Starting phenix.real_space_refine on Sat Feb 17 23:29:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffo_29049/02_2024/8ffo_29049_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffo_29049/02_2024/8ffo_29049.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffo_29049/02_2024/8ffo_29049_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffo_29049/02_2024/8ffo_29049_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffo_29049/02_2024/8ffo_29049_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffo_29049/02_2024/8ffo_29049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffo_29049/02_2024/8ffo_29049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffo_29049/02_2024/8ffo_29049_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffo_29049/02_2024/8ffo_29049_neut_updated.pdb" } resolution = 3.5 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= 0.003 sd= 0.040 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 16 5.49 5 S 136 5.16 5 C 13132 2.51 5 N 3272 2.21 5 O 3544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20100 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4839 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 2 Chain: "B" Number of atoms: 4839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4839 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 2 Chain: "C" Number of atoms: 4839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4839 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 2 Chain: "D" Number of atoms: 4839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4839 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 2 Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'CPL': 4, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-3': 3, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'CPL': 4, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-3': 3, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'CPL': 4, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-3': 3, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'CPL': 4, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-3': 3, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 10.59, per 1000 atoms: 0.53 Number of scatterers: 20100 At special positions: 0 Unit cell: (136.95, 136.95, 121.18, 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 136 16.00 P 16 15.00 O 3544 8.00 N 3272 7.00 C 13132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.73 Conformation dependent library (CDL) restraints added in 3.0 seconds 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 8 sheets defined 59.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.584A pdb=" N ARG A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 209 through 222 removed outlier: 3.988A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.916A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.898A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 348 Processing helix chain 'A' and resid 380 through 410 Proline residue: A 405 - end of helix removed outlier: 3.701A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 423 through 444 Processing helix chain 'A' and resid 450 through 471 removed outlier: 3.728A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 486 removed outlier: 4.007A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 4.998A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 553 through 565 Processing helix chain 'A' and resid 569 through 607 removed outlier: 3.894A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.584A pdb=" N ARG B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 209 through 222 removed outlier: 3.988A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.916A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 303 through 309 Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.898A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 348 Processing helix chain 'B' and resid 380 through 410 Proline residue: B 405 - end of helix removed outlier: 3.701A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 423 through 444 Processing helix chain 'B' and resid 450 through 471 removed outlier: 3.728A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY B 471 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 486 removed outlier: 4.007A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 511 removed outlier: 4.998A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 553 through 565 Processing helix chain 'B' and resid 569 through 607 removed outlier: 3.894A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.584A pdb=" N ARG C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 130 through 139 Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 209 through 222 removed outlier: 3.988A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.916A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.898A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 348 Processing helix chain 'C' and resid 380 through 410 Proline residue: C 405 - end of helix removed outlier: 3.701A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 423 through 444 Processing helix chain 'C' and resid 450 through 471 removed outlier: 3.728A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY C 471 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 486 removed outlier: 4.007A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 511 removed outlier: 4.998A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 553 through 565 Processing helix chain 'C' and resid 569 through 607 removed outlier: 3.894A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.584A pdb=" N ARG D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 209 through 222 removed outlier: 3.988A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.916A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 303 through 309 Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.898A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 348 Processing helix chain 'D' and resid 380 through 410 Proline residue: D 405 - end of helix removed outlier: 3.701A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 423 through 444 Processing helix chain 'D' and resid 450 through 471 removed outlier: 3.728A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG D 470 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY D 471 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 486 removed outlier: 4.007A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 511 removed outlier: 4.998A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 553 through 565 Processing helix chain 'D' and resid 569 through 607 removed outlier: 3.894A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing sheet with id= A, first strand: chain 'A' and resid 630 through 636 removed outlier: 3.760A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= C, first strand: chain 'B' and resid 630 through 636 removed outlier: 3.760A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 352 through 354 Processing sheet with id= E, first strand: chain 'C' and resid 630 through 636 removed outlier: 3.760A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 352 through 354 Processing sheet with id= G, first strand: chain 'D' and resid 630 through 636 removed outlier: 3.760A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 352 through 354 940 hydrogen bonds defined for protein. 2736 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: 6.49 Time building geometry restraints manager: 8.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3472 1.33 - 1.45: 5232 1.45 - 1.58: 11580 1.58 - 1.71: 32 1.71 - 1.83: 232 Bond restraints: 20548 Sorted by residual: bond pdb=" O4P CPL C 801 " pdb=" P CPL C 801 " ideal model delta sigma weight residual 1.648 1.834 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" O4P CPL B 801 " pdb=" P CPL B 801 " ideal model delta sigma weight residual 1.648 1.834 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" O4P CPL D 801 " pdb=" P CPL D 801 " ideal model delta sigma weight residual 1.648 1.834 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" O4P CPL A 807 " pdb=" P CPL A 807 " ideal model delta sigma weight residual 1.648 1.834 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" C2 CPL A 807 " pdb=" C3 CPL A 807 " ideal model delta sigma weight residual 1.511 1.634 -0.123 2.00e-02 2.50e+03 3.80e+01 ... (remaining 20543 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.85: 472 105.85 - 112.89: 11008 112.89 - 119.92: 7396 119.92 - 126.96: 8736 126.96 - 133.99: 248 Bond angle restraints: 27860 Sorted by residual: angle pdb=" O3P CPL B 801 " pdb=" P CPL B 801 " pdb=" O4P CPL B 801 " ideal model delta sigma weight residual 93.29 107.88 -14.59 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O3P CPL C 801 " pdb=" P CPL C 801 " pdb=" O4P CPL C 801 " ideal model delta sigma weight residual 93.29 107.88 -14.59 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O3P CPL D 801 " pdb=" P CPL D 801 " pdb=" O4P CPL D 801 " ideal model delta sigma weight residual 93.29 107.88 -14.59 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O3P CPL A 807 " pdb=" P CPL A 807 " pdb=" O4P CPL A 807 " ideal model delta sigma weight residual 93.29 107.88 -14.59 3.00e+00 1.11e-01 2.37e+01 angle pdb=" C12 CPL C 801 " pdb=" C11 CPL C 801 " pdb=" O3 CPL C 801 " ideal model delta sigma weight residual 111.42 122.50 -11.08 3.00e+00 1.11e-01 1.36e+01 ... (remaining 27855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 12440 34.82 - 69.65: 196 69.65 - 104.47: 24 104.47 - 139.29: 4 139.29 - 174.11: 12 Dihedral angle restraints: 12676 sinusoidal: 5624 harmonic: 7052 Sorted by residual: dihedral pdb=" C3 CPL C 801 " pdb=" C1 CPL C 801 " pdb=" C2 CPL C 801 " pdb=" O3P CPL C 801 " ideal model delta sinusoidal sigma weight residual 72.09 -113.80 -174.11 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL B 801 " pdb=" C1 CPL B 801 " pdb=" C2 CPL B 801 " pdb=" O3P CPL B 801 " ideal model delta sinusoidal sigma weight residual 72.09 -113.80 -174.11 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL D 801 " pdb=" C1 CPL D 801 " pdb=" C2 CPL D 801 " pdb=" O3P CPL D 801 " ideal model delta sinusoidal sigma weight residual 72.09 -113.80 -174.11 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2928 0.075 - 0.150: 212 0.150 - 0.224: 20 0.224 - 0.299: 0 0.299 - 0.374: 4 Chirality restraints: 3164 Sorted by residual: chirality pdb=" C2 CPL A 807 " pdb=" C1 CPL A 807 " pdb=" C3 CPL A 807 " pdb=" O2 CPL A 807 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C2 CPL D 801 " pdb=" C1 CPL D 801 " pdb=" C3 CPL D 801 " pdb=" O2 CPL D 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C2 CPL B 801 " pdb=" C1 CPL B 801 " pdb=" C3 CPL B 801 " pdb=" O2 CPL B 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 3161 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG A 805 " -0.111 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C22 ERG A 805 " 0.109 2.00e-02 2.50e+03 pdb=" C23 ERG A 805 " 0.113 2.00e-02 2.50e+03 pdb=" C24 ERG A 805 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG B 806 " 0.111 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C22 ERG B 806 " -0.109 2.00e-02 2.50e+03 pdb=" C23 ERG B 806 " -0.113 2.00e-02 2.50e+03 pdb=" C24 ERG B 806 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG C 806 " 0.111 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C22 ERG C 806 " -0.109 2.00e-02 2.50e+03 pdb=" C23 ERG C 806 " -0.113 2.00e-02 2.50e+03 pdb=" C24 ERG C 806 " 0.112 2.00e-02 2.50e+03 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5452 2.81 - 3.33: 18072 3.33 - 3.86: 33500 3.86 - 4.38: 39332 4.38 - 4.90: 68556 Nonbonded interactions: 164912 Sorted by model distance: nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.289 2.440 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.289 2.440 nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.289 2.440 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR C 336 " pdb=" OG SER C 464 " model vdw 2.318 2.440 ... (remaining 164907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 638 or resid 803 through 804)) selection = (chain 'B' and (resid 29 through 638 or resid 803 through 804)) selection = (chain 'C' and (resid 29 through 638 or resid 803 through 804)) selection = (chain 'D' and (resid 29 through 638 or resid 803 through 804)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 6.070 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 53.700 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.140 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.008 0.186 20548 Z= 0.498 Angle : 0.766 14.594 27860 Z= 0.369 Chirality : 0.044 0.374 3164 Planarity : 0.007 0.111 3428 Dihedral : 14.481 174.114 8116 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.15), residues: 2392 helix: -1.02 (0.11), residues: 1468 sheet: -3.42 (0.36), residues: 124 loop : -1.51 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 593 HIS 0.003 0.001 HIS D 201 PHE 0.012 0.001 PHE B 169 TYR 0.011 0.001 TYR D 555 ARG 0.002 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 504 time to evaluate : 2.574 Fit side-chains REVERT: A 130 LEU cc_start: 0.8959 (tp) cc_final: 0.8712 (tp) REVERT: A 217 ASN cc_start: 0.8431 (t0) cc_final: 0.8218 (m-40) REVERT: A 262 LYS cc_start: 0.9057 (mtpm) cc_final: 0.8813 (mtpp) REVERT: A 340 MET cc_start: 0.8592 (mmm) cc_final: 0.8308 (tpt) REVERT: A 364 ASP cc_start: 0.8531 (t0) cc_final: 0.8253 (t0) REVERT: A 370 GLN cc_start: 0.8232 (mt0) cc_final: 0.8001 (mt0) REVERT: A 474 MET cc_start: 0.6755 (ptp) cc_final: 0.6145 (ptt) REVERT: B 130 LEU cc_start: 0.8964 (tp) cc_final: 0.8714 (tp) REVERT: B 217 ASN cc_start: 0.8430 (t0) cc_final: 0.8218 (m-40) REVERT: B 262 LYS cc_start: 0.9054 (mtpm) cc_final: 0.8809 (mtpp) REVERT: B 340 MET cc_start: 0.8596 (mmm) cc_final: 0.8319 (tpt) REVERT: B 364 ASP cc_start: 0.8532 (t0) cc_final: 0.8255 (t0) REVERT: B 370 GLN cc_start: 0.8233 (mt0) cc_final: 0.8000 (mt0) REVERT: B 474 MET cc_start: 0.6760 (ptp) cc_final: 0.6152 (ptt) REVERT: C 130 LEU cc_start: 0.8968 (tp) cc_final: 0.8717 (tp) REVERT: C 217 ASN cc_start: 0.8432 (t0) cc_final: 0.8216 (m-40) REVERT: C 262 LYS cc_start: 0.9052 (mtpm) cc_final: 0.8808 (mtpp) REVERT: C 340 MET cc_start: 0.8594 (mmm) cc_final: 0.8317 (tpt) REVERT: C 364 ASP cc_start: 0.8529 (t0) cc_final: 0.8253 (t0) REVERT: C 370 GLN cc_start: 0.8228 (mt0) cc_final: 0.8000 (mt0) REVERT: C 474 MET cc_start: 0.6751 (ptp) cc_final: 0.6142 (ptt) REVERT: D 130 LEU cc_start: 0.8965 (tp) cc_final: 0.8712 (tp) REVERT: D 217 ASN cc_start: 0.8430 (t0) cc_final: 0.8217 (m-40) REVERT: D 262 LYS cc_start: 0.9054 (mtpm) cc_final: 0.8808 (mtpp) REVERT: D 340 MET cc_start: 0.8596 (mmm) cc_final: 0.8312 (tpt) REVERT: D 364 ASP cc_start: 0.8528 (t0) cc_final: 0.8249 (t0) REVERT: D 370 GLN cc_start: 0.8233 (mt0) cc_final: 0.8002 (mt0) REVERT: D 474 MET cc_start: 0.6749 (ptp) cc_final: 0.6140 (ptt) outliers start: 4 outliers final: 0 residues processed: 508 average time/residue: 0.3489 time to fit residues: 263.9972 Evaluate side-chains 304 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 185 HIS A 192 GLN A 208 ASN A 214 GLN A 310 GLN A 582 HIS B 128 GLN B 185 HIS B 192 GLN B 208 ASN B 214 GLN B 310 GLN B 582 HIS C 128 GLN C 185 HIS C 192 GLN C 208 ASN C 214 GLN C 310 GLN C 582 HIS D 128 GLN D 185 HIS D 192 GLN D 208 ASN D 214 GLN D 310 GLN D 582 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 20548 Z= 0.454 Angle : 0.628 6.742 27860 Z= 0.317 Chirality : 0.042 0.180 3164 Planarity : 0.005 0.054 3428 Dihedral : 14.860 174.490 3532 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.53 % Allowed : 9.00 % Favored : 89.46 % 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: -0.90 (0.16), residues: 2392 helix: 0.09 (0.13), residues: 1468 sheet: -3.46 (0.37), residues: 124 loop : -1.22 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 495 HIS 0.003 0.001 HIS A 122 PHE 0.015 0.002 PHE B 425 TYR 0.019 0.002 TYR A 621 ARG 0.004 0.001 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 332 time to evaluate : 2.204 Fit side-chains REVERT: A 217 ASN cc_start: 0.8664 (t0) cc_final: 0.8337 (m-40) REVERT: A 262 LYS cc_start: 0.9081 (mtpm) cc_final: 0.8878 (mtpp) REVERT: A 474 MET cc_start: 0.7095 (ptp) cc_final: 0.6600 (ptt) REVERT: A 497 MET cc_start: 0.8022 (mtp) cc_final: 0.7747 (mtp) REVERT: A 554 MET cc_start: 0.8599 (mmm) cc_final: 0.8257 (mmm) REVERT: B 217 ASN cc_start: 0.8663 (t0) cc_final: 0.8337 (m-40) REVERT: B 262 LYS cc_start: 0.9082 (mtpm) cc_final: 0.8879 (mtpp) REVERT: B 474 MET cc_start: 0.7098 (ptp) cc_final: 0.6603 (ptt) REVERT: B 497 MET cc_start: 0.8016 (mtp) cc_final: 0.7750 (mtp) REVERT: B 554 MET cc_start: 0.8596 (mmm) cc_final: 0.8258 (mmm) REVERT: C 217 ASN cc_start: 0.8664 (t0) cc_final: 0.8337 (m-40) REVERT: C 262 LYS cc_start: 0.9080 (mtpm) cc_final: 0.8878 (mtpp) REVERT: C 474 MET cc_start: 0.7091 (ptp) cc_final: 0.6592 (ptt) REVERT: C 497 MET cc_start: 0.8008 (mtp) cc_final: 0.7742 (mtp) REVERT: C 554 MET cc_start: 0.8594 (mmm) cc_final: 0.8250 (mmm) REVERT: D 217 ASN cc_start: 0.8663 (t0) cc_final: 0.8336 (m-40) REVERT: D 262 LYS cc_start: 0.9080 (mtpm) cc_final: 0.8878 (mtpp) REVERT: D 474 MET cc_start: 0.7093 (ptp) cc_final: 0.6599 (ptt) REVERT: D 497 MET cc_start: 0.8017 (mtp) cc_final: 0.7740 (mtp) REVERT: D 554 MET cc_start: 0.8596 (mmm) cc_final: 0.8251 (mmm) outliers start: 32 outliers final: 24 residues processed: 356 average time/residue: 0.2982 time to fit residues: 166.9667 Evaluate side-chains 296 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 272 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 0.1980 chunk 194 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 596 GLN B 208 ASN B 596 GLN C 31 GLN C 208 ASN C 596 GLN D 74 GLN D 208 ASN D 596 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20548 Z= 0.206 Angle : 0.493 6.199 27860 Z= 0.242 Chirality : 0.037 0.134 3164 Planarity : 0.004 0.049 3428 Dihedral : 14.441 174.086 3532 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.92 % Allowed : 10.97 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.17), residues: 2392 helix: 0.85 (0.13), residues: 1472 sheet: -3.39 (0.37), residues: 124 loop : -1.01 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 495 HIS 0.002 0.000 HIS C 201 PHE 0.009 0.001 PHE C 169 TYR 0.017 0.001 TYR A 621 ARG 0.003 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 284 time to evaluate : 2.290 Fit side-chains REVERT: A 217 ASN cc_start: 0.8605 (t0) cc_final: 0.8269 (m-40) REVERT: A 474 MET cc_start: 0.7047 (ptp) cc_final: 0.6502 (ptt) REVERT: A 554 MET cc_start: 0.8545 (mmm) cc_final: 0.8161 (mmm) REVERT: B 217 ASN cc_start: 0.8603 (t0) cc_final: 0.8267 (m-40) REVERT: B 474 MET cc_start: 0.7047 (ptp) cc_final: 0.6505 (ptt) REVERT: B 554 MET cc_start: 0.8539 (mmm) cc_final: 0.8160 (mmm) REVERT: C 217 ASN cc_start: 0.8606 (t0) cc_final: 0.8270 (m-40) REVERT: C 474 MET cc_start: 0.7040 (ptp) cc_final: 0.6493 (ptt) REVERT: C 554 MET cc_start: 0.8536 (mmm) cc_final: 0.8151 (mmm) REVERT: D 217 ASN cc_start: 0.8601 (t0) cc_final: 0.8266 (m-40) REVERT: D 474 MET cc_start: 0.7042 (ptp) cc_final: 0.6498 (ptt) REVERT: D 554 MET cc_start: 0.8540 (mmm) cc_final: 0.8151 (mmm) outliers start: 40 outliers final: 24 residues processed: 316 average time/residue: 0.2908 time to fit residues: 145.7110 Evaluate side-chains 296 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 272 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 146 optimal weight: 0.0370 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 0.0030 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 overall best weight: 0.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 91 ASN A 208 ASN A 214 GLN A 369 GLN A 636 HIS B 31 GLN B 91 ASN B 208 ASN B 214 GLN B 369 GLN B 636 HIS C 91 ASN C 208 ASN C 214 GLN C 369 GLN C 636 HIS D 31 GLN D 91 ASN D 208 ASN D 214 GLN D 369 GLN D 636 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20548 Z= 0.122 Angle : 0.453 6.391 27860 Z= 0.219 Chirality : 0.035 0.152 3164 Planarity : 0.003 0.045 3428 Dihedral : 13.827 173.030 3532 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.30 % Allowed : 11.54 % Favored : 86.16 % 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: 0.53 (0.17), residues: 2392 helix: 1.36 (0.13), residues: 1472 sheet: -3.35 (0.37), residues: 124 loop : -0.86 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 495 HIS 0.002 0.000 HIS A 165 PHE 0.009 0.001 PHE A 611 TYR 0.018 0.001 TYR A 621 ARG 0.005 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 292 time to evaluate : 2.090 Fit side-chains REVERT: A 160 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8579 (pp) REVERT: A 217 ASN cc_start: 0.8537 (t0) cc_final: 0.8216 (m-40) REVERT: A 267 GLN cc_start: 0.8549 (mt0) cc_final: 0.8226 (mt0) REVERT: A 474 MET cc_start: 0.6994 (ptp) cc_final: 0.6457 (ptt) REVERT: B 160 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8580 (pp) REVERT: B 217 ASN cc_start: 0.8536 (t0) cc_final: 0.8217 (m-40) REVERT: B 267 GLN cc_start: 0.8545 (mt0) cc_final: 0.8222 (mt0) REVERT: B 474 MET cc_start: 0.6994 (ptp) cc_final: 0.6461 (ptt) REVERT: C 160 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8578 (pp) REVERT: C 217 ASN cc_start: 0.8539 (t0) cc_final: 0.8218 (m-40) REVERT: C 267 GLN cc_start: 0.8537 (mt0) cc_final: 0.8217 (mt0) REVERT: C 474 MET cc_start: 0.6989 (ptp) cc_final: 0.6451 (ptt) REVERT: D 160 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8578 (pp) REVERT: D 217 ASN cc_start: 0.8538 (t0) cc_final: 0.8219 (m-40) REVERT: D 267 GLN cc_start: 0.8546 (mt0) cc_final: 0.8221 (mt0) REVERT: D 474 MET cc_start: 0.6990 (ptp) cc_final: 0.6456 (ptt) outliers start: 48 outliers final: 28 residues processed: 332 average time/residue: 0.2893 time to fit residues: 152.5746 Evaluate side-chains 328 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 296 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 616 SER Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 616 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 208 ASN B 51 GLN B 208 ASN C 51 GLN C 208 ASN D 51 GLN D 208 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20548 Z= 0.260 Angle : 0.501 6.228 27860 Z= 0.247 Chirality : 0.038 0.152 3164 Planarity : 0.004 0.048 3428 Dihedral : 13.882 172.594 3532 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.92 % Allowed : 13.27 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.17), residues: 2392 helix: 1.43 (0.13), residues: 1468 sheet: -3.34 (0.37), residues: 124 loop : -0.75 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 495 HIS 0.002 0.001 HIS C 636 PHE 0.011 0.001 PHE A 169 TYR 0.013 0.001 TYR B 526 ARG 0.004 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 288 time to evaluate : 2.275 Fit side-chains REVERT: A 160 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8599 (pp) REVERT: A 217 ASN cc_start: 0.8598 (t0) cc_final: 0.8209 (m-40) REVERT: A 300 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8299 (mmmt) REVERT: A 474 MET cc_start: 0.6905 (ptp) cc_final: 0.6326 (ptt) REVERT: A 554 MET cc_start: 0.8435 (mmm) cc_final: 0.8173 (mmm) REVERT: B 160 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 217 ASN cc_start: 0.8597 (t0) cc_final: 0.8210 (m-40) REVERT: B 300 LYS cc_start: 0.8639 (mtmm) cc_final: 0.8297 (mmmt) REVERT: B 474 MET cc_start: 0.6909 (ptp) cc_final: 0.6332 (ptt) REVERT: B 554 MET cc_start: 0.8428 (mmm) cc_final: 0.8175 (mmm) REVERT: C 160 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8599 (pp) REVERT: C 217 ASN cc_start: 0.8597 (t0) cc_final: 0.8210 (m-40) REVERT: C 300 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8295 (mmmt) REVERT: C 474 MET cc_start: 0.6895 (ptp) cc_final: 0.6315 (ptt) REVERT: C 554 MET cc_start: 0.8429 (mmm) cc_final: 0.8170 (mmm) REVERT: D 160 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8599 (pp) REVERT: D 217 ASN cc_start: 0.8598 (t0) cc_final: 0.8209 (m-40) REVERT: D 300 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8296 (mmmt) REVERT: D 474 MET cc_start: 0.6900 (ptp) cc_final: 0.6322 (ptt) REVERT: D 554 MET cc_start: 0.8434 (mmm) cc_final: 0.8166 (mmm) outliers start: 40 outliers final: 28 residues processed: 320 average time/residue: 0.3039 time to fit residues: 152.9329 Evaluate side-chains 300 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 268 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.2980 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 208 ASN C 208 ASN D 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20548 Z= 0.271 Angle : 0.504 6.331 27860 Z= 0.248 Chirality : 0.038 0.157 3164 Planarity : 0.004 0.046 3428 Dihedral : 13.922 172.433 3532 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.68 % Allowed : 13.07 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2392 helix: 1.46 (0.13), residues: 1468 sheet: -3.32 (0.38), residues: 124 loop : -0.74 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 495 HIS 0.002 0.001 HIS D 201 PHE 0.011 0.001 PHE B 169 TYR 0.013 0.001 TYR B 526 ARG 0.004 0.000 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 276 time to evaluate : 2.124 Fit side-chains REVERT: A 160 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8601 (pp) REVERT: A 217 ASN cc_start: 0.8605 (t0) cc_final: 0.8205 (m-40) REVERT: A 300 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8246 (mmtt) REVERT: A 474 MET cc_start: 0.6953 (ptp) cc_final: 0.6357 (ptt) REVERT: A 554 MET cc_start: 0.8479 (mmm) cc_final: 0.8199 (mmm) REVERT: B 160 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8603 (pp) REVERT: B 217 ASN cc_start: 0.8602 (t0) cc_final: 0.8205 (m-40) REVERT: B 300 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8245 (mmtt) REVERT: B 474 MET cc_start: 0.6958 (ptp) cc_final: 0.6364 (ptt) REVERT: B 554 MET cc_start: 0.8469 (mmm) cc_final: 0.8197 (mmm) REVERT: C 160 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8601 (pp) REVERT: C 217 ASN cc_start: 0.8605 (t0) cc_final: 0.8206 (m-40) REVERT: C 300 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8242 (mmtt) REVERT: C 474 MET cc_start: 0.6944 (ptp) cc_final: 0.6350 (ptt) REVERT: C 554 MET cc_start: 0.8469 (mmm) cc_final: 0.8192 (mmm) REVERT: D 160 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8603 (pp) REVERT: D 217 ASN cc_start: 0.8607 (t0) cc_final: 0.8206 (m-40) REVERT: D 300 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8243 (mmtt) REVERT: D 474 MET cc_start: 0.6951 (ptp) cc_final: 0.6356 (ptt) REVERT: D 554 MET cc_start: 0.8475 (mmm) cc_final: 0.8190 (mmm) outliers start: 56 outliers final: 32 residues processed: 324 average time/residue: 0.2944 time to fit residues: 149.9247 Evaluate side-chains 304 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 268 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 195 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 0.0470 chunk 144 optimal weight: 0.2980 chunk 141 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 208 ASN C 208 ASN D 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20548 Z= 0.129 Angle : 0.454 7.081 27860 Z= 0.222 Chirality : 0.036 0.177 3164 Planarity : 0.003 0.044 3428 Dihedral : 13.567 171.586 3532 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.30 % Allowed : 13.46 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2392 helix: 1.74 (0.13), residues: 1468 sheet: -3.30 (0.37), residues: 124 loop : -0.66 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 593 HIS 0.002 0.000 HIS C 201 PHE 0.010 0.001 PHE C 611 TYR 0.011 0.001 TYR A 621 ARG 0.004 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 284 time to evaluate : 2.403 Fit side-chains REVERT: A 160 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8593 (pp) REVERT: A 217 ASN cc_start: 0.8552 (t0) cc_final: 0.8174 (m-40) REVERT: A 267 GLN cc_start: 0.8567 (mt0) cc_final: 0.8242 (mt0) REVERT: A 300 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8283 (mmmt) REVERT: A 474 MET cc_start: 0.6879 (ptp) cc_final: 0.6281 (ptt) REVERT: A 554 MET cc_start: 0.8397 (mmm) cc_final: 0.8111 (mmm) REVERT: A 635 ASN cc_start: 0.8310 (p0) cc_final: 0.8007 (p0) REVERT: B 160 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8594 (pp) REVERT: B 217 ASN cc_start: 0.8546 (t0) cc_final: 0.8171 (m-40) REVERT: B 267 GLN cc_start: 0.8559 (mt0) cc_final: 0.8241 (mt0) REVERT: B 300 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8282 (mmmt) REVERT: B 474 MET cc_start: 0.6880 (ptp) cc_final: 0.6283 (ptt) REVERT: B 554 MET cc_start: 0.8389 (mmm) cc_final: 0.8109 (mmm) REVERT: B 635 ASN cc_start: 0.8306 (p0) cc_final: 0.8008 (p0) REVERT: C 160 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8593 (pp) REVERT: C 217 ASN cc_start: 0.8551 (t0) cc_final: 0.8174 (m-40) REVERT: C 267 GLN cc_start: 0.8553 (mt0) cc_final: 0.8235 (mt0) REVERT: C 300 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8280 (mmmt) REVERT: C 474 MET cc_start: 0.6866 (ptp) cc_final: 0.6268 (ptt) REVERT: C 554 MET cc_start: 0.8386 (mmm) cc_final: 0.8101 (mmm) REVERT: C 635 ASN cc_start: 0.8320 (p0) cc_final: 0.8027 (p0) REVERT: D 160 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8592 (pp) REVERT: D 217 ASN cc_start: 0.8551 (t0) cc_final: 0.8175 (m-40) REVERT: D 267 GLN cc_start: 0.8562 (mt0) cc_final: 0.8240 (mt0) REVERT: D 300 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8281 (mmmt) REVERT: D 474 MET cc_start: 0.6873 (ptp) cc_final: 0.6275 (ptt) REVERT: D 554 MET cc_start: 0.8393 (mmm) cc_final: 0.8100 (mmm) REVERT: D 635 ASN cc_start: 0.8311 (p0) cc_final: 0.8005 (p0) outliers start: 48 outliers final: 32 residues processed: 324 average time/residue: 0.3009 time to fit residues: 153.1852 Evaluate side-chains 312 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 0.0070 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20548 Z= 0.140 Angle : 0.443 7.163 27860 Z= 0.214 Chirality : 0.036 0.178 3164 Planarity : 0.003 0.041 3428 Dihedral : 13.273 169.767 3532 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.92 % Allowed : 13.84 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2392 helix: 1.85 (0.13), residues: 1468 sheet: -3.26 (0.38), residues: 124 loop : -0.65 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 593 HIS 0.002 0.000 HIS D 201 PHE 0.007 0.001 PHE A 169 TYR 0.009 0.001 TYR A 621 ARG 0.003 0.000 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 288 time to evaluate : 3.145 Fit side-chains REVERT: A 160 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 217 ASN cc_start: 0.8512 (t0) cc_final: 0.8181 (m-40) REVERT: A 267 GLN cc_start: 0.8573 (mt0) cc_final: 0.8236 (mt0) REVERT: A 300 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8295 (mmmt) REVERT: A 474 MET cc_start: 0.6908 (ptp) cc_final: 0.6312 (ptt) REVERT: A 554 MET cc_start: 0.8375 (mmm) cc_final: 0.8117 (mmm) REVERT: B 160 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8610 (pp) REVERT: B 217 ASN cc_start: 0.8509 (t0) cc_final: 0.8181 (m-40) REVERT: B 267 GLN cc_start: 0.8566 (mt0) cc_final: 0.8235 (mt0) REVERT: B 300 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8294 (mmmt) REVERT: B 474 MET cc_start: 0.6908 (ptp) cc_final: 0.6309 (ptt) REVERT: B 554 MET cc_start: 0.8364 (mmm) cc_final: 0.8112 (mmm) REVERT: C 160 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8608 (pp) REVERT: C 217 ASN cc_start: 0.8510 (t0) cc_final: 0.8179 (m-40) REVERT: C 267 GLN cc_start: 0.8561 (mt0) cc_final: 0.8229 (mt0) REVERT: C 300 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8291 (mmmt) REVERT: C 474 MET cc_start: 0.6899 (ptp) cc_final: 0.6301 (ptt) REVERT: C 554 MET cc_start: 0.8365 (mmm) cc_final: 0.8110 (mmm) REVERT: D 160 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8609 (pp) REVERT: D 217 ASN cc_start: 0.8512 (t0) cc_final: 0.8183 (m-40) REVERT: D 267 GLN cc_start: 0.8567 (mt0) cc_final: 0.8235 (mt0) REVERT: D 300 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8292 (mmmt) REVERT: D 474 MET cc_start: 0.6903 (ptp) cc_final: 0.6306 (ptt) REVERT: D 554 MET cc_start: 0.8366 (mmm) cc_final: 0.8104 (mmm) outliers start: 40 outliers final: 32 residues processed: 324 average time/residue: 0.3170 time to fit residues: 162.2934 Evaluate side-chains 308 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 272 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.9980 chunk 221 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 0.0370 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 214 optimal weight: 7.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 208 ASN C 208 ASN D 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20548 Z= 0.135 Angle : 0.444 7.408 27860 Z= 0.214 Chirality : 0.035 0.175 3164 Planarity : 0.003 0.041 3428 Dihedral : 13.110 168.811 3532 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.92 % Allowed : 14.03 % Favored : 84.05 % 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: 1.22 (0.17), residues: 2392 helix: 1.95 (0.14), residues: 1468 sheet: -3.25 (0.38), residues: 124 loop : -0.62 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 593 HIS 0.002 0.000 HIS D 201 PHE 0.014 0.001 PHE D 611 TYR 0.008 0.001 TYR B 555 ARG 0.007 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 288 time to evaluate : 2.344 Fit side-chains REVERT: A 160 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8621 (pp) REVERT: A 217 ASN cc_start: 0.8551 (t0) cc_final: 0.8188 (m-40) REVERT: A 267 GLN cc_start: 0.8546 (mt0) cc_final: 0.8218 (mt0) REVERT: A 282 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 300 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8294 (mmmt) REVERT: A 474 MET cc_start: 0.6918 (ptp) cc_final: 0.6317 (ptt) REVERT: A 554 MET cc_start: 0.8344 (mmm) cc_final: 0.8068 (mmm) REVERT: B 160 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8622 (pp) REVERT: B 217 ASN cc_start: 0.8549 (t0) cc_final: 0.8189 (m-40) REVERT: B 267 GLN cc_start: 0.8538 (mt0) cc_final: 0.8217 (mt0) REVERT: B 282 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 300 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8292 (mmmt) REVERT: B 474 MET cc_start: 0.6916 (ptp) cc_final: 0.6319 (ptt) REVERT: B 554 MET cc_start: 0.8333 (mmm) cc_final: 0.8066 (mmm) REVERT: C 160 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8621 (pp) REVERT: C 217 ASN cc_start: 0.8552 (t0) cc_final: 0.8188 (m-40) REVERT: C 267 GLN cc_start: 0.8535 (mt0) cc_final: 0.8214 (mt0) REVERT: C 282 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7447 (mt-10) REVERT: C 300 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8290 (mmmt) REVERT: C 474 MET cc_start: 0.6907 (ptp) cc_final: 0.6306 (ptt) REVERT: C 554 MET cc_start: 0.8331 (mmm) cc_final: 0.8058 (mmm) REVERT: D 160 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8621 (pp) REVERT: D 217 ASN cc_start: 0.8551 (t0) cc_final: 0.8188 (m-40) REVERT: D 267 GLN cc_start: 0.8540 (mt0) cc_final: 0.8215 (mt0) REVERT: D 282 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7452 (mt-10) REVERT: D 300 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8290 (mmmt) REVERT: D 474 MET cc_start: 0.6909 (ptp) cc_final: 0.6311 (ptt) REVERT: D 554 MET cc_start: 0.8334 (mmm) cc_final: 0.8056 (mmm) outliers start: 40 outliers final: 32 residues processed: 320 average time/residue: 0.2979 time to fit residues: 150.1635 Evaluate side-chains 312 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.0970 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 0.0370 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 0.0060 chunk 116 optimal weight: 2.9990 overall best weight: 0.6276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 20548 Z= 0.209 Angle : 0.997 59.011 27860 Z= 0.597 Chirality : 0.039 0.485 3164 Planarity : 0.004 0.069 3428 Dihedral : 13.131 168.805 3532 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.34 % Favored : 98.49 % Rotamer: Outliers : 1.34 % Allowed : 14.61 % Favored : 84.05 % 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: 1.21 (0.17), residues: 2392 helix: 1.95 (0.14), residues: 1468 sheet: -3.25 (0.38), residues: 124 loop : -0.65 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 593 HIS 0.002 0.000 HIS D 201 PHE 0.014 0.001 PHE D 611 TYR 0.008 0.001 TYR B 555 ARG 0.006 0.000 ARG D 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 276 time to evaluate : 2.197 Fit side-chains REVERT: A 160 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8622 (pp) REVERT: A 217 ASN cc_start: 0.8546 (t0) cc_final: 0.8185 (m-40) REVERT: A 267 GLN cc_start: 0.8574 (mt0) cc_final: 0.8218 (mt0) REVERT: A 300 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8294 (mmmt) REVERT: A 474 MET cc_start: 0.6917 (ptp) cc_final: 0.6316 (ptt) REVERT: A 554 MET cc_start: 0.8343 (mmm) cc_final: 0.8067 (mmm) REVERT: B 160 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8623 (pp) REVERT: B 217 ASN cc_start: 0.8545 (t0) cc_final: 0.8186 (m-40) REVERT: B 267 GLN cc_start: 0.8567 (mt0) cc_final: 0.8217 (mt0) REVERT: B 300 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8292 (mmmt) REVERT: B 474 MET cc_start: 0.6916 (ptp) cc_final: 0.6318 (ptt) REVERT: B 554 MET cc_start: 0.8332 (mmm) cc_final: 0.8064 (mmm) REVERT: C 160 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8621 (pp) REVERT: C 217 ASN cc_start: 0.8548 (t0) cc_final: 0.8185 (m-40) REVERT: C 267 GLN cc_start: 0.8565 (mt0) cc_final: 0.8215 (mt0) REVERT: C 300 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8290 (mmmt) REVERT: C 474 MET cc_start: 0.6905 (ptp) cc_final: 0.6305 (ptt) REVERT: C 554 MET cc_start: 0.8330 (mmm) cc_final: 0.8056 (mmm) REVERT: D 160 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8622 (pp) REVERT: D 217 ASN cc_start: 0.8547 (t0) cc_final: 0.8185 (m-40) REVERT: D 267 GLN cc_start: 0.8569 (mt0) cc_final: 0.8215 (mt0) REVERT: D 300 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8290 (mmmt) REVERT: D 474 MET cc_start: 0.6908 (ptp) cc_final: 0.6311 (ptt) REVERT: D 554 MET cc_start: 0.8334 (mmm) cc_final: 0.8056 (mmm) outliers start: 28 outliers final: 24 residues processed: 300 average time/residue: 0.2828 time to fit residues: 136.2442 Evaluate side-chains 308 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.125013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.099640 restraints weight = 24114.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099722 restraints weight = 18218.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100175 restraints weight = 15234.661| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 20548 Z= 0.209 Angle : 0.997 59.008 27860 Z= 0.597 Chirality : 0.039 0.485 3164 Planarity : 0.004 0.069 3428 Dihedral : 13.131 168.805 3532 Min Nonbonded Distance : 1.370 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.34 % Favored : 98.49 % Rotamer: Outliers : 1.34 % Allowed : 14.80 % Favored : 83.86 % 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: 1.21 (0.17), residues: 2392 helix: 1.95 (0.14), residues: 1468 sheet: -3.25 (0.38), residues: 124 loop : -0.65 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 593 HIS 0.002 0.000 HIS D 201 PHE 0.014 0.001 PHE D 611 TYR 0.008 0.001 TYR B 555 ARG 0.006 0.000 ARG D 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.05 seconds wall clock time: 71 minutes 25.18 seconds (4285.18 seconds total)