Starting phenix.real_space_refine on Mon Jun 16 14:11:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0p_22606/06_2025/7k0p_22606.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0p_22606/06_2025/7k0p_22606.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/7k0p_22606/06_2025/7k0p_22606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0p_22606/06_2025/7k0p_22606.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0p_22606/06_2025/7k0p_22606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0p_22606/06_2025/7k0p_22606.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.094 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 12000 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 88 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18572 Number of models: 1 Model: "" Number of chains: 14 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'TYR: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: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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: "E" 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" 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: "G" 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1236 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} 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-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 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-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" 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-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 36 Chain: "H" 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-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 11.47, per 1000 atoms: 0.62 Number of scatterers: 18572 At special positions: 0 Unit cell: (92.46, 120.6, 153.765, 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 12000 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: 4.82 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 98 helices and 12 sheets defined 55.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.603A pdb=" N LEU A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 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: 3.677A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.122A 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 Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.907A pdb=" N VAL A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.706A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.372A 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 removed outlier: 3.568A pdb=" N ASN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.715A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.730A 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 removed outlier: 3.652A pdb=" N LYS B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 134 removed outlier: 5.463A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 removed outlier: 3.636A pdb=" N GLU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.871A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.761A 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 347 through 352 removed outlier: 4.036A pdb=" N ALA B 351 " --> pdb=" O HIS B 347 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 352' Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.716A pdb=" N TYR B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.590A pdb=" N ALA B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 455 removed outlier: 3.765A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.909A 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 removed outlier: 3.531A pdb=" N ALA C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 removed outlier: 4.694A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 40 removed outlier: 3.780A pdb=" N ILE D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) 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 116 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 120 through 136 removed outlier: 3.781A pdb=" N LEU D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.512A pdb=" N HIS D 143 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.706A pdb=" N GLY D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 19 Processing helix chain 'E' and resid 21 through 40 Processing helix chain 'E' and resid 53 through 64 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: 3.637A pdb=" N LEU E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 179 removed outlier: 4.152A 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 Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 288 through 294 Processing helix chain 'E' and resid 321 through 332 removed outlier: 4.772A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.292A 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: 4.254A pdb=" N ALA E 364 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 422 removed outlier: 3.949A 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 '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 127 through 134 removed outlier: 3.684A pdb=" N ARG F 131 " --> pdb=" O MET F 128 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP F 132 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 200 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.583A pdb=" N GLU F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 250 Proline residue: F 247 - end of helix removed outlier: 3.530A pdb=" N VAL F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) 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 347 through 352 removed outlier: 3.904A pdb=" N ALA F 351 " --> pdb=" O HIS F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 364 Processing helix chain 'F' and resid 391 through 401 Processing helix chain 'F' and resid 402 through 408 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 435 through 457 removed outlier: 3.549A pdb=" N VAL F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY F 457 " --> pdb=" O LEU F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.975A pdb=" N GLY F 480 " --> pdb=" O PRO F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 536 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: 4.766A pdb=" N MET H 17 " --> pdb=" O THR H 14 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER H 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 40 removed outlier: 3.639A pdb=" N ILE H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 65 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 removed outlier: 3.799A pdb=" N LEU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 139 No H-bonds generated for 'chain 'H' and resid 137 through 139' Processing helix chain 'H' and resid 146 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 7.063A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.872A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.275A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.961A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.672A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.822A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 4.276A pdb=" N VAL E 94 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 160 through 164 removed outlier: 3.756A pdb=" N LEU E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG E 240 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N PHE E 272 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLU E 274 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 244 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE E 184 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL E 243 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE E 186 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLU E 245 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASP E 188 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE E 209 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E 187 " --> pdb=" O PHE E 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 383 through 386 removed outlier: 4.235A pdb=" N THR E 427 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 145 through 152 removed outlier: 7.146A pdb=" N VAL F 146 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE F 167 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE F 148 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN F 165 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU F 150 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY F 492 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 171 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.643A pdb=" N ILE F 310 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.505A pdb=" N ARG F 507 " --> pdb=" O VAL F 496 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2739 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: 5.36 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5891 1.34 - 1.46: 2690 1.46 - 1.57: 10207 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18960 Sorted by residual: bond pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.73e+01 bond pdb=" O12 POV B 602 " pdb=" P POV B 602 " ideal model delta sigma weight residual 1.657 1.740 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" O12 POV F 602 " pdb=" P POV F 602 " ideal model delta sigma weight residual 1.657 1.740 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.85e+00 ... (remaining 18955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 25510 3.58 - 7.15: 102 7.15 - 10.73: 3 10.73 - 14.30: 0 14.30 - 17.88: 4 Bond angle restraints: 25619 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 127.79 109.91 17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C28 POV H 901 " pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 127.79 109.94 17.85 3.00e+00 1.11e-01 3.54e+01 angle pdb=" C29 POV D 901 " pdb="C210 POV D 901 " pdb="C211 POV D 901 " ideal model delta sigma weight residual 127.67 110.20 17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" C29 POV H 901 " pdb="C210 POV H 901 " pdb="C211 POV H 901 " ideal model delta sigma weight residual 127.67 110.22 17.45 3.00e+00 1.11e-01 3.38e+01 angle pdb=" N GLU E 414 " pdb=" CA GLU E 414 " pdb=" CB GLU E 414 " ideal model delta sigma weight residual 110.28 116.82 -6.54 1.55e+00 4.16e-01 1.78e+01 ... (remaining 25614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.26: 10881 26.26 - 52.53: 432 52.53 - 78.79: 50 78.79 - 105.06: 9 105.06 - 131.32: 1 Dihedral angle restraints: 11373 sinusoidal: 4587 harmonic: 6786 Sorted by residual: dihedral pdb=" C5A PLP F 601 " pdb=" O4P PLP F 601 " pdb=" P PLP F 601 " pdb=" O1P PLP F 601 " ideal model delta sinusoidal sigma weight residual 76.43 -54.89 131.32 1 2.00e+01 2.50e-03 3.98e+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 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR B 501 " pdb=" C THR B 501 " pdb=" N PRO B 502 " pdb=" CA PRO B 502 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 11370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2006 0.038 - 0.076: 591 0.076 - 0.113: 216 0.113 - 0.151: 38 0.151 - 0.189: 3 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 8.92e-01 chirality pdb=" CA PHE F 498 " pdb=" N PHE F 498 " pdb=" C PHE F 498 " pdb=" CB PHE F 498 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CB THR D 74 " pdb=" CA THR D 74 " pdb=" OG1 THR D 74 " pdb=" CG2 THR D 74 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 2851 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO B 413 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 901 " 0.026 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C29 POV D 901 " -0.026 2.00e-02 2.50e+03 pdb="C210 POV D 901 " -0.026 2.00e-02 2.50e+03 pdb="C211 POV D 901 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 412 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO F 413 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 413 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 413 " -0.027 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 945 2.73 - 3.27: 18036 3.27 - 3.81: 29317 3.81 - 4.36: 35595 4.36 - 4.90: 63976 Nonbonded interactions: 147869 Sorted by model distance: nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.183 3.040 nonbonded pdb=" OE2 GLU A 56 " pdb=" NH2 ARG F 302 " model vdw 2.213 3.120 nonbonded pdb=" OD2 ASP F 259 " pdb=" OH TYR F 318 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 355 " pdb=" OE2 GLU B 361 " model vdw 2.220 3.040 nonbonded pdb=" OE2 GLU H 9 " pdb=" OH TYR H 91 " model vdw 2.230 3.040 ... (remaining 147864 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' selection = (chain 'F' and (resid 53 through 544 or resid 601 or (resid 602 and (name C1 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or na \ me O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) \ or resid 603)) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 8 through 69 or resid 101 through 102)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 1 through 147 or (resid 148 and (name N or name CA or name \ C or name O or name CB )) or resid 149 through 153 or resid 901 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 42.130 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.005 0.187 18962 Z= 0.230 Angle : 0.715 17.880 25619 Z= 0.386 Chirality : 0.043 0.189 2854 Planarity : 0.005 0.069 3245 Dihedral : 13.774 131.321 7029 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2326 helix: 1.83 (0.16), residues: 1109 sheet: -0.56 (0.39), residues: 182 loop : -0.49 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 32 HIS 0.006 0.001 HIS E 292 PHE 0.018 0.002 PHE E 209 TYR 0.023 0.002 TYR E 166 ARG 0.006 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.14396 ( 960) hydrogen bonds : angle 5.68832 ( 2739) covalent geometry : bond 0.00491 (18960) covalent geometry : angle 0.71463 (25619) Misc. bond : bond 0.02872 ( 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 212 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 2.084 Fit side-chains REVERT: E 236 ARG cc_start: 0.7318 (ttp-110) cc_final: 0.6760 (tpt170) REVERT: F 161 LYS cc_start: 0.8287 (mttt) cc_final: 0.7528 (mmtt) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3383 time to fit residues: 107.1133 Evaluate side-chains 173 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS F 125 ASN F 154 HIS H 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110664 restraints weight = 25276.747| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.27 r_work: 0.3358 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18962 Z= 0.193 Angle : 0.575 6.661 25619 Z= 0.305 Chirality : 0.043 0.186 2854 Planarity : 0.005 0.067 3245 Dihedral : 7.078 103.886 2715 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.67 % Allowed : 4.65 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2326 helix: 1.86 (0.15), residues: 1135 sheet: -0.29 (0.38), residues: 199 loop : -0.45 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 32 HIS 0.006 0.001 HIS B 403 PHE 0.021 0.002 PHE E 209 TYR 0.018 0.002 TYR B 539 ARG 0.004 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.05344 ( 960) hydrogen bonds : angle 4.63098 ( 2739) covalent geometry : bond 0.00471 (18960) covalent geometry : angle 0.57501 (25619) Misc. bond : bond 0.00007 ( 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 204 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 2.227 Fit side-chains revert: symmetry clash REVERT: B 392 LYS cc_start: 0.7935 (tttm) cc_final: 0.7663 (tttp) REVERT: C 47 MET cc_start: 0.6335 (tmm) cc_final: 0.6030 (tmm) REVERT: E 236 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.6948 (tpt170) REVERT: F 161 LYS cc_start: 0.8302 (mttt) cc_final: 0.7403 (mmtt) outliers start: 13 outliers final: 9 residues processed: 199 average time/residue: 0.3352 time to fit residues: 101.1063 Evaluate side-chains 180 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 56 optimal weight: 0.3980 chunk 161 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 245 ASN E 77 HIS F 154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112328 restraints weight = 25120.851| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.27 r_work: 0.3387 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18962 Z= 0.139 Angle : 0.510 6.591 25619 Z= 0.270 Chirality : 0.041 0.178 2854 Planarity : 0.004 0.055 3245 Dihedral : 6.547 83.958 2715 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.78 % Allowed : 6.51 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2326 helix: 2.14 (0.16), residues: 1127 sheet: -0.07 (0.37), residues: 219 loop : -0.54 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 PHE 0.018 0.001 PHE E 209 TYR 0.015 0.001 TYR D 26 ARG 0.002 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 960) hydrogen bonds : angle 4.32677 ( 2739) covalent geometry : bond 0.00330 (18960) covalent geometry : angle 0.50957 (25619) Misc. bond : bond 0.00102 ( 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 205 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 3.598 Fit side-chains revert: symmetry clash REVERT: B 392 LYS cc_start: 0.7877 (tttm) cc_final: 0.7610 (tttp) REVERT: C 47 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.6006 (tmm) REVERT: D 17 MET cc_start: 0.8642 (mmt) cc_final: 0.8417 (mmt) REVERT: E 236 ARG cc_start: 0.7733 (ttp-110) cc_final: 0.6925 (tpt170) REVERT: F 161 LYS cc_start: 0.8293 (mttt) cc_final: 0.7391 (mmtt) REVERT: H 76 ASP cc_start: 0.8829 (p0) cc_final: 0.8518 (p0) REVERT: H 96 THR cc_start: 0.7819 (m) cc_final: 0.7493 (p) outliers start: 15 outliers final: 9 residues processed: 198 average time/residue: 0.3811 time to fit residues: 115.1458 Evaluate side-chains 184 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 59 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 191 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS E 91 HIS E 428 GLN F 154 HIS H 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112755 restraints weight = 25186.359| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.26 r_work: 0.3377 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18962 Z= 0.135 Angle : 0.499 6.698 25619 Z= 0.263 Chirality : 0.041 0.175 2854 Planarity : 0.004 0.052 3245 Dihedral : 6.244 67.916 2715 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.14 % Allowed : 8.11 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2326 helix: 2.25 (0.16), residues: 1127 sheet: -0.10 (0.37), residues: 219 loop : -0.54 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 PHE 0.017 0.001 PHE E 209 TYR 0.015 0.001 TYR D 26 ARG 0.003 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 960) hydrogen bonds : angle 4.17494 ( 2739) covalent geometry : bond 0.00321 (18960) covalent geometry : angle 0.49894 (25619) Misc. bond : bond 0.00084 ( 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 214 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 2.016 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 155 ASP cc_start: 0.8024 (t0) cc_final: 0.7804 (t0) REVERT: B 392 LYS cc_start: 0.7837 (tttm) cc_final: 0.7587 (tttp) REVERT: C 47 MET cc_start: 0.6217 (tmm) cc_final: 0.6002 (tmm) REVERT: F 161 LYS cc_start: 0.8304 (mttt) cc_final: 0.7402 (mmtt) REVERT: H 76 ASP cc_start: 0.8846 (p0) cc_final: 0.8552 (p0) REVERT: H 96 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7456 (p) outliers start: 22 outliers final: 13 residues processed: 208 average time/residue: 0.3160 time to fit residues: 99.9837 Evaluate side-chains 198 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain H residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 231 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 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 177 ASN E 77 HIS E 114 ASN F 154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112659 restraints weight = 25334.634| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.27 r_work: 0.3393 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18962 Z= 0.139 Angle : 0.499 6.921 25619 Z= 0.263 Chirality : 0.041 0.173 2854 Planarity : 0.004 0.052 3245 Dihedral : 6.098 65.662 2715 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.45 % Allowed : 9.20 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2326 helix: 2.27 (0.15), residues: 1133 sheet: -0.14 (0.37), residues: 219 loop : -0.52 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 PHE 0.026 0.001 PHE F 90 TYR 0.014 0.001 TYR D 26 ARG 0.002 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 960) hydrogen bonds : angle 4.10352 ( 2739) covalent geometry : bond 0.00332 (18960) covalent geometry : angle 0.49893 (25619) Misc. bond : bond 0.00095 ( 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 221 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 2.064 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8534 (mp) REVERT: B 155 ASP cc_start: 0.8074 (t0) cc_final: 0.7816 (t0) REVERT: B 392 LYS cc_start: 0.7815 (tttm) cc_final: 0.7564 (tttp) REVERT: C 47 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5835 (tmm) REVERT: F 161 LYS cc_start: 0.8284 (mttt) cc_final: 0.7373 (mmtt) REVERT: H 76 ASP cc_start: 0.8792 (p0) cc_final: 0.8509 (p0) REVERT: H 96 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7437 (p) outliers start: 28 outliers final: 17 residues processed: 212 average time/residue: 0.3150 time to fit residues: 102.1902 Evaluate side-chains 208 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain H residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 chunk 54 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS F 154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.139747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113969 restraints weight = 25258.699| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.27 r_work: 0.3405 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18962 Z= 0.110 Angle : 0.476 7.099 25619 Z= 0.252 Chirality : 0.040 0.169 2854 Planarity : 0.004 0.051 3245 Dihedral : 5.897 64.613 2715 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.29 % Allowed : 10.03 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.18), residues: 2326 helix: 2.35 (0.16), residues: 1137 sheet: -0.33 (0.39), residues: 200 loop : -0.42 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 PHE 0.014 0.001 PHE E 209 TYR 0.019 0.001 TYR A 23 ARG 0.003 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 960) hydrogen bonds : angle 3.98436 ( 2739) covalent geometry : bond 0.00253 (18960) covalent geometry : angle 0.47617 (25619) Misc. bond : bond 0.00071 ( 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 221 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 2.294 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8568 (mp) REVERT: B 155 ASP cc_start: 0.7998 (t0) cc_final: 0.7758 (t0) REVERT: C 47 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5885 (tmm) REVERT: F 57 ARG cc_start: 0.7002 (ptm160) cc_final: 0.6758 (ptm160) REVERT: F 95 ARG cc_start: 0.8114 (tpt90) cc_final: 0.7648 (mmm160) REVERT: F 161 LYS cc_start: 0.8288 (mttt) cc_final: 0.7403 (mmtt) REVERT: F 487 LEU cc_start: 0.8125 (tp) cc_final: 0.7827 (tp) REVERT: H 76 ASP cc_start: 0.8792 (p0) cc_final: 0.8518 (p0) REVERT: H 96 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7467 (p) outliers start: 25 outliers final: 17 residues processed: 213 average time/residue: 0.3167 time to fit residues: 103.3199 Evaluate side-chains 205 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain H residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 77 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 221 optimal weight: 0.0000 chunk 157 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN D 88 GLN E 77 HIS F 154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113544 restraints weight = 25055.512| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.26 r_work: 0.3398 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18962 Z= 0.124 Angle : 0.485 7.200 25619 Z= 0.256 Chirality : 0.041 0.171 2854 Planarity : 0.004 0.051 3245 Dihedral : 5.760 65.429 2715 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.55 % Allowed : 10.18 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2326 helix: 2.37 (0.16), residues: 1137 sheet: -0.34 (0.39), residues: 200 loop : -0.42 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 PHE 0.015 0.001 PHE E 209 TYR 0.013 0.001 TYR D 26 ARG 0.002 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 960) hydrogen bonds : angle 3.97402 ( 2739) covalent geometry : bond 0.00296 (18960) covalent geometry : angle 0.48485 (25619) Misc. bond : bond 0.00076 ( 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 220 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 2.229 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 155 ASP cc_start: 0.8034 (t0) cc_final: 0.7832 (t0) REVERT: C 47 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5898 (tmm) REVERT: F 57 ARG cc_start: 0.6974 (ptm160) cc_final: 0.6708 (ptm160) REVERT: F 95 ARG cc_start: 0.8080 (tpt90) cc_final: 0.7615 (mmm160) REVERT: F 161 LYS cc_start: 0.8293 (mttt) cc_final: 0.7398 (mmtt) REVERT: F 252 LYS cc_start: 0.8750 (tppt) cc_final: 0.8487 (tttt) REVERT: F 487 LEU cc_start: 0.8148 (tp) cc_final: 0.7855 (tp) REVERT: H 74 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8117 (t) REVERT: H 96 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7486 (p) outliers start: 30 outliers final: 22 residues processed: 211 average time/residue: 0.3216 time to fit residues: 103.8863 Evaluate side-chains 209 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain F residue 286 GLN Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 223 optimal weight: 0.0770 chunk 37 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 119 optimal weight: 0.3980 chunk 162 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS F 154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114733 restraints weight = 25060.181| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.27 r_work: 0.3420 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 0.033 18962 Z= 0.108 Angle : 0.471 7.249 25619 Z= 0.248 Chirality : 0.040 0.168 2854 Planarity : 0.004 0.050 3245 Dihedral : 5.602 64.816 2715 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.50 % Allowed : 10.54 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2326 helix: 2.42 (0.15), residues: 1149 sheet: -0.32 (0.39), residues: 200 loop : -0.37 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 32 HIS 0.003 0.000 HIS E 24 PHE 0.013 0.001 PHE E 209 TYR 0.017 0.001 TYR A 23 ARG 0.002 0.000 ARG F 450 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 960) hydrogen bonds : angle 3.91283 ( 2739) covalent geometry : bond 0.00250 (18960) covalent geometry : angle 0.47056 (25619) Misc. bond : bond 0.00058 ( 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 221 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 2.119 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8533 (mp) REVERT: C 47 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.5840 (tmm) REVERT: F 57 ARG cc_start: 0.7029 (ptm160) cc_final: 0.6760 (ptm160) REVERT: F 95 ARG cc_start: 0.8040 (tpt90) cc_final: 0.7581 (mmm160) REVERT: F 161 LYS cc_start: 0.8268 (mttt) cc_final: 0.7381 (mmtt) REVERT: F 252 LYS cc_start: 0.8726 (tppt) cc_final: 0.8467 (tttt) REVERT: H 96 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7412 (p) outliers start: 29 outliers final: 19 residues processed: 213 average time/residue: 0.3297 time to fit residues: 107.4212 Evaluate side-chains 205 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain F residue 286 GLN Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 169 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 142 optimal weight: 0.4980 chunk 138 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS E 114 ASN F 154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114642 restraints weight = 25220.907| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.28 r_work: 0.3418 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18962 Z= 0.110 Angle : 0.476 6.877 25619 Z= 0.251 Chirality : 0.040 0.169 2854 Planarity : 0.004 0.050 3245 Dihedral : 5.539 65.335 2715 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.29 % Allowed : 11.06 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2326 helix: 2.37 (0.15), residues: 1161 sheet: -0.28 (0.40), residues: 190 loop : -0.40 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 32 HIS 0.003 0.001 HIS E 24 PHE 0.032 0.001 PHE F 90 TYR 0.012 0.001 TYR D 26 ARG 0.002 0.000 ARG F 207 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 960) hydrogen bonds : angle 3.88913 ( 2739) covalent geometry : bond 0.00257 (18960) covalent geometry : angle 0.47649 (25619) Misc. bond : bond 0.00053 ( 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 212 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 2.060 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8527 (mp) REVERT: A 472 LEU cc_start: 0.6627 (mm) cc_final: 0.6396 (mm) REVERT: B 155 ASP cc_start: 0.7813 (t0) cc_final: 0.7504 (t0) REVERT: C 47 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5829 (tmm) REVERT: F 57 ARG cc_start: 0.7040 (ptm160) cc_final: 0.6758 (ptm160) REVERT: F 95 ARG cc_start: 0.8038 (tpt90) cc_final: 0.7587 (mmm160) REVERT: F 161 LYS cc_start: 0.8266 (mttt) cc_final: 0.7380 (mmtt) REVERT: F 252 LYS cc_start: 0.8730 (tppt) cc_final: 0.8427 (tttt) REVERT: H 76 ASP cc_start: 0.8764 (p0) cc_final: 0.8460 (p0) REVERT: H 96 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7398 (p) outliers start: 25 outliers final: 18 residues processed: 205 average time/residue: 0.3357 time to fit residues: 103.9032 Evaluate side-chains 201 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain F residue 286 GLN Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 32 optimal weight: 0.3980 chunk 127 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 171 optimal weight: 0.0970 chunk 117 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS E 114 ASN F 154 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115595 restraints weight = 25009.699| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.27 r_work: 0.3421 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18962 Z= 0.102 Angle : 0.465 7.288 25619 Z= 0.245 Chirality : 0.040 0.169 2854 Planarity : 0.004 0.049 3245 Dihedral : 5.476 64.934 2715 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.29 % Allowed : 11.37 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2326 helix: 2.42 (0.16), residues: 1159 sheet: -0.23 (0.40), residues: 190 loop : -0.36 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 32 HIS 0.003 0.000 HIS E 24 PHE 0.013 0.001 PHE E 168 TYR 0.017 0.001 TYR A 23 ARG 0.002 0.000 ARG F 450 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 960) hydrogen bonds : angle 3.84627 ( 2739) covalent geometry : bond 0.00235 (18960) covalent geometry : angle 0.46498 (25619) Misc. bond : bond 0.00044 ( 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 214 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 2.227 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8195 (t0) cc_final: 0.7955 (m-30) REVERT: A 432 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 155 ASP cc_start: 0.7805 (t0) cc_final: 0.7518 (t0) REVERT: C 47 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.5858 (tmm) REVERT: F 57 ARG cc_start: 0.7045 (ptm160) cc_final: 0.6760 (ptm160) REVERT: F 95 ARG cc_start: 0.8009 (tpt90) cc_final: 0.7575 (mmm160) REVERT: F 161 LYS cc_start: 0.8274 (mttt) cc_final: 0.7391 (mmtt) REVERT: F 252 LYS cc_start: 0.8737 (tppt) cc_final: 0.8413 (tttt) REVERT: F 440 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6642 (mp10) REVERT: H 76 ASP cc_start: 0.8768 (p0) cc_final: 0.8464 (p0) REVERT: H 96 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7402 (p) outliers start: 25 outliers final: 20 residues processed: 206 average time/residue: 0.3282 time to fit residues: 102.8336 Evaluate side-chains 206 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain F residue 286 GLN Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 440 GLN Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 204 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 135 optimal weight: 0.0980 chunk 50 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 188 optimal weight: 0.2980 chunk 16 optimal weight: 0.3980 chunk 160 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS F 154 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115525 restraints weight = 24934.084| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.27 r_work: 0.3425 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 18962 Z= 0.139 Angle : 0.669 59.200 25619 Z= 0.398 Chirality : 0.042 0.804 2854 Planarity : 0.004 0.053 3245 Dihedral : 5.497 64.947 2715 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.29 % Allowed : 11.68 % Favored : 87.03 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2326 helix: 2.42 (0.15), residues: 1159 sheet: -0.24 (0.40), residues: 190 loop : -0.36 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 32 HIS 0.003 0.000 HIS E 24 PHE 0.012 0.001 PHE E 168 TYR 0.012 0.001 TYR D 26 ARG 0.002 0.000 ARG F 450 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 960) hydrogen bonds : angle 3.84498 ( 2739) covalent geometry : bond 0.00280 (18960) covalent geometry : angle 0.66855 (25619) Misc. bond : bond 0.00045 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10227.15 seconds wall clock time: 178 minutes 37.92 seconds (10717.92 seconds total)