Starting phenix.real_space_refine on Sun Jun 15 08:08:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j5r_5777/06_2025/3j5r_5777.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j5r_5777/06_2025/3j5r_5777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j5r_5777/06_2025/3j5r_5777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j5r_5777/06_2025/3j5r_5777.map" model { file = "/net/cci-nas-00/data/ceres_data/3j5r_5777/06_2025/3j5r_5777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j5r_5777/06_2025/3j5r_5777.cif" } resolution = 4.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 11388 2.51 5 N 2904 2.21 5 O 3192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17564 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4338 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 88} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 560} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 208 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4338 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 88} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 560} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 208 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4338 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 88} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 560} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 208 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4338 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 88} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 560} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 208 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 10.01, per 1000 atoms: 0.57 Number of scatterers: 17564 At special positions: 0 Unit cell: (132.5, 132.5, 119.129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 3192 8.00 N 2904 7.00 C 11388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 2.2 seconds 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 71.1% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'B' and resid 113 through 123 removed outlier: 3.560A pdb=" N ILE B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 170 through 183 removed outlier: 4.313A pdb=" N ALA B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 406 through 413 removed outlier: 4.550A pdb=" N HIS B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP B 411 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET B 412 " --> pdb=" O ASN B 408 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 413' Processing helix chain 'B' and resid 417 through 429 removed outlier: 3.544A pdb=" N TRP B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.607A pdb=" N PHE B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 499 removed outlier: 3.794A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 487 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 533 removed outlier: 3.756A pdb=" N PHE B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 556 removed outlier: 3.980A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 580 removed outlier: 3.529A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 599 Processing helix chain 'B' and resid 629 through 643 removed outlier: 4.194A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 670 Processing helix chain 'B' and resid 670 through 687 removed outlier: 4.021A pdb=" N MET B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 711 removed outlier: 3.988A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 123 removed outlier: 3.560A pdb=" N ILE A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 170 through 183 removed outlier: 4.313A pdb=" N ALA A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 406 through 413 removed outlier: 4.550A pdb=" N HIS A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A 412 " --> pdb=" O ASN A 408 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 413' Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.545A pdb=" N TRP A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.608A pdb=" N PHE A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 499 removed outlier: 3.793A pdb=" N ASP A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 533 removed outlier: 3.756A pdb=" N PHE A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 556 removed outlier: 3.980A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.529A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 599 Processing helix chain 'A' and resid 629 through 643 removed outlier: 4.194A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 670 Processing helix chain 'A' and resid 670 through 687 removed outlier: 4.021A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 711 removed outlier: 3.989A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 170 through 183 removed outlier: 4.312A pdb=" N ALA C 174 " --> pdb=" O ASN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'C' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 406 through 413 removed outlier: 4.549A pdb=" N HIS C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP C 411 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET C 412 " --> pdb=" O ASN C 408 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 413' Processing helix chain 'C' and resid 417 through 429 removed outlier: 3.544A pdb=" N TRP C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.607A pdb=" N PHE C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 499 removed outlier: 3.794A pdb=" N ASP C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 533 removed outlier: 3.757A pdb=" N PHE C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 556 removed outlier: 3.980A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 580 removed outlier: 3.530A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 599 Processing helix chain 'C' and resid 629 through 643 removed outlier: 4.194A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 670 Processing helix chain 'C' and resid 670 through 687 removed outlier: 4.022A pdb=" N MET C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET C 682 " --> pdb=" O LEU C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 711 removed outlier: 3.988A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE C 696 " --> pdb=" O GLU C 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP C 697 " --> pdb=" O SER C 693 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 170 through 183 removed outlier: 4.313A pdb=" N ALA D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 191 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 345 through 355 Processing helix chain 'D' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 406 through 413 removed outlier: 4.549A pdb=" N HIS D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP D 411 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET D 412 " --> pdb=" O ASN D 408 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 406 through 413' Processing helix chain 'D' and resid 417 through 429 removed outlier: 3.545A pdb=" N TRP D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.607A pdb=" N PHE D 436 " --> pdb=" O ARG D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 499 removed outlier: 3.794A pdb=" N ASP D 471 " --> pdb=" O ASN D 467 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 487 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE D 488 " --> pdb=" O GLY D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 533 removed outlier: 3.756A pdb=" N PHE D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 556 removed outlier: 3.980A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 580 removed outlier: 3.529A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 599 Processing helix chain 'D' and resid 629 through 643 removed outlier: 4.194A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 670 Processing helix chain 'D' and resid 670 through 687 removed outlier: 4.021A pdb=" N MET D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 711 removed outlier: 3.988A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP D 697 " --> pdb=" O SER D 693 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'B' and resid 378 through 382 Processing sheet with id=B, first strand: chain 'A' and resid 378 through 382 Processing sheet with id=C, first strand: chain 'C' and resid 378 through 382 Processing sheet with id=D, first strand: chain 'D' and resid 378 through 382 1048 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 5596 1.36 - 1.52: 7792 1.52 - 1.68: 4388 1.68 - 1.85: 108 1.85 - 2.01: 24 Bond restraints: 17908 Sorted by residual: bond pdb=" CG MET A 162 " pdb=" SD MET A 162 " ideal model delta sigma weight residual 1.803 2.007 -0.204 2.50e-02 1.60e+03 6.67e+01 bond pdb=" CG MET D 162 " pdb=" SD MET D 162 " ideal model delta sigma weight residual 1.803 2.007 -0.204 2.50e-02 1.60e+03 6.65e+01 bond pdb=" CG MET B 162 " pdb=" SD MET B 162 " ideal model delta sigma weight residual 1.803 2.007 -0.204 2.50e-02 1.60e+03 6.64e+01 bond pdb=" CG MET C 162 " pdb=" SD MET C 162 " ideal model delta sigma weight residual 1.803 2.006 -0.203 2.50e-02 1.60e+03 6.60e+01 bond pdb=" CG MET A 214 " pdb=" SD MET A 214 " ideal model delta sigma weight residual 1.803 1.970 -0.167 2.50e-02 1.60e+03 4.48e+01 ... (remaining 17903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 23503 3.65 - 7.30: 769 7.30 - 10.94: 36 10.94 - 14.59: 16 14.59 - 18.24: 20 Bond angle restraints: 24344 Sorted by residual: angle pdb=" N VAL C 415 " pdb=" CA VAL C 415 " pdb=" C VAL C 415 " ideal model delta sigma weight residual 110.72 124.61 -13.89 1.01e+00 9.80e-01 1.89e+02 angle pdb=" N VAL A 415 " pdb=" CA VAL A 415 " pdb=" C VAL A 415 " ideal model delta sigma weight residual 110.72 124.61 -13.89 1.01e+00 9.80e-01 1.89e+02 angle pdb=" N VAL B 415 " pdb=" CA VAL B 415 " pdb=" C VAL B 415 " ideal model delta sigma weight residual 110.72 124.60 -13.88 1.01e+00 9.80e-01 1.89e+02 angle pdb=" N VAL D 415 " pdb=" CA VAL D 415 " pdb=" C VAL D 415 " ideal model delta sigma weight residual 110.72 124.60 -13.88 1.01e+00 9.80e-01 1.89e+02 angle pdb=" N ASP B 383 " pdb=" CA ASP B 383 " pdb=" C ASP B 383 " ideal model delta sigma weight residual 111.07 121.74 -10.67 1.07e+00 8.73e-01 9.95e+01 ... (remaining 24339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.92: 9326 24.92 - 49.84: 966 49.84 - 74.76: 172 74.76 - 99.68: 20 99.68 - 124.60: 8 Dihedral angle restraints: 10492 sinusoidal: 3584 harmonic: 6908 Sorted by residual: dihedral pdb=" CA GLY D 244 " pdb=" C GLY D 244 " pdb=" N PHE D 245 " pdb=" CA PHE D 245 " ideal model delta harmonic sigma weight residual 180.00 55.40 124.60 0 5.00e+00 4.00e-02 6.21e+02 dihedral pdb=" CA GLY C 244 " pdb=" C GLY C 244 " pdb=" N PHE C 245 " pdb=" CA PHE C 245 " ideal model delta harmonic sigma weight residual 180.00 55.42 124.58 0 5.00e+00 4.00e-02 6.21e+02 dihedral pdb=" CA GLY B 244 " pdb=" C GLY B 244 " pdb=" N PHE B 245 " pdb=" CA PHE B 245 " ideal model delta harmonic sigma weight residual 180.00 55.46 124.54 0 5.00e+00 4.00e-02 6.20e+02 ... (remaining 10489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2283 0.105 - 0.210: 493 0.210 - 0.315: 68 0.315 - 0.420: 16 0.420 - 0.526: 8 Chirality restraints: 2868 Sorted by residual: chirality pdb=" CA GLU A 249 " pdb=" N GLU A 249 " pdb=" C GLU A 249 " pdb=" CB GLU A 249 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CA GLU D 249 " pdb=" N GLU D 249 " pdb=" C GLU D 249 " pdb=" CB GLU D 249 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CA GLU B 249 " pdb=" N GLU B 249 " pdb=" C GLU B 249 " pdb=" CB GLU B 249 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.88e+00 ... (remaining 2865 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 686 " 0.053 2.00e-02 2.50e+03 1.10e-01 1.21e+02 pdb=" C VAL D 686 " -0.190 2.00e-02 2.50e+03 pdb=" O VAL D 686 " 0.075 2.00e-02 2.50e+03 pdb=" N ASN D 687 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 686 " 0.053 2.00e-02 2.50e+03 1.10e-01 1.20e+02 pdb=" C VAL B 686 " -0.190 2.00e-02 2.50e+03 pdb=" O VAL B 686 " 0.075 2.00e-02 2.50e+03 pdb=" N ASN B 687 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 686 " -0.053 2.00e-02 2.50e+03 1.10e-01 1.20e+02 pdb=" C VAL A 686 " 0.190 2.00e-02 2.50e+03 pdb=" O VAL A 686 " -0.075 2.00e-02 2.50e+03 pdb=" N ASN A 687 " -0.062 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 71 1.94 - 2.68: 1111 2.68 - 3.42: 27695 3.42 - 4.16: 42248 4.16 - 4.90: 72983 Nonbonded interactions: 144108 Sorted by model distance: nonbonded pdb=" OE1 GLN C 519 " pdb=" N GLY C 548 " model vdw 1.204 3.120 nonbonded pdb=" OE1 GLN A 519 " pdb=" N GLY A 548 " model vdw 1.204 3.120 nonbonded pdb=" OE1 GLN B 519 " pdb=" N GLY B 548 " model vdw 1.205 3.120 nonbonded pdb=" OE1 GLN D 519 " pdb=" N GLY D 548 " model vdw 1.205 3.120 nonbonded pdb=" O ASP B 601 " pdb=" ND2 ASN B 652 " model vdw 1.369 3.120 ... (remaining 144103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 38.500 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4867 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 : 0.011 0.204 17908 Z= 0.640 Angle : 1.571 18.239 24344 Z= 1.086 Chirality : 0.091 0.526 2868 Planarity : 0.007 0.110 3072 Dihedral : 20.247 124.597 6052 Min Nonbonded Distance : 1.204 Molprobity Statistics. All-atom Clashscore : 84.36 Ramachandran Plot: Outliers : 1.21 % Allowed : 7.80 % Favored : 90.99 % Rotamer: Outliers : 28.64 % Allowed : 15.75 % Favored : 55.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 1.06 % 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: -0.91 (0.17), residues: 2308 helix: 0.14 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -1.76 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 272 HIS 0.007 0.002 HIS C 289 PHE 0.024 0.001 PHE D 235 TYR 0.022 0.001 TYR B 309 ARG 0.005 0.001 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.26719 ( 1048) hydrogen bonds : angle 8.66466 ( 3048) covalent geometry : bond 0.01076 (17908) covalent geometry : angle 1.57118 (24344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 480 poor density : 429 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.2268 (OUTLIER) cc_final: -0.2576 (pt) REVERT: B 158 LEU cc_start: 0.3596 (OUTLIER) cc_final: 0.3356 (tp) REVERT: B 218 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7438 (p) REVERT: B 394 SER cc_start: 0.5460 (OUTLIER) cc_final: 0.5159 (t) REVERT: B 421 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5827 (tp) REVERT: B 545 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6584 (tp) REVERT: B 668 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6719 (pp) REVERT: B 681 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5306 (pp) REVERT: A 136 LEU cc_start: -0.2703 (OUTLIER) cc_final: -0.2958 (pt) REVERT: A 158 LEU cc_start: 0.3769 (OUTLIER) cc_final: 0.3560 (tp) REVERT: A 218 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7405 (p) REVERT: A 421 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5739 (tp) REVERT: A 668 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6758 (pp) REVERT: A 681 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5121 (pp) REVERT: C 136 LEU cc_start: -0.2953 (OUTLIER) cc_final: -0.3578 (pt) REVERT: C 218 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7647 (p) REVERT: C 421 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5786 (tp) REVERT: C 545 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6652 (tp) REVERT: C 647 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6668 (tm) REVERT: C 660 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7504 (pt) REVERT: C 668 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.6030 (pp) REVERT: C 681 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.4823 (pp) REVERT: D 136 LEU cc_start: -0.2305 (OUTLIER) cc_final: -0.2626 (pt) REVERT: D 218 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7552 (p) REVERT: D 394 SER cc_start: 0.5436 (OUTLIER) cc_final: 0.5227 (t) REVERT: D 421 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5817 (tp) REVERT: D 668 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6748 (pp) REVERT: D 681 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5006 (pp) outliers start: 480 outliers final: 129 residues processed: 772 average time/residue: 0.3093 time to fit residues: 349.5678 Evaluate side-chains 433 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 276 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 120 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 184 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN B 289 HIS B 533 GLN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 GLN D 164 ASN D 289 HIS D 533 GLN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.111901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060421 restraints weight = 53245.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.060090 restraints weight = 61685.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.060090 restraints weight = 64520.348| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 17908 Z= 0.276 Angle : 1.001 14.095 24344 Z= 0.519 Chirality : 0.049 0.416 2868 Planarity : 0.006 0.074 3072 Dihedral : 7.996 76.777 2548 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.87 % Allowed : 3.90 % Favored : 95.23 % Rotamer: Outliers : 1.73 % Allowed : 3.52 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: -0.35 (0.17), residues: 2308 helix: 0.47 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.43 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 697 HIS 0.004 0.002 HIS A 289 PHE 0.033 0.003 PHE B 434 TYR 0.042 0.003 TYR D 555 ARG 0.004 0.001 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.06670 ( 1048) hydrogen bonds : angle 5.74389 ( 3048) covalent geometry : bond 0.00574 (17908) covalent geometry : angle 1.00092 (24344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 324 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 MET cc_start: 0.9544 (mmp) cc_final: 0.9298 (mmm) REVERT: B 448 PHE cc_start: 0.9476 (t80) cc_final: 0.9062 (t80) REVERT: B 522 PHE cc_start: 0.9458 (m-80) cc_final: 0.9129 (m-80) REVERT: B 545 LEU cc_start: 0.9662 (tt) cc_final: 0.9380 (tp) REVERT: B 547 MET cc_start: 0.8929 (ptp) cc_final: 0.8587 (ptm) REVERT: B 549 TRP cc_start: 0.7442 (m100) cc_final: 0.6388 (m100) REVERT: B 591 PHE cc_start: 0.9355 (m-80) cc_final: 0.9094 (m-80) REVERT: A 445 MET cc_start: 0.9539 (mmp) cc_final: 0.9225 (mmm) REVERT: A 448 PHE cc_start: 0.9522 (t80) cc_final: 0.9098 (t80) REVERT: A 522 PHE cc_start: 0.9474 (m-80) cc_final: 0.9110 (m-80) REVERT: A 538 VAL cc_start: 0.9512 (OUTLIER) cc_final: 0.9138 (m) REVERT: A 547 MET cc_start: 0.8923 (ptp) cc_final: 0.8596 (ptm) REVERT: A 549 TRP cc_start: 0.7857 (m100) cc_final: 0.6962 (m100) REVERT: A 580 PHE cc_start: 0.9173 (t80) cc_final: 0.8698 (t80) REVERT: A 591 PHE cc_start: 0.9340 (m-80) cc_final: 0.9092 (m-80) REVERT: C 308 MET cc_start: 0.9525 (mtm) cc_final: 0.9258 (mpp) REVERT: C 448 PHE cc_start: 0.9467 (t80) cc_final: 0.9032 (t80) REVERT: C 522 PHE cc_start: 0.9333 (m-80) cc_final: 0.9086 (m-80) REVERT: C 538 VAL cc_start: 0.9489 (OUTLIER) cc_final: 0.9101 (m) REVERT: C 541 MET cc_start: 0.9531 (ptt) cc_final: 0.9289 (ppp) REVERT: C 549 TRP cc_start: 0.7391 (m100) cc_final: 0.6284 (m100) REVERT: C 568 MET cc_start: 0.9262 (ttp) cc_final: 0.8983 (ttm) REVERT: C 572 MET cc_start: 0.8128 (mtm) cc_final: 0.7698 (ptp) REVERT: C 580 PHE cc_start: 0.9593 (t80) cc_final: 0.9307 (t80) REVERT: C 635 LEU cc_start: 0.9667 (mm) cc_final: 0.9440 (pp) REVERT: D 445 MET cc_start: 0.9552 (mmp) cc_final: 0.9289 (mmm) REVERT: D 448 PHE cc_start: 0.9549 (t80) cc_final: 0.9103 (t80) REVERT: D 522 PHE cc_start: 0.9477 (m-80) cc_final: 0.9077 (m-80) REVERT: D 538 VAL cc_start: 0.9599 (OUTLIER) cc_final: 0.9201 (m) REVERT: D 545 LEU cc_start: 0.9672 (pp) cc_final: 0.9458 (pp) REVERT: D 547 MET cc_start: 0.8962 (ptp) cc_final: 0.8663 (ptp) REVERT: D 549 TRP cc_start: 0.7799 (m100) cc_final: 0.6970 (m100) REVERT: D 568 MET cc_start: 0.9612 (ttp) cc_final: 0.9359 (ttm) REVERT: D 569 ILE cc_start: 0.9428 (tt) cc_final: 0.9192 (pt) REVERT: D 572 MET cc_start: 0.9360 (mmp) cc_final: 0.8790 (ptm) REVERT: D 591 PHE cc_start: 0.9470 (m-80) cc_final: 0.9234 (m-80) REVERT: D 647 LEU cc_start: 0.9386 (tt) cc_final: 0.9070 (tt) outliers start: 29 outliers final: 4 residues processed: 348 average time/residue: 0.2361 time to fit residues: 133.8113 Evaluate side-chains 250 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 243 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 131 optimal weight: 10.0000 chunk 176 optimal weight: 40.0000 chunk 146 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 40.0000 chunk 173 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN B 652 ASN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 GLN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 GLN C 676 ASN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 GLN D 560 GLN D 652 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.097385 restraints weight = 26166.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.097263 restraints weight = 39869.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.097245 restraints weight = 40682.093| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17908 Z= 0.175 Angle : 0.860 15.899 24344 Z= 0.436 Chirality : 0.043 0.340 2868 Planarity : 0.005 0.073 3072 Dihedral : 7.159 66.511 2548 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.85 % Favored : 93.63 % Rotamer: Outliers : 0.60 % Allowed : 5.37 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: 0.06 (0.17), residues: 2308 helix: 0.79 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.25 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 697 HIS 0.005 0.001 HIS C 206 PHE 0.030 0.002 PHE C 543 TYR 0.029 0.002 TYR C 555 ARG 0.008 0.000 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 1048) hydrogen bonds : angle 5.08677 ( 3048) covalent geometry : bond 0.00355 (17908) covalent geometry : angle 0.85972 (24344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 318 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 541 MET cc_start: 0.9670 (ptt) cc_final: 0.9397 (ppp) REVERT: B 562 MET cc_start: 0.9256 (mmp) cc_final: 0.8968 (mmm) REVERT: B 572 MET cc_start: 0.7914 (ptm) cc_final: 0.7578 (ptt) REVERT: B 580 PHE cc_start: 0.9274 (t80) cc_final: 0.8662 (t80) REVERT: B 591 PHE cc_start: 0.9497 (m-80) cc_final: 0.9123 (m-80) REVERT: B 642 ILE cc_start: 0.7935 (mt) cc_final: 0.7634 (mt) REVERT: B 644 MET cc_start: 0.8880 (tpp) cc_final: 0.8504 (tpp) REVERT: A 445 MET cc_start: 0.9536 (mmp) cc_final: 0.9143 (mmm) REVERT: A 448 PHE cc_start: 0.9571 (t80) cc_final: 0.9228 (t80) REVERT: A 522 PHE cc_start: 0.9508 (m-80) cc_final: 0.9118 (m-80) REVERT: A 547 MET cc_start: 0.9221 (ptp) cc_final: 0.9000 (ptp) REVERT: A 549 TRP cc_start: 0.8042 (m100) cc_final: 0.7006 (m100) REVERT: A 572 MET cc_start: 0.7838 (ptm) cc_final: 0.7489 (ptt) REVERT: A 580 PHE cc_start: 0.9329 (t80) cc_final: 0.8756 (t80) REVERT: A 591 PHE cc_start: 0.9486 (m-80) cc_final: 0.9164 (m-80) REVERT: C 426 TRP cc_start: 0.8283 (t-100) cc_final: 0.7961 (t-100) REVERT: C 448 PHE cc_start: 0.9587 (t80) cc_final: 0.9271 (t80) REVERT: C 549 TRP cc_start: 0.7783 (m100) cc_final: 0.7333 (m100) REVERT: C 568 MET cc_start: 0.9205 (ttp) cc_final: 0.8851 (ttm) REVERT: C 569 ILE cc_start: 0.8634 (pt) cc_final: 0.8328 (pt) REVERT: C 572 MET cc_start: 0.8282 (mtm) cc_final: 0.7769 (ptp) REVERT: C 580 PHE cc_start: 0.9580 (t80) cc_final: 0.9006 (t80) REVERT: C 591 PHE cc_start: 0.9444 (m-10) cc_final: 0.9227 (m-10) REVERT: C 659 PHE cc_start: 0.9112 (t80) cc_final: 0.8911 (t80) REVERT: D 445 MET cc_start: 0.9536 (mmp) cc_final: 0.9297 (mmm) REVERT: D 448 PHE cc_start: 0.9550 (t80) cc_final: 0.9176 (t80) REVERT: D 522 PHE cc_start: 0.9464 (m-80) cc_final: 0.9050 (m-80) REVERT: D 543 PHE cc_start: 0.9489 (m-80) cc_final: 0.9283 (m-80) REVERT: D 549 TRP cc_start: 0.8010 (m100) cc_final: 0.6967 (m100) REVERT: D 568 MET cc_start: 0.9577 (ttp) cc_final: 0.9200 (ptm) REVERT: D 572 MET cc_start: 0.9262 (mmp) cc_final: 0.8710 (ptm) REVERT: D 591 PHE cc_start: 0.9523 (m-80) cc_final: 0.9142 (m-80) REVERT: D 597 THR cc_start: 0.8684 (p) cc_final: 0.8248 (p) REVERT: D 647 LEU cc_start: 0.9362 (tt) cc_final: 0.9017 (mp) outliers start: 10 outliers final: 0 residues processed: 327 average time/residue: 0.2273 time to fit residues: 121.1527 Evaluate side-chains 239 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 162 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 94 optimal weight: 0.0970 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.111064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.061605 restraints weight = 52950.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.061495 restraints weight = 63540.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.061490 restraints weight = 64768.268| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17908 Z= 0.160 Angle : 0.834 16.808 24344 Z= 0.418 Chirality : 0.042 0.265 2868 Planarity : 0.006 0.098 3072 Dihedral : 6.875 62.001 2548 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.42 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: 0.15 (0.18), residues: 2308 helix: 0.81 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -1.09 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 697 HIS 0.003 0.001 HIS B 206 PHE 0.027 0.002 PHE C 543 TYR 0.026 0.002 TYR B 555 ARG 0.005 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 1048) hydrogen bonds : angle 4.97907 ( 3048) covalent geometry : bond 0.00329 (17908) covalent geometry : angle 0.83355 (24344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 308 MET cc_start: 0.9364 (mmm) cc_final: 0.9032 (mmm) REVERT: B 445 MET cc_start: 0.9553 (mmp) cc_final: 0.9325 (mmm) REVERT: B 448 PHE cc_start: 0.9739 (t80) cc_final: 0.9195 (t80) REVERT: B 549 TRP cc_start: 0.8268 (m100) cc_final: 0.7055 (m100) REVERT: B 580 PHE cc_start: 0.8982 (t80) cc_final: 0.8411 (t80) REVERT: B 591 PHE cc_start: 0.9402 (m-80) cc_final: 0.9166 (m-80) REVERT: B 637 LEU cc_start: 0.9599 (mt) cc_final: 0.9353 (pp) REVERT: A 308 MET cc_start: 0.9406 (mmm) cc_final: 0.9062 (mmm) REVERT: A 445 MET cc_start: 0.9500 (mmp) cc_final: 0.9258 (mmm) REVERT: A 448 PHE cc_start: 0.9733 (t80) cc_final: 0.9430 (t80) REVERT: A 522 PHE cc_start: 0.9463 (m-80) cc_final: 0.9087 (m-80) REVERT: A 543 PHE cc_start: 0.9621 (m-80) cc_final: 0.9294 (m-80) REVERT: A 547 MET cc_start: 0.9126 (ptp) cc_final: 0.8816 (ptp) REVERT: A 549 TRP cc_start: 0.8372 (m100) cc_final: 0.7095 (m100) REVERT: A 580 PHE cc_start: 0.9078 (t80) cc_final: 0.8482 (t80) REVERT: A 591 PHE cc_start: 0.9309 (m-80) cc_final: 0.9059 (m-80) REVERT: C 426 TRP cc_start: 0.8546 (t-100) cc_final: 0.8209 (t-100) REVERT: C 448 PHE cc_start: 0.9757 (t80) cc_final: 0.9408 (t80) REVERT: C 543 PHE cc_start: 0.9565 (m-80) cc_final: 0.9251 (m-80) REVERT: C 549 TRP cc_start: 0.8184 (m100) cc_final: 0.7024 (m100) REVERT: C 568 MET cc_start: 0.9122 (ttp) cc_final: 0.8751 (ttm) REVERT: C 569 ILE cc_start: 0.8411 (pt) cc_final: 0.8106 (pt) REVERT: C 572 MET cc_start: 0.7909 (mtm) cc_final: 0.7322 (ptp) REVERT: C 580 PHE cc_start: 0.9441 (t80) cc_final: 0.8920 (t80) REVERT: C 659 PHE cc_start: 0.9235 (t80) cc_final: 0.8984 (t80) REVERT: D 308 MET cc_start: 0.9395 (mmm) cc_final: 0.9064 (mmm) REVERT: D 445 MET cc_start: 0.9554 (mmp) cc_final: 0.9315 (mmm) REVERT: D 448 PHE cc_start: 0.9730 (t80) cc_final: 0.9378 (t80) REVERT: D 549 TRP cc_start: 0.8247 (m100) cc_final: 0.7065 (m100) REVERT: D 562 MET cc_start: 0.9321 (mmp) cc_final: 0.9085 (mmm) REVERT: D 568 MET cc_start: 0.9526 (ttp) cc_final: 0.9106 (ptm) REVERT: D 569 ILE cc_start: 0.9446 (pt) cc_final: 0.9086 (pt) REVERT: D 572 MET cc_start: 0.9265 (mmp) cc_final: 0.8753 (mtp) REVERT: D 573 ILE cc_start: 0.8996 (pt) cc_final: 0.8724 (pt) REVERT: D 580 PHE cc_start: 0.8874 (t80) cc_final: 0.8318 (t80) REVERT: D 591 PHE cc_start: 0.9435 (m-80) cc_final: 0.9165 (m-80) REVERT: D 597 THR cc_start: 0.8780 (p) cc_final: 0.8526 (p) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2329 time to fit residues: 112.9527 Evaluate side-chains 248 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 26 optimal weight: 4.9990 chunk 118 optimal weight: 70.0000 chunk 133 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 235 optimal weight: 40.0000 chunk 226 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 234 optimal weight: 0.4980 chunk 200 optimal weight: 7.9990 chunk 177 optimal weight: 60.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN B 202 GLN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN A 202 GLN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN C 202 GLN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 GLN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN D 533 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.108430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059215 restraints weight = 60904.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059215 restraints weight = 69573.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059215 restraints weight = 69573.877| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.7484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17908 Z= 0.179 Angle : 0.788 17.981 24344 Z= 0.398 Chirality : 0.041 0.214 2868 Planarity : 0.005 0.086 3072 Dihedral : 6.317 50.423 2548 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.16 % Favored : 94.50 % Rotamer: Outliers : 0.18 % Allowed : 3.34 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: 0.08 (0.18), residues: 2308 helix: 0.74 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.16 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 697 HIS 0.006 0.001 HIS B 206 PHE 0.026 0.002 PHE C 304 TYR 0.022 0.002 TYR C 631 ARG 0.007 0.000 ARG B 701 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 1048) hydrogen bonds : angle 4.73373 ( 3048) covalent geometry : bond 0.00350 (17908) covalent geometry : angle 0.78801 (24344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 279 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 TRP cc_start: 0.8833 (t-100) cc_final: 0.8284 (t-100) REVERT: B 445 MET cc_start: 0.9578 (mmp) cc_final: 0.9266 (mmm) REVERT: B 549 TRP cc_start: 0.8403 (m100) cc_final: 0.7419 (m100) REVERT: B 580 PHE cc_start: 0.8934 (t80) cc_final: 0.8158 (t80) REVERT: B 591 PHE cc_start: 0.9419 (m-80) cc_final: 0.9215 (m-80) REVERT: B 642 ILE cc_start: 0.7294 (mt) cc_final: 0.6992 (mt) REVERT: A 445 MET cc_start: 0.9418 (mmp) cc_final: 0.9130 (mmm) REVERT: A 543 PHE cc_start: 0.9609 (m-80) cc_final: 0.9354 (m-80) REVERT: A 549 TRP cc_start: 0.8332 (m100) cc_final: 0.7518 (m100) REVERT: A 580 PHE cc_start: 0.9017 (t80) cc_final: 0.8346 (t80) REVERT: A 591 PHE cc_start: 0.9413 (m-80) cc_final: 0.9148 (m-80) REVERT: C 426 TRP cc_start: 0.8716 (t-100) cc_final: 0.8375 (t-100) REVERT: C 438 PHE cc_start: 0.9637 (t80) cc_final: 0.9426 (t80) REVERT: C 543 PHE cc_start: 0.9555 (m-80) cc_final: 0.9316 (m-80) REVERT: C 549 TRP cc_start: 0.8163 (m100) cc_final: 0.7431 (m100) REVERT: C 568 MET cc_start: 0.9172 (ttp) cc_final: 0.8811 (ttm) REVERT: C 569 ILE cc_start: 0.8538 (pt) cc_final: 0.8270 (pt) REVERT: C 572 MET cc_start: 0.8100 (mtm) cc_final: 0.7637 (mtp) REVERT: C 591 PHE cc_start: 0.9416 (m-10) cc_final: 0.9185 (m-10) REVERT: C 659 PHE cc_start: 0.9306 (t80) cc_final: 0.9003 (t80) REVERT: D 445 MET cc_start: 0.9483 (mmp) cc_final: 0.9281 (mmm) REVERT: D 549 TRP cc_start: 0.8297 (m100) cc_final: 0.7712 (m100) REVERT: D 568 MET cc_start: 0.9544 (ttp) cc_final: 0.9132 (ptt) REVERT: D 569 ILE cc_start: 0.9531 (pt) cc_final: 0.9252 (pt) REVERT: D 572 MET cc_start: 0.9324 (mmp) cc_final: 0.8879 (ptp) REVERT: D 573 ILE cc_start: 0.9178 (pt) cc_final: 0.8874 (pt) REVERT: D 580 PHE cc_start: 0.8896 (t80) cc_final: 0.8366 (t80) REVERT: D 591 PHE cc_start: 0.9448 (m-80) cc_final: 0.9071 (m-80) REVERT: D 644 MET cc_start: 0.8595 (tpp) cc_final: 0.8297 (tpp) outliers start: 3 outliers final: 0 residues processed: 282 average time/residue: 0.2321 time to fit residues: 108.6309 Evaluate side-chains 233 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 10.0000 chunk 83 optimal weight: 0.0000 chunk 218 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 176 optimal weight: 40.0000 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN D 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.102931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.054393 restraints weight = 56696.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.054393 restraints weight = 57119.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.054393 restraints weight = 57119.140| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.8135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17908 Z= 0.281 Angle : 0.877 20.489 24344 Z= 0.449 Chirality : 0.042 0.193 2868 Planarity : 0.006 0.080 3072 Dihedral : 6.400 52.053 2548 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.24 % Favored : 93.41 % Rotamer: Outliers : 0.12 % Allowed : 4.00 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: -0.10 (0.18), residues: 2308 helix: 0.54 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -1.08 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP C 697 HIS 0.005 0.002 HIS D 320 PHE 0.030 0.002 PHE C 640 TYR 0.041 0.002 TYR C 554 ARG 0.007 0.001 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.04866 ( 1048) hydrogen bonds : angle 5.02865 ( 3048) covalent geometry : bond 0.00546 (17908) covalent geometry : angle 0.87694 (24344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 TRP cc_start: 0.7871 (t-100) cc_final: 0.7575 (t-100) REVERT: B 438 PHE cc_start: 0.9374 (t80) cc_final: 0.9144 (t80) REVERT: B 549 TRP cc_start: 0.7537 (m100) cc_final: 0.7192 (m100) REVERT: B 580 PHE cc_start: 0.8233 (t80) cc_final: 0.7836 (t80) REVERT: B 660 ILE cc_start: 0.9460 (pt) cc_final: 0.9192 (pt) REVERT: A 549 TRP cc_start: 0.7149 (m100) cc_final: 0.6836 (m100) REVERT: A 660 ILE cc_start: 0.9431 (pt) cc_final: 0.9122 (pt) REVERT: C 549 TRP cc_start: 0.6954 (m100) cc_final: 0.6640 (m100) REVERT: C 568 MET cc_start: 0.8619 (ttp) cc_final: 0.8374 (ttp) REVERT: C 580 PHE cc_start: 0.8387 (t80) cc_final: 0.8013 (t80) REVERT: C 591 PHE cc_start: 0.9173 (m-10) cc_final: 0.8843 (m-10) REVERT: C 670 THR cc_start: 0.7459 (p) cc_final: 0.6864 (p) REVERT: D 549 TRP cc_start: 0.7434 (m100) cc_final: 0.7193 (m100) REVERT: D 568 MET cc_start: 0.9400 (ttp) cc_final: 0.9009 (ptm) REVERT: D 569 ILE cc_start: 0.9336 (pt) cc_final: 0.8959 (pt) REVERT: D 572 MET cc_start: 0.8914 (mmp) cc_final: 0.8507 (mtp) REVERT: D 573 ILE cc_start: 0.8757 (pt) cc_final: 0.8449 (pt) REVERT: D 580 PHE cc_start: 0.8144 (t80) cc_final: 0.7789 (t80) REVERT: D 591 PHE cc_start: 0.9166 (m-80) cc_final: 0.8964 (m-80) outliers start: 2 outliers final: 0 residues processed: 255 average time/residue: 0.2301 time to fit residues: 97.4519 Evaluate side-chains 189 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 187 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 1 optimal weight: 30.0000 chunk 183 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.107883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.058018 restraints weight = 52197.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.058018 restraints weight = 54081.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.058018 restraints weight = 54081.111| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.8388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17908 Z= 0.143 Angle : 0.796 18.411 24344 Z= 0.391 Chirality : 0.041 0.174 2868 Planarity : 0.005 0.073 3072 Dihedral : 5.863 44.767 2548 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.33 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: 0.13 (0.18), residues: 2308 helix: 0.87 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 272 HIS 0.003 0.001 HIS A 289 PHE 0.018 0.001 PHE A 245 TYR 0.021 0.002 TYR B 401 ARG 0.003 0.000 ARG D 557 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 1048) hydrogen bonds : angle 4.59957 ( 3048) covalent geometry : bond 0.00296 (17908) covalent geometry : angle 0.79601 (24344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 TRP cc_start: 0.7845 (t-100) cc_final: 0.7534 (t-100) REVERT: B 549 TRP cc_start: 0.7359 (m100) cc_final: 0.7142 (m100) REVERT: B 580 PHE cc_start: 0.8121 (t80) cc_final: 0.7610 (t80) REVERT: B 642 ILE cc_start: 0.4696 (mt) cc_final: 0.4413 (mt) REVERT: B 644 MET cc_start: 0.7042 (mmp) cc_final: 0.6800 (mmm) REVERT: B 660 ILE cc_start: 0.9429 (pt) cc_final: 0.9201 (pt) REVERT: A 549 TRP cc_start: 0.7283 (m100) cc_final: 0.6976 (m100) REVERT: A 565 TYR cc_start: 0.7903 (t80) cc_final: 0.7170 (t80) REVERT: A 569 ILE cc_start: 0.8388 (pt) cc_final: 0.8103 (pt) REVERT: A 572 MET cc_start: 0.6769 (ptp) cc_final: 0.6545 (ptt) REVERT: A 580 PHE cc_start: 0.8203 (t80) cc_final: 0.7454 (t80) REVERT: A 660 ILE cc_start: 0.9336 (pt) cc_final: 0.9052 (pt) REVERT: A 678 LEU cc_start: 0.9312 (tp) cc_final: 0.9073 (tp) REVERT: C 426 TRP cc_start: 0.7328 (t-100) cc_final: 0.7058 (t-100) REVERT: C 568 MET cc_start: 0.8944 (ttp) cc_final: 0.8549 (ttm) REVERT: C 569 ILE cc_start: 0.8149 (pt) cc_final: 0.7570 (pt) REVERT: C 573 ILE cc_start: 0.8430 (pt) cc_final: 0.8003 (pt) REVERT: C 580 PHE cc_start: 0.8350 (t80) cc_final: 0.8079 (t80) REVERT: C 660 ILE cc_start: 0.9378 (pt) cc_final: 0.9123 (pt) REVERT: D 568 MET cc_start: 0.9430 (ttp) cc_final: 0.9153 (ptp) REVERT: D 569 ILE cc_start: 0.9296 (pt) cc_final: 0.8968 (pt) REVERT: D 572 MET cc_start: 0.8833 (mmp) cc_final: 0.8452 (mtp) REVERT: D 573 ILE cc_start: 0.8750 (pt) cc_final: 0.8374 (pt) REVERT: D 580 PHE cc_start: 0.8051 (t80) cc_final: 0.7412 (t80) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2301 time to fit residues: 104.7916 Evaluate side-chains 215 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 235 optimal weight: 40.0000 chunk 171 optimal weight: 1.9990 chunk 168 optimal weight: 0.0000 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 80.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** 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 = 0.3775 r_free = 0.3775 target = 0.108894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057815 restraints weight = 56572.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057816 restraints weight = 56267.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057816 restraints weight = 56259.452| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 moved from start: 0.8552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17908 Z= 0.146 Angle : 0.801 17.448 24344 Z= 0.398 Chirality : 0.041 0.174 2868 Planarity : 0.005 0.071 3072 Dihedral : 5.698 45.215 2548 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.07 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: 0.13 (0.18), residues: 2308 helix: 0.88 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP D 549 HIS 0.003 0.001 HIS A 289 PHE 0.034 0.002 PHE A 496 TYR 0.022 0.002 TYR A 554 ARG 0.005 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 1048) hydrogen bonds : angle 4.54747 ( 3048) covalent geometry : bond 0.00304 (17908) covalent geometry : angle 0.80080 (24344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 ILE cc_start: 0.7712 (mt) cc_final: 0.7440 (mt) REVERT: B 247 PHE cc_start: 0.8421 (p90) cc_final: 0.8103 (p90) REVERT: B 426 TRP cc_start: 0.7913 (t-100) cc_final: 0.7571 (t-100) REVERT: B 549 TRP cc_start: 0.7350 (m100) cc_final: 0.7075 (m100) REVERT: B 580 PHE cc_start: 0.7982 (t80) cc_final: 0.7241 (t80) REVERT: B 586 VAL cc_start: 0.8802 (t) cc_final: 0.8564 (t) REVERT: B 660 ILE cc_start: 0.9438 (pt) cc_final: 0.9214 (pt) REVERT: A 549 TRP cc_start: 0.7120 (m100) cc_final: 0.6814 (m100) REVERT: A 580 PHE cc_start: 0.8134 (t80) cc_final: 0.7501 (t80) REVERT: A 660 ILE cc_start: 0.9366 (pt) cc_final: 0.9115 (pt) REVERT: C 426 TRP cc_start: 0.7473 (t-100) cc_final: 0.7187 (t-100) REVERT: C 524 LEU cc_start: 0.9419 (tt) cc_final: 0.9208 (mt) REVERT: C 549 TRP cc_start: 0.6681 (m-90) cc_final: 0.5819 (m-90) REVERT: C 550 THR cc_start: 0.8526 (p) cc_final: 0.8270 (p) REVERT: C 568 MET cc_start: 0.8923 (ttp) cc_final: 0.8654 (ttm) REVERT: C 569 ILE cc_start: 0.8112 (pt) cc_final: 0.7777 (pt) REVERT: C 580 PHE cc_start: 0.8264 (t80) cc_final: 0.8044 (t80) REVERT: D 445 MET cc_start: 0.9426 (mmp) cc_final: 0.9101 (mmm) REVERT: D 568 MET cc_start: 0.9419 (ttp) cc_final: 0.9145 (ptp) REVERT: D 569 ILE cc_start: 0.9293 (pt) cc_final: 0.8954 (pt) REVERT: D 572 MET cc_start: 0.8838 (mmp) cc_final: 0.8459 (mtp) REVERT: D 573 ILE cc_start: 0.8780 (pt) cc_final: 0.8406 (pt) REVERT: D 580 PHE cc_start: 0.8048 (t80) cc_final: 0.7355 (t80) REVERT: D 642 ILE cc_start: 0.5261 (mt) cc_final: 0.4943 (mt) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2257 time to fit residues: 99.6039 Evaluate side-chains 212 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 77 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 118 optimal weight: 70.0000 chunk 129 optimal weight: 4.9990 chunk 119 optimal weight: 40.0000 chunk 166 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** 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 = 0.3770 r_free = 0.3770 target = 0.109224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056835 restraints weight = 56463.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056702 restraints weight = 56249.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056702 restraints weight = 55746.547| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 moved from start: 0.8821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17908 Z= 0.162 Angle : 0.811 16.481 24344 Z= 0.406 Chirality : 0.042 0.203 2868 Planarity : 0.005 0.065 3072 Dihedral : 5.523 43.815 2548 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.37 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.06 (0.18), residues: 2308 helix: 0.83 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : -1.35 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP D 549 HIS 0.002 0.001 HIS C 289 PHE 0.035 0.002 PHE D 543 TYR 0.028 0.002 TYR A 554 ARG 0.004 0.000 ARG D 557 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 1048) hydrogen bonds : angle 4.57683 ( 3048) covalent geometry : bond 0.00338 (17908) covalent geometry : angle 0.81111 (24344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 ILE cc_start: 0.7493 (mt) cc_final: 0.7220 (mt) REVERT: B 247 PHE cc_start: 0.8338 (p90) cc_final: 0.8004 (p90) REVERT: B 426 TRP cc_start: 0.7983 (t-100) cc_final: 0.7626 (t-100) REVERT: B 549 TRP cc_start: 0.7212 (m100) cc_final: 0.6911 (m100) REVERT: B 580 PHE cc_start: 0.8027 (t80) cc_final: 0.7356 (t80) REVERT: B 586 VAL cc_start: 0.8912 (t) cc_final: 0.8699 (t) REVERT: A 549 TRP cc_start: 0.7219 (m100) cc_final: 0.6877 (m100) REVERT: A 580 PHE cc_start: 0.8134 (t80) cc_final: 0.7522 (t80) REVERT: A 660 ILE cc_start: 0.9329 (pt) cc_final: 0.9109 (pt) REVERT: C 549 TRP cc_start: 0.6382 (m-90) cc_final: 0.5934 (m-90) REVERT: C 550 THR cc_start: 0.8508 (p) cc_final: 0.8299 (p) REVERT: C 568 MET cc_start: 0.8988 (ttp) cc_final: 0.8732 (ttm) REVERT: C 569 ILE cc_start: 0.8153 (pt) cc_final: 0.7918 (pt) REVERT: C 580 PHE cc_start: 0.8258 (t80) cc_final: 0.8026 (t80) REVERT: C 591 PHE cc_start: 0.9266 (m-10) cc_final: 0.9026 (m-10) REVERT: C 659 PHE cc_start: 0.9351 (t80) cc_final: 0.9129 (t80) REVERT: C 660 ILE cc_start: 0.9428 (pt) cc_final: 0.9182 (pt) REVERT: D 445 MET cc_start: 0.9508 (mmp) cc_final: 0.9156 (mmm) REVERT: D 549 TRP cc_start: 0.6931 (m-90) cc_final: 0.6476 (m-90) REVERT: D 568 MET cc_start: 0.9434 (ttp) cc_final: 0.9168 (ptp) REVERT: D 569 ILE cc_start: 0.9359 (pt) cc_final: 0.9055 (pt) REVERT: D 572 MET cc_start: 0.8828 (mmp) cc_final: 0.8447 (mtp) REVERT: D 573 ILE cc_start: 0.8785 (pt) cc_final: 0.8449 (pt) REVERT: D 580 PHE cc_start: 0.8014 (t80) cc_final: 0.7339 (t80) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2336 time to fit residues: 99.3996 Evaluate side-chains 197 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 97 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 176 optimal weight: 40.0000 chunk 150 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 166 optimal weight: 0.0770 chunk 201 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 213 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 GLN ** 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 = 0.3781 r_free = 0.3781 target = 0.110884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.056431 restraints weight = 56065.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.056314 restraints weight = 57061.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.056314 restraints weight = 57484.322| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.8935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17908 Z= 0.143 Angle : 0.799 15.203 24344 Z= 0.399 Chirality : 0.041 0.188 2868 Planarity : 0.005 0.064 3072 Dihedral : 5.387 42.865 2548 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.85 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.01 (0.18), residues: 2308 helix: 0.84 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : -1.46 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 549 HIS 0.002 0.001 HIS C 289 PHE 0.037 0.002 PHE A 438 TYR 0.024 0.002 TYR A 554 ARG 0.007 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 1048) hydrogen bonds : angle 4.50061 ( 3048) covalent geometry : bond 0.00301 (17908) covalent geometry : angle 0.79905 (24344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 ILE cc_start: 0.7032 (mt) cc_final: 0.6704 (mt) REVERT: B 247 PHE cc_start: 0.8091 (p90) cc_final: 0.7816 (p90) REVERT: B 426 TRP cc_start: 0.7898 (t-100) cc_final: 0.7569 (t-100) REVERT: B 549 TRP cc_start: 0.7230 (m100) cc_final: 0.6877 (m100) REVERT: B 565 TYR cc_start: 0.8016 (t80) cc_final: 0.7671 (t80) REVERT: B 580 PHE cc_start: 0.7937 (t80) cc_final: 0.7240 (t80) REVERT: B 586 VAL cc_start: 0.8723 (t) cc_final: 0.8517 (t) REVERT: A 438 PHE cc_start: 0.8960 (m-80) cc_final: 0.8543 (m-80) REVERT: A 549 TRP cc_start: 0.6958 (m100) cc_final: 0.6544 (m100) REVERT: A 580 PHE cc_start: 0.8133 (t80) cc_final: 0.7503 (t80) REVERT: A 642 ILE cc_start: 0.4143 (mt) cc_final: 0.3802 (mt) REVERT: A 660 ILE cc_start: 0.9302 (pt) cc_final: 0.9068 (pt) REVERT: C 549 TRP cc_start: 0.6256 (m-90) cc_final: 0.5657 (m-90) REVERT: C 568 MET cc_start: 0.8978 (ttp) cc_final: 0.8694 (ttm) REVERT: C 569 ILE cc_start: 0.7950 (pt) cc_final: 0.7637 (pt) REVERT: C 580 PHE cc_start: 0.8110 (t80) cc_final: 0.7843 (t80) REVERT: C 591 PHE cc_start: 0.9262 (m-10) cc_final: 0.9035 (m-10) REVERT: C 644 MET cc_start: 0.7347 (mmp) cc_final: 0.7135 (mmm) REVERT: C 662 LEU cc_start: 0.8978 (tt) cc_final: 0.8711 (tt) REVERT: D 445 MET cc_start: 0.9532 (mmp) cc_final: 0.9158 (mmm) REVERT: D 549 TRP cc_start: 0.6801 (m-90) cc_final: 0.6374 (m-90) REVERT: D 568 MET cc_start: 0.9417 (ttp) cc_final: 0.9164 (ptp) REVERT: D 569 ILE cc_start: 0.9343 (pt) cc_final: 0.9025 (pt) REVERT: D 572 MET cc_start: 0.8744 (mmp) cc_final: 0.8385 (mtp) REVERT: D 573 ILE cc_start: 0.8655 (pt) cc_final: 0.8294 (pt) REVERT: D 580 PHE cc_start: 0.7972 (t80) cc_final: 0.7298 (t80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2274 time to fit residues: 100.2281 Evaluate side-chains 204 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 1 optimal weight: 50.0000 chunk 178 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 GLN ** 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 = 0.3740 r_free = 0.3740 target = 0.106738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055723 restraints weight = 57675.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055727 restraints weight = 57483.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055727 restraints weight = 57446.128| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5530 moved from start: 0.9179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17908 Z= 0.188 Angle : 0.802 15.985 24344 Z= 0.409 Chirality : 0.042 0.199 2868 Planarity : 0.005 0.061 3072 Dihedral : 5.361 41.299 2548 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.93 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.01 (0.18), residues: 2308 helix: 0.81 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.41 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 549 HIS 0.004 0.001 HIS C 289 PHE 0.063 0.002 PHE A 434 TYR 0.025 0.002 TYR A 554 ARG 0.005 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 1048) hydrogen bonds : angle 4.62410 ( 3048) covalent geometry : bond 0.00381 (17908) covalent geometry : angle 0.80186 (24344) =============================================================================== Job complete usr+sys time: 5805.50 seconds wall clock time: 101 minutes 35.23 seconds (6095.23 seconds total)