' and (resid 10 through 418 or (resid 503 and (name C02 or name C03 or \ name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13 or name C14 or name C15)) or (resid 504 and \ (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C \ 08 or name C09 or name C10 or name C11 or name C12 or name C13)) or (resid 506 a \ nd (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) selection = (chain 'D' and (resid 10 through 418 or (resid 503 and (name C02 or name C03 or \ name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13 or name C14 or name C15)) or (resid 504 and \ (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C \ 08 or name C09 or name C10 or name C11 or name C12 or name C13)) or (resid 506 a \ nd (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.120 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 37.790 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.010 0.237 13276 Z= 0.662 Angle : 2.228 47.676 17948 Z= 0.984 Chirality : 0.070 0.312 2092 Planarity : 0.008 0.080 2176 Dihedral : 18.817 158.050 5104 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.08 % Allowed : 3.35 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1548 helix: 1.16 (0.17), residues: 980 sheet: 0.27 (0.47), residues: 88 loop : -0.72 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.005 TRP A 18 HIS 0.006 0.002 HIS D 232 PHE 0.026 0.003 PHE A 309 TYR 0.023 0.003 TYR D 25 ARG 0.008 0.001 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 2 residues processed: 154 average time/residue: 1.4044 time to fit residues: 234.3857 Evaluate side-chains 44 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain D residue 404 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 0.0370 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13276 Z= 0.215 Angle : 0.759 10.186 17948 Z= 0.351 Chirality : 0.039 0.136 2092 Planarity : 0.005 0.053 2176 Dihedral : 18.303 155.145 2140 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.38 % Allowed : 9.38 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.22), residues: 1548 helix: 1.30 (0.17), residues: 1024 sheet: 0.34 (0.49), residues: 96 loop : -0.68 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 18 HIS 0.003 0.001 HIS A 232 PHE 0.010 0.001 PHE C 242 TYR 0.014 0.001 TYR C 170 ARG 0.009 0.000 ARG C 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 48 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7735 (pp) outliers start: 32 outliers final: 3 residues processed: 75 average time/residue: 1.6509 time to fit residues: 134.3252 Evaluate side-chains 36 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain D residue 404 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13276 Z= 0.395 Angle : 0.786 10.550 17948 Z= 0.378 Chirality : 0.043 0.169 2092 Planarity : 0.005 0.042 2176 Dihedral : 16.208 129.357 2138 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.75 % Allowed : 11.76 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1548 helix: 1.41 (0.17), residues: 988 sheet: 0.38 (0.56), residues: 96 loop : -0.79 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 18 HIS 0.003 0.001 HIS C 316 PHE 0.014 0.002 PHE A 242 TYR 0.033 0.002 TYR A 211 ARG 0.011 0.001 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 41 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 5 residues processed: 70 average time/residue: 1.4835 time to fit residues: 113.4208 Evaluate side-chains 33 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 210 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13276 Z= 0.198 Angle : 0.665 8.875 17948 Z= 0.310 Chirality : 0.038 0.199 2092 Planarity : 0.004 0.040 2176 Dihedral : 15.084 131.271 2136 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.71 % Allowed : 14.81 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.22), residues: 1548 helix: 1.72 (0.17), residues: 984 sheet: 0.28 (0.56), residues: 96 loop : -0.64 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.002 0.001 HIS D 281 PHE 0.010 0.001 PHE D 386 TYR 0.012 0.001 TYR A 170 ARG 0.004 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 33 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7809 (t80) outliers start: 23 outliers final: 4 residues processed: 53 average time/residue: 1.1764 time to fit residues: 70.1251 Evaluate side-chains 32 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 213 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 2 optimal weight: 0.0670 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13276 Z= 0.239 Angle : 0.667 14.629 17948 Z= 0.310 Chirality : 0.039 0.169 2092 Planarity : 0.004 0.040 2176 Dihedral : 14.323 131.419 2136 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.83 % Allowed : 14.58 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1548 helix: 1.78 (0.17), residues: 984 sheet: 0.23 (0.56), residues: 96 loop : -0.57 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.002 0.001 HIS B 292 PHE 0.017 0.001 PHE D 386 TYR 0.011 0.001 TYR B 175 ARG 0.002 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 33 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 MET cc_start: 0.6600 (pmm) cc_final: 0.6265 (pmt) outliers start: 38 outliers final: 7 residues processed: 66 average time/residue: 0.9883 time to fit residues: 74.2755 Evaluate side-chains 35 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 210 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 10.0000 chunk 125 optimal weight: 0.0030 chunk 69 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13276 Z= 0.168 Angle : 0.677 11.022 17948 Z= 0.308 Chirality : 0.039 0.185 2092 Planarity : 0.004 0.033 2176 Dihedral : 13.608 131.716 2136 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.93 % Allowed : 16.44 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.23), residues: 1548 helix: 1.88 (0.17), residues: 984 sheet: 0.20 (0.55), residues: 96 loop : -0.54 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 264 HIS 0.001 0.000 HIS C 281 PHE 0.018 0.001 PHE B 386 TYR 0.010 0.001 TYR B 128 ARG 0.003 0.000 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 35 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 5 residues processed: 60 average time/residue: 1.2799 time to fit residues: 85.4204 Evaluate side-chains 31 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 407 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13276 Z= 0.193 Angle : 0.667 9.718 17948 Z= 0.307 Chirality : 0.038 0.156 2092 Planarity : 0.004 0.036 2176 Dihedral : 13.241 132.541 2136 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.64 % Allowed : 16.67 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1548 helix: 1.97 (0.17), residues: 984 sheet: 0.25 (0.55), residues: 96 loop : -0.55 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 18 HIS 0.001 0.001 HIS C 281 PHE 0.017 0.001 PHE C 397 TYR 0.010 0.001 TYR C 170 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 29 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7159 (t80) outliers start: 22 outliers final: 7 residues processed: 49 average time/residue: 1.1307 time to fit residues: 62.6320 Evaluate side-chains 34 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 329 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 0.0370 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.0470 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13276 Z= 0.185 Angle : 0.672 10.844 17948 Z= 0.304 Chirality : 0.038 0.168 2092 Planarity : 0.004 0.036 2176 Dihedral : 12.850 130.542 2136 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.19 % Allowed : 17.19 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.23), residues: 1548 helix: 2.02 (0.17), residues: 984 sheet: 0.29 (0.55), residues: 96 loop : -0.55 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 18 HIS 0.002 0.000 HIS C 281 PHE 0.016 0.001 PHE D 386 TYR 0.009 0.001 TYR A 128 ARG 0.002 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 30 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8018 (p) REVERT: A 386 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7279 (t80) outliers start: 16 outliers final: 6 residues processed: 45 average time/residue: 1.3119 time to fit residues: 66.0104 Evaluate side-chains 34 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 329 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 144 optimal weight: 0.1980 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 0.0030 chunk 110 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13276 Z= 0.161 Angle : 0.677 11.708 17948 Z= 0.302 Chirality : 0.038 0.172 2092 Planarity : 0.004 0.034 2176 Dihedral : 12.374 131.313 2136 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.04 % Allowed : 17.19 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.23), residues: 1548 helix: 2.07 (0.17), residues: 988 sheet: 0.23 (0.55), residues: 96 loop : -0.46 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 155 HIS 0.002 0.000 HIS C 281 PHE 0.018 0.001 PHE D 386 TYR 0.010 0.001 TYR B 25 ARG 0.002 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 29 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8058 (p) REVERT: B 22 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7994 (p) outliers start: 14 outliers final: 5 residues processed: 42 average time/residue: 1.5875 time to fit residues: 73.4711 Evaluate side-chains 32 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 329 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13276 Z= 0.217 Angle : 0.694 11.951 17948 Z= 0.314 Chirality : 0.039 0.149 2092 Planarity : 0.004 0.035 2176 Dihedral : 12.432 131.571 2136 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.74 % Allowed : 17.63 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.23), residues: 1548 helix: 2.07 (0.17), residues: 988 sheet: 0.25 (0.55), residues: 96 loop : -0.63 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.002 0.001 HIS A 281 PHE 0.016 0.001 PHE A 386 TYR 0.010 0.001 TYR A 170 ARG 0.002 0.000 ARG B 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 26 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8103 (p) REVERT: A 386 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7279 (t80) outliers start: 10 outliers final: 6 residues processed: 36 average time/residue: 1.3310 time to fit residues: 53.9578 Evaluate side-chains 34 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 329 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.083877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.058338 restraints weight = 52223.729| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.03 r_work: 0.3149 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13276 Z= 0.166 Angle : 0.676 11.732 17948 Z= 0.302 Chirality : 0.038 0.154 2092 Planarity : 0.004 0.034 2176 Dihedral : 12.186 131.629 2136 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.89 % Allowed : 17.49 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.23), residues: 1548 helix: 2.12 (0.17), residues: 988 sheet: 0.25 (0.55), residues: 96 loop : -0.59 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 18 HIS 0.002 0.000 HIS C 281 PHE 0.013 0.001 PHE C 397 TYR 0.009 0.001 TYR C 170 ARG 0.001 0.000 ARG B 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3258.21 seconds wall clock time: 59 minutes 38.71 seconds (3578.71 seconds total)