Starting phenix.real_space_refine on Tue Nov 18 23:58:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0o_22605/11_2025/7k0o_22605.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0o_22605/11_2025/7k0o_22605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0o_22605/11_2025/7k0o_22605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0o_22605/11_2025/7k0o_22605.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0o_22605/11_2025/7k0o_22605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0o_22605/11_2025/7k0o_22605.cif" } resolution = 3.1 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= 0.101 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 100 5.16 5 C 11986 2.51 5 N 3116 2.21 5 O 3352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18558 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'PLP': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Restraints were copied for chains: E, F, G, H Time building chain proxies: 6.36, per 1000 atoms: 0.34 Number of scatterers: 18558 At special positions: 0 Unit cell: (149.745, 135.675, 118.59, 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 100 16.00 P 4 15.00 O 3352 8.00 N 3116 7.00 C 11986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 922.7 milliseconds 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 14 sheets defined 54.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.520A pdb=" N ALA A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.713A pdb=" N LEU A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.693A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.666A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.191A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.749A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 removed outlier: 3.535A pdb=" N HIS A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.678A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 360 through 378 removed outlier: 4.298A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.557A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 Processing helix chain 'B' and resid 67 through 94 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.742A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.708A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.887A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.057A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 55 Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'D' and resid 11 through 19 removed outlier: 4.704A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 Processing helix chain 'D' and resid 44 through 66 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 96 through 117 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 120 through 136 Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.567A pdb=" N GLY D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 150 " --> pdb=" O ILE D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 150' Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.520A pdb=" N ALA E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 removed outlier: 3.713A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 64 removed outlier: 3.694A pdb=" N TRP E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.667A pdb=" N LEU E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 179 removed outlier: 4.191A pdb=" N ILE E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 213 through 231 removed outlier: 3.749A pdb=" N LEU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 288 through 294 removed outlier: 3.535A pdb=" N HIS E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 332 removed outlier: 4.679A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 359 Processing helix chain 'E' and resid 360 through 378 removed outlier: 4.298A pdb=" N ALA E 364 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 422 removed outlier: 3.557A pdb=" N ASP E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 473 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 30 through 55 Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.704A pdb=" N MET H 17 " --> pdb=" O THR H 14 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER H 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 39 Processing helix chain 'H' and resid 44 through 66 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 90 through 93 Processing helix chain 'H' and resid 96 through 117 Proline residue: H 106 - end of helix Processing helix chain 'H' and resid 120 through 136 Processing helix chain 'H' and resid 146 through 150 removed outlier: 3.567A pdb=" N GLY H 149 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 150 " --> pdb=" O ILE H 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 146 through 150' Processing helix chain 'F' and resid 67 through 94 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 116 through 119 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 130 through 134 Processing helix chain 'F' and resid 186 through 200 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.741A pdb=" N GLU F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 250 removed outlier: 3.708A pdb=" N ASN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 263 through 273 Processing helix chain 'F' and resid 284 through 299 Processing helix chain 'F' and resid 326 through 338 Processing helix chain 'F' and resid 358 through 364 Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 391 through 402 Processing helix chain 'F' and resid 402 through 407 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 433 through 455 removed outlier: 3.887A pdb=" N VAL F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 4.058A pdb=" N GLY F 480 " --> pdb=" O PRO F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 536 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.328A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 164 removed outlier: 7.057A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.208A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.986A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.646A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.820A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 94 through 95 Processing sheet with id=AA9, first strand: chain 'E' and resid 101 through 102 removed outlier: 6.329A pdb=" N ILE E 101 " --> pdb=" O ALA E 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 160 through 164 removed outlier: 7.058A pdb=" N ILE E 271 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER E 304 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU E 273 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ASN E 306 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG E 240 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE E 272 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU E 274 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL E 244 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP E 188 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU E 245 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE E 209 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL E 187 " --> pdb=" O PHE E 209 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 383 through 386 removed outlier: 4.207A pdb=" N THR E 427 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 145 through 152 removed outlier: 6.987A pdb=" N VAL F 146 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE F 167 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE F 148 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN F 165 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU F 150 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY F 492 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE F 171 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.646A pdb=" N ILE F 310 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.820A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2727 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: 4.15 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 4454 1.45 - 1.57: 10754 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18946 Sorted by residual: bond pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" O12 POV F 601 " pdb=" P POV F 601 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O12 POV B 602 " pdb=" P POV B 602 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CA PRO B 413 " pdb=" C PRO B 413 " ideal model delta sigma weight residual 1.517 1.547 -0.029 9.30e-03 1.16e+04 1.00e+01 ... (remaining 18941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 25475 3.54 - 7.09: 119 7.09 - 10.63: 6 10.63 - 14.17: 0 14.17 - 17.72: 4 Bond angle restraints: 25604 Sorted by residual: angle pdb=" C28 POV D 901 " pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 127.79 110.07 17.72 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C28 POV H 901 " pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 127.79 110.08 17.71 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C29 POV H 901 " pdb="C210 POV H 901 " pdb="C211 POV H 901 " ideal model delta sigma weight residual 127.67 110.03 17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" C29 POV D 901 " pdb="C210 POV D 901 " pdb="C211 POV D 901 " ideal model delta sigma weight residual 127.67 110.05 17.62 3.00e+00 1.11e-01 3.45e+01 angle pdb=" CA PRO F 413 " pdb=" C PRO F 413 " pdb=" N PRO F 414 " ideal model delta sigma weight residual 117.93 124.26 -6.33 1.20e+00 6.94e-01 2.78e+01 ... (remaining 25599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10442 17.80 - 35.60: 746 35.60 - 53.40: 152 53.40 - 71.20: 12 71.20 - 88.99: 14 Dihedral angle restraints: 11366 sinusoidal: 4580 harmonic: 6786 Sorted by residual: dihedral pdb=" CA LYS D 79 " pdb=" C LYS D 79 " pdb=" N ALA D 80 " pdb=" CA ALA D 80 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LYS H 79 " pdb=" C LYS H 79 " pdb=" N ALA H 80 " pdb=" CA ALA H 80 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA VAL D 93 " pdb=" C VAL D 93 " pdb=" N GLN D 94 " pdb=" CA GLN D 94 " ideal model delta harmonic sigma weight residual 180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 11363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1882 0.038 - 0.076: 683 0.076 - 0.114: 227 0.114 - 0.152: 56 0.152 - 0.190: 6 Chirality restraints: 2854 Sorted by residual: chirality pdb=" CA THR H 105 " pdb=" N THR H 105 " pdb=" C THR H 105 " pdb=" CB THR H 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA THR D 105 " pdb=" N THR D 105 " pdb=" C THR D 105 " pdb=" CB THR D 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA PRO B 413 " pdb=" N PRO B 413 " pdb=" C PRO B 413 " pdb=" CB PRO B 413 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 2851 not shown) Planarity restraints: 3244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 469 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO F 470 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 470 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 470 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO B 470 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 502 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.027 5.00e-02 4.00e+02 ... (remaining 3241 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 516 2.71 - 3.26: 18077 3.26 - 3.80: 28687 3.80 - 4.35: 37141 4.35 - 4.90: 65235 Nonbonded interactions: 149656 Sorted by model distance: nonbonded pdb=" O VAL D 10 " pdb=" OG1 THR D 74 " model vdw 2.161 3.040 nonbonded pdb=" O VAL H 10 " pdb=" OG1 THR H 74 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" OD1 ASP B 522 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR F 448 " pdb=" OD1 ASP F 522 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.266 3.040 ... (remaining 149651 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 53 through 544) selection = (chain 'F' and resid 53 through 544) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 1 through 902) } 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.600 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 0.190 18948 Z= 0.261 Angle : 0.745 17.715 25604 Z= 0.411 Chirality : 0.045 0.190 2854 Planarity : 0.005 0.050 3244 Dihedral : 13.026 88.995 7022 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.21 % Allowed : 0.67 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2326 helix: 1.76 (0.15), residues: 1092 sheet: -0.25 (0.35), residues: 226 loop : -0.38 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 459 TYR 0.029 0.002 TYR E 166 PHE 0.022 0.002 PHE E 168 TRP 0.014 0.001 TRP G 32 HIS 0.007 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00560 (18946) covalent geometry : angle 0.74500 (25604) hydrogen bonds : bond 0.13470 ( 953) hydrogen bonds : angle 5.86448 ( 2727) Misc. bond : bond 0.02896 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 0.987 Fit side-chains REVERT: A 214 MET cc_start: 0.6571 (mmt) cc_final: 0.6189 (mmt) REVERT: B 285 MET cc_start: 0.8032 (mmt) cc_final: 0.7384 (mmt) REVERT: E 214 MET cc_start: 0.6508 (mmt) cc_final: 0.6166 (mmt) REVERT: F 285 MET cc_start: 0.7993 (mmt) cc_final: 0.7333 (mmt) outliers start: 4 outliers final: 0 residues processed: 233 average time/residue: 0.1694 time to fit residues: 58.4599 Evaluate side-chains 193 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.0570 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112762 restraints weight = 22485.950| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.71 r_work: 0.3124 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18948 Z= 0.128 Angle : 0.515 7.142 25604 Z= 0.277 Chirality : 0.042 0.179 2854 Planarity : 0.005 0.047 3244 Dihedral : 6.896 74.111 2710 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.72 % Allowed : 6.36 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.17), residues: 2326 helix: 1.98 (0.15), residues: 1134 sheet: -0.09 (0.35), residues: 226 loop : -0.21 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.014 0.001 TYR D 26 PHE 0.016 0.001 PHE E 168 TRP 0.013 0.001 TRP G 32 HIS 0.005 0.001 HIS H 143 Details of bonding type rmsd covalent geometry : bond 0.00289 (18946) covalent geometry : angle 0.51545 (25604) hydrogen bonds : bond 0.04599 ( 953) hydrogen bonds : angle 4.61027 ( 2727) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.730 Fit side-chains REVERT: A 55 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8370 (pttp) REVERT: A 150 ASP cc_start: 0.7328 (m-30) cc_final: 0.7107 (m-30) REVERT: B 285 MET cc_start: 0.8198 (mmt) cc_final: 0.7661 (mmt) REVERT: B 423 MET cc_start: 0.8504 (ttm) cc_final: 0.8247 (mtt) REVERT: D 79 LYS cc_start: 0.8390 (mmmm) cc_final: 0.7880 (tppt) REVERT: D 89 MET cc_start: 0.8680 (ttm) cc_final: 0.8460 (ttm) REVERT: E 55 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8347 (pttp) REVERT: E 150 ASP cc_start: 0.7334 (m-30) cc_final: 0.7123 (m-30) REVERT: H 79 LYS cc_start: 0.8375 (mmmm) cc_final: 0.7812 (tppt) REVERT: H 89 MET cc_start: 0.8681 (ttm) cc_final: 0.8443 (ttm) REVERT: F 285 MET cc_start: 0.8201 (mmt) cc_final: 0.7644 (mmt) REVERT: F 423 MET cc_start: 0.8499 (ttm) cc_final: 0.8237 (mtt) outliers start: 14 outliers final: 8 residues processed: 215 average time/residue: 0.1662 time to fit residues: 52.9975 Evaluate side-chains 207 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 245 ASN E 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.135894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103683 restraints weight = 22923.221| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.16 r_work: 0.3057 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18948 Z= 0.174 Angle : 0.538 6.241 25604 Z= 0.288 Chirality : 0.044 0.176 2854 Planarity : 0.005 0.050 3244 Dihedral : 6.607 72.130 2710 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.09 % Allowed : 8.07 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2326 helix: 1.92 (0.15), residues: 1124 sheet: -0.14 (0.35), residues: 224 loop : -0.37 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 136 TYR 0.015 0.002 TYR D 26 PHE 0.016 0.002 PHE E 209 TRP 0.014 0.001 TRP G 32 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00420 (18946) covalent geometry : angle 0.53834 (25604) hydrogen bonds : bond 0.04929 ( 953) hydrogen bonds : angle 4.51348 ( 2727) Misc. bond : bond 0.00094 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.6994 (m-30) cc_final: 0.6782 (m-30) REVERT: B 281 LYS cc_start: 0.8502 (mtpt) cc_final: 0.7688 (mptt) REVERT: B 285 MET cc_start: 0.7833 (mmt) cc_final: 0.7092 (mmt) REVERT: H 113 THR cc_start: 0.7819 (t) cc_final: 0.7528 (p) REVERT: F 281 LYS cc_start: 0.8499 (mtpt) cc_final: 0.7682 (mptt) REVERT: F 285 MET cc_start: 0.7800 (mmt) cc_final: 0.7070 (mmt) outliers start: 21 outliers final: 13 residues processed: 215 average time/residue: 0.1581 time to fit residues: 51.0160 Evaluate side-chains 206 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 192 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103670 restraints weight = 22995.247| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.13 r_work: 0.3051 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18948 Z= 0.186 Angle : 0.547 7.567 25604 Z= 0.293 Chirality : 0.044 0.174 2854 Planarity : 0.005 0.050 3244 Dihedral : 6.579 74.130 2710 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.81 % Allowed : 9.46 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2326 helix: 1.87 (0.15), residues: 1120 sheet: -0.24 (0.34), residues: 224 loop : -0.45 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 459 TYR 0.015 0.002 TYR D 26 PHE 0.017 0.002 PHE E 209 TRP 0.016 0.001 TRP C 32 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00453 (18946) covalent geometry : angle 0.54731 (25604) hydrogen bonds : bond 0.04934 ( 953) hydrogen bonds : angle 4.47248 ( 2727) Misc. bond : bond 0.00100 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7450 (tp40) cc_final: 0.6901 (tt0) REVERT: B 126 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8279 (tt) REVERT: B 281 LYS cc_start: 0.8415 (mtpt) cc_final: 0.7632 (mptt) REVERT: D 79 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8156 (tttm) REVERT: E 407 GLN cc_start: 0.7439 (tp40) cc_final: 0.6896 (tt0) REVERT: H 79 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8178 (tttm) REVERT: F 126 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8275 (tt) REVERT: F 281 LYS cc_start: 0.8432 (mtpt) cc_final: 0.7633 (mptt) outliers start: 35 outliers final: 22 residues processed: 223 average time/residue: 0.1630 time to fit residues: 54.8542 Evaluate side-chains 216 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 141 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 231 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 428 GLN E 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109969 restraints weight = 22626.573| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.87 r_work: 0.3123 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18948 Z= 0.122 Angle : 0.486 7.845 25604 Z= 0.262 Chirality : 0.041 0.165 2854 Planarity : 0.005 0.050 3244 Dihedral : 6.247 73.782 2710 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.45 % Allowed : 10.96 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.31 (0.17), residues: 2326 helix: 2.04 (0.15), residues: 1134 sheet: 0.15 (0.32), residues: 246 loop : -0.33 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 459 TYR 0.012 0.001 TYR H 26 PHE 0.014 0.001 PHE E 209 TRP 0.014 0.001 TRP G 32 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00281 (18946) covalent geometry : angle 0.48645 (25604) hydrogen bonds : bond 0.04090 ( 953) hydrogen bonds : angle 4.33437 ( 2727) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7715 (tp40) cc_final: 0.7164 (tt0) REVERT: B 285 MET cc_start: 0.8099 (mmt) cc_final: 0.7586 (mmt) REVERT: D 79 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8358 (tttm) REVERT: D 113 THR cc_start: 0.8090 (t) cc_final: 0.7764 (p) REVERT: D 119 TYR cc_start: 0.7255 (m-80) cc_final: 0.6731 (m-80) REVERT: E 407 GLN cc_start: 0.7705 (tp40) cc_final: 0.7146 (tt0) REVERT: H 79 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8375 (tttm) REVERT: H 113 THR cc_start: 0.8015 (t) cc_final: 0.7702 (p) REVERT: F 285 MET cc_start: 0.8102 (mmt) cc_final: 0.7593 (mmt) outliers start: 28 outliers final: 18 residues processed: 222 average time/residue: 0.1582 time to fit residues: 53.0400 Evaluate side-chains 209 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 0.0370 chunk 223 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN F 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109917 restraints weight = 22562.933| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.86 r_work: 0.3101 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18948 Z= 0.125 Angle : 0.489 8.774 25604 Z= 0.262 Chirality : 0.041 0.164 2854 Planarity : 0.005 0.050 3244 Dihedral : 6.179 74.679 2710 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.55 % Allowed : 12.10 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.17), residues: 2326 helix: 2.07 (0.15), residues: 1136 sheet: 0.23 (0.32), residues: 246 loop : -0.33 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 459 TYR 0.012 0.001 TYR D 26 PHE 0.017 0.001 PHE H 115 TRP 0.014 0.001 TRP G 32 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00289 (18946) covalent geometry : angle 0.48875 (25604) hydrogen bonds : bond 0.04072 ( 953) hydrogen bonds : angle 4.29972 ( 2727) Misc. bond : bond 0.00074 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.707 Fit side-chains REVERT: A 407 GLN cc_start: 0.7620 (tp40) cc_final: 0.7051 (tt0) REVERT: B 126 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8586 (tt) REVERT: B 285 MET cc_start: 0.8059 (mmt) cc_final: 0.7587 (mmt) REVERT: D 79 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8394 (tttm) REVERT: D 89 MET cc_start: 0.8636 (ttm) cc_final: 0.8404 (ttm) REVERT: D 113 THR cc_start: 0.8095 (t) cc_final: 0.7764 (p) REVERT: E 407 GLN cc_start: 0.7620 (tp40) cc_final: 0.7042 (tt0) REVERT: H 79 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8420 (tttm) REVERT: H 113 THR cc_start: 0.8023 (t) cc_final: 0.7702 (p) REVERT: F 126 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8583 (tt) REVERT: F 285 MET cc_start: 0.8049 (mmt) cc_final: 0.7573 (mmt) outliers start: 30 outliers final: 19 residues processed: 222 average time/residue: 0.1605 time to fit residues: 53.7439 Evaluate side-chains 211 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 209 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 120 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN E 428 GLN F 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110325 restraints weight = 22866.718| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.74 r_work: 0.3118 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18948 Z= 0.145 Angle : 0.512 8.960 25604 Z= 0.272 Chirality : 0.043 0.172 2854 Planarity : 0.005 0.051 3244 Dihedral : 6.218 74.990 2710 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.55 % Allowed : 12.51 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.17), residues: 2326 helix: 2.03 (0.15), residues: 1138 sheet: 0.00 (0.35), residues: 220 loop : -0.41 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 459 TYR 0.013 0.001 TYR H 26 PHE 0.015 0.001 PHE E 168 TRP 0.014 0.001 TRP G 32 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00345 (18946) covalent geometry : angle 0.51210 (25604) hydrogen bonds : bond 0.04319 ( 953) hydrogen bonds : angle 4.34304 ( 2727) Misc. bond : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.797 Fit side-chains REVERT: B 126 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8610 (tt) REVERT: B 281 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8408 (mptt) REVERT: B 285 MET cc_start: 0.8135 (mmt) cc_final: 0.7729 (mmt) REVERT: D 79 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8352 (tttm) REVERT: E 407 GLN cc_start: 0.7648 (tp40) cc_final: 0.7446 (tp40) REVERT: H 79 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8475 (tttm) REVERT: H 113 THR cc_start: 0.8054 (t) cc_final: 0.7724 (p) REVERT: F 126 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8615 (tt) REVERT: F 281 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8402 (mptt) REVERT: F 285 MET cc_start: 0.8090 (mmt) cc_final: 0.7663 (mmt) outliers start: 30 outliers final: 20 residues processed: 221 average time/residue: 0.1582 time to fit residues: 52.5057 Evaluate side-chains 216 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 226 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN F 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118317 restraints weight = 22407.474| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.60 r_work: 0.3104 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18948 Z= 0.112 Angle : 0.479 8.182 25604 Z= 0.257 Chirality : 0.041 0.162 2854 Planarity : 0.004 0.049 3244 Dihedral : 6.068 74.465 2710 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.65 % Allowed : 12.77 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.38 (0.17), residues: 2326 helix: 2.15 (0.15), residues: 1138 sheet: 0.09 (0.35), residues: 220 loop : -0.35 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 459 TYR 0.011 0.001 TYR H 26 PHE 0.019 0.001 PHE H 115 TRP 0.014 0.001 TRP G 32 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00253 (18946) covalent geometry : angle 0.47930 (25604) hydrogen bonds : bond 0.03797 ( 953) hydrogen bonds : angle 4.26647 ( 2727) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.898 Fit side-chains REVERT: A 407 GLN cc_start: 0.7671 (tp40) cc_final: 0.7313 (tt0) REVERT: B 126 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8578 (tt) REVERT: B 281 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8343 (mmtt) REVERT: B 285 MET cc_start: 0.8059 (mmt) cc_final: 0.7660 (mmt) REVERT: D 79 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8342 (tttm) REVERT: D 113 THR cc_start: 0.8085 (t) cc_final: 0.7767 (p) REVERT: E 407 GLN cc_start: 0.7653 (tp40) cc_final: 0.7100 (tt0) REVERT: H 79 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8339 (tttm) REVERT: H 113 THR cc_start: 0.8060 (t) cc_final: 0.7754 (p) REVERT: F 126 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8579 (tt) REVERT: F 281 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8338 (mmtt) REVERT: F 285 MET cc_start: 0.8055 (mmt) cc_final: 0.7649 (mmt) outliers start: 32 outliers final: 20 residues processed: 221 average time/residue: 0.1589 time to fit residues: 52.6208 Evaluate side-chains 213 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 0 optimal weight: 50.0000 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 100 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN F 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117245 restraints weight = 22609.419| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.41 r_work: 0.3109 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18948 Z= 0.141 Angle : 0.512 11.212 25604 Z= 0.274 Chirality : 0.043 0.175 2854 Planarity : 0.005 0.057 3244 Dihedral : 6.157 75.628 2710 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.45 % Allowed : 13.08 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.17), residues: 2326 helix: 2.08 (0.15), residues: 1142 sheet: -0.00 (0.35), residues: 222 loop : -0.44 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.012 0.001 TYR D 26 PHE 0.016 0.001 PHE E 168 TRP 0.013 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00334 (18946) covalent geometry : angle 0.51211 (25604) hydrogen bonds : bond 0.04203 ( 953) hydrogen bonds : angle 4.30819 ( 2727) Misc. bond : bond 0.00083 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.920 Fit side-chains REVERT: A 407 GLN cc_start: 0.7711 (tp40) cc_final: 0.7341 (tt0) REVERT: B 126 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8591 (tt) REVERT: B 281 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8525 (mptt) REVERT: B 285 MET cc_start: 0.8042 (mmt) cc_final: 0.7682 (mmt) REVERT: D 79 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8296 (tttm) REVERT: D 113 THR cc_start: 0.8126 (t) cc_final: 0.7797 (p) REVERT: E 407 GLN cc_start: 0.7639 (tp40) cc_final: 0.7157 (tt0) REVERT: H 76 ASP cc_start: 0.8860 (p0) cc_final: 0.8584 (p0) REVERT: H 79 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8231 (tttm) REVERT: H 113 THR cc_start: 0.8079 (t) cc_final: 0.7757 (p) REVERT: F 126 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8587 (tt) REVERT: F 281 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8519 (mptt) REVERT: F 285 MET cc_start: 0.8046 (mmt) cc_final: 0.7683 (mmt) outliers start: 28 outliers final: 22 residues processed: 220 average time/residue: 0.1620 time to fit residues: 53.5372 Evaluate side-chains 221 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 504 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 188 optimal weight: 0.8980 chunk 122 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.0370 chunk 114 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 12 optimal weight: 0.0470 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN F 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119710 restraints weight = 22433.202| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.62 r_work: 0.3179 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18948 Z= 0.092 Angle : 0.460 10.061 25604 Z= 0.247 Chirality : 0.040 0.159 2854 Planarity : 0.004 0.056 3244 Dihedral : 5.887 73.246 2710 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.14 % Allowed : 13.50 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.17), residues: 2326 helix: 2.29 (0.15), residues: 1138 sheet: 0.22 (0.33), residues: 250 loop : -0.27 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.010 0.001 TYR H 26 PHE 0.020 0.001 PHE H 115 TRP 0.015 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00191 (18946) covalent geometry : angle 0.46012 (25604) hydrogen bonds : bond 0.03274 ( 953) hydrogen bonds : angle 4.18782 ( 2727) Misc. bond : bond 0.00048 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.740 Fit side-chains REVERT: B 126 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8566 (tt) REVERT: B 281 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8450 (mmtt) REVERT: B 285 MET cc_start: 0.8017 (mmt) cc_final: 0.7700 (mmt) REVERT: C 13 MET cc_start: 0.6873 (tpt) cc_final: 0.5851 (mpp) REVERT: D 79 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8230 (tttm) REVERT: D 113 THR cc_start: 0.8036 (t) cc_final: 0.7739 (p) REVERT: E 407 GLN cc_start: 0.7676 (tp40) cc_final: 0.7183 (tt0) REVERT: G 13 MET cc_start: 0.6882 (tpt) cc_final: 0.5887 (mpp) REVERT: H 76 ASP cc_start: 0.8869 (p0) cc_final: 0.8585 (p0) REVERT: H 79 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8124 (tttm) REVERT: H 113 THR cc_start: 0.8019 (t) cc_final: 0.7726 (p) REVERT: F 126 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8568 (tt) REVERT: F 281 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8441 (mmtt) REVERT: F 285 MET cc_start: 0.8021 (mmt) cc_final: 0.7696 (mmt) outliers start: 22 outliers final: 16 residues processed: 234 average time/residue: 0.1576 time to fit residues: 55.3711 Evaluate side-chains 221 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 101 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 217 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 176 optimal weight: 0.0040 chunk 85 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119428 restraints weight = 22594.411| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.55 r_work: 0.3133 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18948 Z= 0.114 Angle : 0.481 8.293 25604 Z= 0.258 Chirality : 0.042 0.187 2854 Planarity : 0.005 0.061 3244 Dihedral : 5.935 75.639 2710 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.50 % Allowed : 13.39 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.17), residues: 2326 helix: 2.23 (0.15), residues: 1144 sheet: 0.14 (0.35), residues: 220 loop : -0.37 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 459 TYR 0.011 0.001 TYR D 26 PHE 0.014 0.001 PHE E 168 TRP 0.013 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00260 (18946) covalent geometry : angle 0.48060 (25604) hydrogen bonds : bond 0.03704 ( 953) hydrogen bonds : angle 4.21146 ( 2727) Misc. bond : bond 0.00057 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5023.19 seconds wall clock time: 86 minutes 50.91 seconds (5210.91 seconds total)