Starting phenix.real_space_refine on Sat Oct 11 08:39:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r64_18946/10_2025/8r64_18946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r64_18946/10_2025/8r64_18946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r64_18946/10_2025/8r64_18946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r64_18946/10_2025/8r64_18946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r64_18946/10_2025/8r64_18946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r64_18946/10_2025/8r64_18946.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 6 5.21 5 S 74 5.16 5 C 8445 2.51 5 N 2353 2.21 5 O 2534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13429 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2300 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 284} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2306 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 284} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2308 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 284} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2314 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 284} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1971 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 14, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 13, 'ASN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 1956 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 271, 1951 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 117 Conformer: "B" Number of residues, atoms: 271, 1951 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 117 bond proxies already assigned to first conformer: 1979 Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 86 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATHR A 632 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR A 632 " occ=0.50 Time building chain proxies: 3.74, per 1000 atoms: 0.28 Number of scatterers: 13429 At special positions: 0 Unit cell: (135.3, 129.8, 103.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 17 15.00 Mg 6 11.99 O 2534 8.00 N 2353 7.00 C 8445 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: 1.07 Conformation dependent library (CDL) restraints added in 713.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 6 sheets defined 63.6% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 380 through 389 Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 406 through 423 removed outlier: 3.868A pdb=" N LYS B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TRP B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Proline residue: B 420 - end of helix Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 446 through 459 removed outlier: 4.227A pdb=" N GLY B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 removed outlier: 3.889A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 492 Processing helix chain 'B' and resid 514 through 529 removed outlier: 3.613A pdb=" N ARG B 518 " --> pdb=" O HIS B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.768A pdb=" N ARG B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 583 removed outlier: 4.293A pdb=" N LYS B 583 " --> pdb=" O ASN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 600 Processing helix chain 'B' and resid 604 through 617 removed outlier: 3.511A pdb=" N THR B 609 " --> pdb=" O GLY B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 623 Processing helix chain 'B' and resid 640 through 651 removed outlier: 3.754A pdb=" N PHE B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 650 " --> pdb=" O ASN B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 659 through 671 removed outlier: 4.509A pdb=" N TYR B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 665 " --> pdb=" O GLU B 661 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 669 " --> pdb=" O ASN B 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 removed outlier: 4.068A pdb=" N ARG C 375 " --> pdb=" O VAL C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 Processing helix chain 'C' and resid 407 through 423 removed outlier: 4.087A pdb=" N TRP C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 423 through 428 Processing helix chain 'C' and resid 429 through 432 Processing helix chain 'C' and resid 446 through 459 removed outlier: 4.298A pdb=" N GLY C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 471 removed outlier: 3.818A pdb=" N LEU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 490 removed outlier: 3.583A pdb=" N LYS C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 514 through 529 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 552 through 559 removed outlier: 3.788A pdb=" N ARG C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 584 removed outlier: 4.038A pdb=" N LYS C 583 " --> pdb=" O ASN C 579 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 600 Processing helix chain 'C' and resid 604 through 617 removed outlier: 3.619A pdb=" N LEU C 617 " --> pdb=" O ARG C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 623 Processing helix chain 'C' and resid 626 through 631 removed outlier: 3.736A pdb=" N THR C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 636 removed outlier: 3.613A pdb=" N VAL C 636 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.787A pdb=" N PHE C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR C 650 " --> pdb=" O ASN C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' Processing helix chain 'C' and resid 659 through 671 removed outlier: 4.416A pdb=" N TYR C 663 " --> pdb=" O ASP C 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 377 Processing helix chain 'D' and resid 380 through 390 Processing helix chain 'D' and resid 406 through 423 removed outlier: 4.110A pdb=" N TRP D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Proline residue: D 420 - end of helix Processing helix chain 'D' and resid 423 through 428 Processing helix chain 'D' and resid 429 through 432 Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.529A pdb=" N ILE D 450 " --> pdb=" O GLY D 446 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 471 removed outlier: 3.624A pdb=" N LEU D 470 " --> pdb=" O SER D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 492 Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 514 through 529 removed outlier: 3.595A pdb=" N ARG D 518 " --> pdb=" O HIS D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 552 through 559 removed outlier: 3.546A pdb=" N ARG D 557 " --> pdb=" O GLU D 553 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG D 558 " --> pdb=" O ALA D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 583 removed outlier: 4.243A pdb=" N LYS D 583 " --> pdb=" O ASN D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 600 Processing helix chain 'D' and resid 604 through 616 removed outlier: 3.579A pdb=" N THR D 609 " --> pdb=" O GLY D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 623 Processing helix chain 'D' and resid 626 through 631 removed outlier: 4.378A pdb=" N THR D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 649 removed outlier: 3.628A pdb=" N PHE D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 670 removed outlier: 4.262A pdb=" N TYR D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 377 Processing helix chain 'E' and resid 380 through 389 Processing helix chain 'E' and resid 399 through 403 Processing helix chain 'E' and resid 407 through 423 removed outlier: 4.091A pdb=" N TRP E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Proline residue: E 420 - end of helix Processing helix chain 'E' and resid 423 through 428 Processing helix chain 'E' and resid 446 through 458 removed outlier: 3.519A pdb=" N SER E 456 " --> pdb=" O LYS E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 471 removed outlier: 3.947A pdb=" N LEU E 470 " --> pdb=" O SER E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 492 removed outlier: 3.582A pdb=" N LYS E 480 " --> pdb=" O GLY E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 506 removed outlier: 4.325A pdb=" N LEU E 505 " --> pdb=" O GLN E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 530 Processing helix chain 'E' and resid 547 through 551 Processing helix chain 'E' and resid 552 through 559 removed outlier: 3.922A pdb=" N ARG E 558 " --> pdb=" O ALA E 554 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 559 " --> pdb=" O ALA E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 584 removed outlier: 4.188A pdb=" N LYS E 583 " --> pdb=" O ASN E 579 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU E 584 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 600 Processing helix chain 'E' and resid 604 through 617 removed outlier: 3.518A pdb=" N LEU E 617 " --> pdb=" O ARG E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 623 Processing helix chain 'E' and resid 632 through 636 Processing helix chain 'E' and resid 641 through 650 removed outlier: 3.713A pdb=" N GLU E 645 " --> pdb=" O TYR E 641 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN E 646 " --> pdb=" O ILE E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 670 removed outlier: 4.417A pdb=" N LEU E 660 " --> pdb=" O SER E 656 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU E 661 " --> pdb=" O PRO E 657 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU E 662 " --> pdb=" O LYS E 658 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR E 663 " --> pdb=" O ASP E 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 377 removed outlier: 3.547A pdb=" N ARG F 375 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.592A pdb=" N ILE F 391 " --> pdb=" O ILE F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 404 removed outlier: 3.811A pdb=" N ILE F 403 " --> pdb=" O ASN F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.932A pdb=" N TRP F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Proline residue: F 420 - end of helix Processing helix chain 'F' and resid 423 through 428 removed outlier: 3.700A pdb=" N PHE F 427 " --> pdb=" O ARG F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 459 removed outlier: 3.945A pdb=" N GLY F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 471 removed outlier: 4.193A pdb=" N LEU F 470 " --> pdb=" O SER F 466 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR F 471 " --> pdb=" O ALA F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'F' and resid 476 through 492 removed outlier: 3.535A pdb=" N LYS F 480 " --> pdb=" O GLY F 476 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN F 492 " --> pdb=" O VAL F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 506 removed outlier: 4.066A pdb=" N LEU F 505 " --> pdb=" O GLN F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 529 Processing helix chain 'F' and resid 547 through 551 Processing helix chain 'F' and resid 552 through 559 removed outlier: 3.654A pdb=" N ARG F 558 " --> pdb=" O ALA F 554 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 559 " --> pdb=" O ALA F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 582 Processing helix chain 'F' and resid 590 through 600 Processing helix chain 'F' and resid 604 through 617 removed outlier: 3.674A pdb=" N LEU F 617 " --> pdb=" O ARG F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 650 Processing helix chain 'F' and resid 656 through 670 removed outlier: 4.387A pdb=" N LEU F 660 " --> pdb=" O SER F 656 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU F 661 " --> pdb=" O PRO F 657 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU F 662 " --> pdb=" O LYS F 658 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.739A pdb=" N ILE A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.294A pdb=" N ILE A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A 404 " --> pdb=" O TRP A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 404' Processing helix chain 'A' and resid 406 through 418 removed outlier: 3.570A pdb=" N LYS A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 459 removed outlier: 4.310A pdb=" N GLY A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.523A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.713A pdb=" N LYS A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.012A pdb=" N LEU A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 535 removed outlier: 3.870A pdb=" N SER A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 552 through 559 removed outlier: 4.150A pdb=" N ARG A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 4.116A pdb=" N LYS A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 600 Processing helix chain 'A' and resid 604 through 623 Proline residue: A 619 - end of helix Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 640 through 650 removed outlier: 3.656A pdb=" N PHE A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 650 " --> pdb=" O ASN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 671 Processing sheet with id=AA1, first strand: chain 'B' and resid 461 through 465 removed outlier: 6.211A pdb=" N THR B 461 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE B 498 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE B 463 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP B 500 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 465 " --> pdb=" O ASP B 500 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 437 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR B 545 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU B 439 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 461 through 465 removed outlier: 3.884A pdb=" N ASP C 500 " --> pdb=" O ILE C 465 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 561 " --> pdb=" O GLY C 436 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 461 through 465 removed outlier: 6.323A pdb=" N THR D 461 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE D 498 " --> pdb=" O THR D 461 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE D 463 " --> pdb=" O PHE D 498 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP D 500 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE D 465 " --> pdb=" O ASP D 500 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 437 " --> pdb=" O GLY D 543 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR D 545 " --> pdb=" O ILE D 437 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 439 " --> pdb=" O THR D 545 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU D 438 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 461 through 465 removed outlier: 6.200A pdb=" N THR E 461 " --> pdb=" O VAL E 496 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE E 498 " --> pdb=" O THR E 461 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE E 463 " --> pdb=" O PHE E 498 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA E 495 " --> pdb=" O LEU E 540 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL E 542 " --> pdb=" O ALA E 495 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE E 497 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA E 544 " --> pdb=" O ILE E 497 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 499 " --> pdb=" O ALA E 544 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS E 561 " --> pdb=" O GLY E 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 461 through 465 removed outlier: 3.639A pdb=" N ALA F 544 " --> pdb=" O ILE F 499 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE F 437 " --> pdb=" O GLY F 543 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR F 545 " --> pdb=" O ILE F 437 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU F 439 " --> pdb=" O THR F 545 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU F 438 " --> pdb=" O LEU F 563 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 465 removed outlier: 6.262A pdb=" N THR A 461 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE A 498 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A 463 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP A 500 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 465 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA A 495 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL A 542 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE A 497 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA A 544 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 499 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY A 436 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU A 563 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 438 " --> pdb=" O LEU A 563 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1836 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: 2.31 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4457 1.34 - 1.46: 2618 1.46 - 1.58: 6446 1.58 - 1.69: 28 1.69 - 1.81: 115 Bond restraints: 13664 Sorted by residual: bond pdb=" C LEU D 528 " pdb=" N ASP D 529 " ideal model delta sigma weight residual 1.328 1.338 -0.010 8.90e-03 1.26e+04 1.37e+00 bond pdb=" CA VAL D 406 " pdb=" CB VAL D 406 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.31e-02 5.83e+03 1.35e+00 bond pdb=" C LEU A 617 " pdb=" N GLY A 618 " ideal model delta sigma weight residual 1.339 1.331 0.008 7.50e-03 1.78e+04 1.24e+00 bond pdb=" CA ASP D 529 " pdb=" CB ASP D 529 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.45e-02 4.76e+03 1.19e+00 bond pdb=" C4 ADP F 702 " pdb=" C5 ADP F 702 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 ... (remaining 13659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 18276 1.35 - 2.71: 165 2.71 - 4.06: 101 4.06 - 5.42: 15 5.42 - 6.77: 19 Bond angle restraints: 18576 Sorted by residual: angle pdb=" C3' ATP C 702 " pdb=" C4' ATP C 702 " pdb=" O4' ATP C 702 " ideal model delta sigma weight residual 105.22 101.35 3.87 1.30e+00 5.94e-01 8.89e+00 angle pdb=" C3' ATP E 702 " pdb=" C4' ATP E 702 " pdb=" C5' ATP E 702 " ideal model delta sigma weight residual 115.19 110.36 4.83 1.76e+00 3.23e-01 7.55e+00 angle pdb=" C3' ATP D 702 " pdb=" C4' ATP D 702 " pdb=" O4' ATP D 702 " ideal model delta sigma weight residual 105.22 101.73 3.49 1.30e+00 5.94e-01 7.23e+00 angle pdb=" C3' ATP A 702 " pdb=" C4' ATP A 702 " pdb=" C5' ATP A 702 " ideal model delta sigma weight residual 115.19 110.72 4.47 1.76e+00 3.23e-01 6.45e+00 angle pdb=" C3' ATP D 702 " pdb=" C4' ATP D 702 " pdb=" C5' ATP D 702 " ideal model delta sigma weight residual 115.19 110.76 4.43 1.76e+00 3.23e-01 6.34e+00 ... (remaining 18571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.60: 8284 31.60 - 63.20: 151 63.20 - 94.80: 9 94.80 - 126.39: 1 126.39 - 157.99: 2 Dihedral angle restraints: 8447 sinusoidal: 3375 harmonic: 5072 Sorted by residual: dihedral pdb=" C5' ADP F 702 " pdb=" O5' ADP F 702 " pdb=" PA ADP F 702 " pdb=" O2A ADP F 702 " ideal model delta sinusoidal sigma weight residual -60.00 98.00 -157.99 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP F 702 " pdb=" O3A ADP F 702 " pdb=" PA ADP F 702 " pdb=" PB ADP F 702 " ideal model delta sinusoidal sigma weight residual -60.00 81.50 -141.50 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O1B ADP F 702 " pdb=" O3A ADP F 702 " pdb=" PB ADP F 702 " pdb=" PA ADP F 702 " ideal model delta sinusoidal sigma weight residual -60.00 66.37 -126.37 1 2.00e+01 2.50e-03 3.82e+01 ... (remaining 8444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1874 0.061 - 0.123: 262 0.123 - 0.184: 11 0.184 - 0.245: 2 0.245 - 0.307: 13 Chirality restraints: 2162 Sorted by residual: chirality pdb=" C2' ATP C 702 " pdb=" C1' ATP C 702 " pdb=" C3' ATP C 702 " pdb=" O2' ATP C 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ATP B 702 " pdb=" C1' ATP B 702 " pdb=" C3' ATP B 702 " pdb=" O2' ATP B 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C2' ATP D 702 " pdb=" C1' ATP D 702 " pdb=" C3' ATP D 702 " pdb=" O2' ATP D 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 2159 not shown) Planarity restraints: 2376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 618 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO A 619 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP F 419 " 0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO F 420 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO F 420 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 420 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 618 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.39e-01 pdb=" N PRO D 619 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO D 619 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 619 " 0.014 5.00e-02 4.00e+02 ... (remaining 2373 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 99 2.53 - 3.12: 10999 3.12 - 3.72: 20049 3.72 - 4.31: 26854 4.31 - 4.90: 46552 Nonbonded interactions: 104553 Sorted by model distance: nonbonded pdb=" OG1 THR E 448 " pdb="MG MG E 701 " model vdw 1.940 2.170 nonbonded pdb=" OG SER C 516 " pdb=" OE2 GLU G 8 " model vdw 1.953 3.040 nonbonded pdb="MG MG C 701 " pdb=" O2B ATP C 702 " model vdw 1.959 2.170 nonbonded pdb=" OG1 THR A 448 " pdb="MG MG A 701 " model vdw 1.966 2.170 nonbonded pdb="MG MG B 701 " pdb=" O1G ATP B 702 " model vdw 2.037 2.170 ... (remaining 104548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 380 and (name N or name CA or name C or name O or name CB \ )) or resid 381 through 401 or (resid 402 and (name N or name CA or name C or n \ ame O or name CB )) or resid 403 through 406 or (resid 407 and (name N or name C \ A or name C or name O or name CB )) or resid 408 through 448 or (resid 449 and ( \ name N or name CA or name C or name O or name CB )) or resid 450 through 499 or \ (resid 500 and (name N or name CA or name C or name O or name CB )) or resid 501 \ through 528 or (resid 529 and (name N or name CA or name C or name O or name CB \ )) or resid 530 through 568 or (resid 569 through 570 and (name N or name CA or \ name C or name O or name CB )) or resid 571 through 580 or (resid 581 and (name \ N or name CA or name C or name O or name CB )) or resid 582 or (resid 589 throu \ gh 602 and (name N or name CA or name C or name O or name CB )) or resid 603 thr \ ough 612 or (resid 613 through 615 and (name N or name CA or name C or name O or \ name CB )) or resid 616 through 617 or resid 641 or (resid 642 through 650 and \ (name N or name CA or name C or name O or name CB )) or resid 651 or resid 656 t \ hrough 701)) selection = (chain 'B' and ((resid 380 and (name N or name CA or name C or name O or name CB \ )) or resid 381 or (resid 382 and (name N or name CA or name C or name O or nam \ e CB )) or resid 383 through 384 or (resid 385 and (name N or name CA or name C \ or name O or name CB )) or resid 386 through 391 or (resid 392 through 394 and ( \ name N or name CA or name C or name O or name CB )) or resid 395 through 400 or \ (resid 401 through 402 and (name N or name CA or name C or name O or name CB )) \ or resid 403 through 406 or (resid 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 414 or (resid 415 and (name N or name CA or \ name C or name O or name CB )) or resid 416 through 418 or resid 434 or (resid \ 435 and (name N or name CA or name C or name O or name CB )) or resid 436 throug \ h 448 or (resid 449 and (name N or name CA or name C or name O or name CB )) or \ resid 450 through 499 or (resid 500 and (name N or name CA or name C or name O o \ r name CB )) or resid 501 through 507 or (resid 508 through 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 or (resid 513 and (nam \ e N or name CA or name C or name O or name CB )) or resid 514 or (resid 515 and \ (name N or name CA or name C or name O or name CB )) or resid 516 through 517 or \ (resid 518 through 519 and (name N or name CA or name C or name O or name CB )) \ or resid 520 through 522 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 528 or (resid 529 and (name N or name CA o \ r name C or name O or name CB )) or resid 530 through 535 or (resid 536 through \ 537 and (name N or name CA or name C or name O or name CB )) or resid 538 throug \ h 552 or (resid 553 through 555 and (name N or name CA or name C or name O or na \ me CB )) or resid 556 through 560 or (resid 561 and (name N or name CA or name C \ or name O or name CB )) or resid 562 through 568 or (resid 569 through 570 and \ (name N or name CA or name C or name O or name CB )) or resid 571 through 573 or \ (resid 574 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 5 through 580 or (resid 581 and (name N or name CA or name C or name O or name C \ B )) or resid 582 or (resid 589 through 602 and (name N or name CA or name C or \ name O or name CB )) or resid 603 through 612 or (resid 613 through 615 and (nam \ e N or name CA or name C or name O or name CB )) or resid 616 through 617 or res \ id 641 or (resid 642 through 650 and (name N or name CA or name C or name O or n \ ame CB )) or resid 651 or resid 656 through 657 or (resid 658 and (name N or nam \ e CA or name C or name O or name CB )) or resid 659 through 663 or (resid 664 an \ d (name N or name CA or name C or name O or name CB )) or resid 665 through 667 \ or (resid 668 and (name N or name CA or name C or name O or name CB )) or resid \ 669 through 671 or resid 701)) selection = (chain 'C' and ((resid 380 and (name N or name CA or name C or name O or name CB \ )) or resid 381 or (resid 382 and (name N or name CA or name C or name O or nam \ e CB )) or resid 383 through 384 or (resid 385 and (name N or name CA or name C \ or name O or name CB )) or resid 386 through 391 or (resid 392 through 394 and ( \ name N or name CA or name C or name O or name CB )) or resid 395 through 401 or \ (resid 402 and (name N or name CA or name C or name O or name CB )) or resid 403 \ through 406 or (resid 407 and (name N or name CA or name C or name O or name CB \ )) or resid 408 through 414 or (resid 415 and (name N or name CA or name C or n \ ame O or name CB )) or resid 416 through 418 or resid 434 or (resid 435 and (nam \ e N or name CA or name C or name O or name CB )) or resid 436 through 448 or (re \ sid 449 and (name N or name CA or name C or name O or name CB )) or resid 450 th \ rough 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) \ or resid 501 through 507 or (resid 508 through 509 and (name N or name CA or na \ me C or name O or name CB )) or (resid 510 through 513 and (name N or name CA or \ name C or name O or name CB )) or resid 514 or (resid 515 and (name N or name C \ A or name C or name O or name CB )) or resid 516 through 517 or (resid 518 throu \ gh 519 and (name N or name CA or name C or name O or name CB )) or resid 520 thr \ ough 522 or (resid 523 and (name N or name CA or name C or name O or name CB )) \ or resid 524 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 535 or (resid 536 through 537 and (name N o \ r name CA or name C or name O or name CB )) or resid 538 through 552 or (resid 5 \ 53 through 555 and (name N or name CA or name C or name O or name CB )) or resid \ 556 through 560 or (resid 561 and (name N or name CA or name C or name O or nam \ e CB )) or resid 562 through 568 or (resid 569 through 570 and (name N or name C \ A or name C or name O or name CB )) or resid 571 through 573 or (resid 574 and ( \ name N or name CA or name C or name O or name CB )) or resid 575 through 580 or \ (resid 581 and (name N or name CA or name C or name O or name CB )) or resid 582 \ or (resid 589 through 602 and (name N or name CA or name C or name O or name CB \ )) or resid 603 through 612 or (resid 613 through 615 and (name N or name CA or \ name C or name O or name CB )) or resid 616 through 617 or resid 641 or (resid \ 642 through 650 and (name N or name CA or name C or name O or name CB )) or resi \ d 651 or resid 656 through 657 or (resid 658 and (name N or name CA or name C or \ name O or name CB )) or resid 659 through 660 or (resid 661 and (name N or name \ CA or name C or name O or name CB )) or resid 662 through 663 or (resid 664 and \ (name N or name CA or name C or name O or name CB )) or resid 665 through 667 o \ r (resid 668 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 69 through 671 or resid 701)) selection = (chain 'D' and (resid 380 through 384 or (resid 385 and (name N or name CA or na \ me C or name O or name CB )) or resid 386 through 391 or (resid 392 through 394 \ and (name N or name CA or name C or name O or name CB )) or resid 395 through 40 \ 0 or (resid 401 through 402 and (name N or name CA or name C or name O or name C \ B )) or resid 403 through 406 or (resid 407 and (name N or name CA or name C or \ name O or name CB )) or resid 408 through 414 or (resid 415 and (name N or name \ CA or name C or name O or name CB )) or resid 416 through 418 or resid 434 or (r \ esid 435 and (name N or name CA or name C or name O or name CB )) or resid 436 t \ hrough 448 or (resid 449 and (name N or name CA or name C or name O or name CB ) \ ) or resid 450 through 499 or (resid 500 and (name N or name CA or name C or nam \ e O or name CB )) or resid 501 through 507 or (resid 508 through 509 and (name N \ or name CA or name C or name O or name CB )) or resid 510 or (resid 511 and (na \ me N or name CA or name C or name O or name CB )) or resid 512 or (resid 513 and \ (name N or name CA or name C or name O or name CB )) or resid 514 or (resid 515 \ and (name N or name CA or name C or name O or name CB )) or resid 516 through 5 \ 17 or (resid 518 through 519 and (name N or name CA or name C or name O or name \ CB )) or resid 520 through 522 or (resid 523 and (name N or name CA or name C or \ name O or name CB )) or resid 524 through 528 or (resid 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 536 or (resid 537 and \ (name N or name CA or name C or name O or name CB )) or resid 538 through 552 o \ r (resid 553 through 555 and (name N or name CA or name C or name O or name CB ) \ ) or resid 556 through 560 or (resid 561 and (name N or name CA or name C or nam \ e O or name CB )) or resid 562 through 568 or (resid 569 through 570 and (name N \ or name CA or name C or name O or name CB )) or resid 571 through 573 or (resid \ 574 and (name N or name CA or name C or name O or name CB )) or resid 575 throu \ gh 580 or (resid 581 and (name N or name CA or name C or name O or name CB )) or \ resid 582 or (resid 589 through 602 and (name N or name CA or name C or name O \ or name CB )) or resid 603 through 612 or (resid 613 through 615 and (name N or \ name CA or name C or name O or name CB )) or resid 616 through 617 or resid 641 \ or (resid 642 through 650 and (name N or name CA or name C or name O or name CB \ )) or resid 651 or resid 656 through 657 or (resid 658 and (name N or name CA or \ name C or name O or name CB )) or resid 659 through 660 or (resid 661 and (name \ N or name CA or name C or name O or name CB )) or resid 662 through 663 or (res \ id 664 and (name N or name CA or name C or name O or name CB )) or resid 665 thr \ ough 667 or (resid 668 and (name N or name CA or name C or name O or name CB )) \ or resid 669 through 671 or resid 701)) selection = (chain 'E' and (resid 380 through 381 or (resid 382 and (name N or name CA or na \ me C or name O or name CB )) or resid 383 through 384 or (resid 385 and (name N \ or name CA or name C or name O or name CB )) or resid 386 through 391 or (resid \ 392 through 394 and (name N or name CA or name C or name O or name CB )) or resi \ d 395 through 400 or (resid 401 through 402 and (name N or name CA or name C or \ name O or name CB )) or resid 403 through 406 or (resid 407 and (name N or name \ CA or name C or name O or name CB )) or resid 408 through 414 or (resid 415 and \ (name N or name CA or name C or name O or name CB )) or resid 416 through 418 or \ resid 434 or (resid 435 and (name N or name CA or name C or name O or name CB ) \ ) or resid 436 through 448 or (resid 449 and (name N or name CA or name C or nam \ e O or name CB )) or resid 450 through 499 or (resid 500 and (name N or name CA \ or name C or name O or name CB )) or resid 501 through 507 or (resid 508 through \ 509 and (name N or name CA or name C or name O or name CB )) or resid 510 or (r \ esid 511 and (name N or name CA or name C or name O or name CB )) or resid 512 o \ r (resid 513 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 14 or (resid 515 and (name N or name CA or name C or name O or name CB )) or res \ id 516 through 517 or (resid 518 through 519 and (name N or name CA or name C or \ name O or name CB )) or resid 520 through 522 or (resid 523 and (name N or name \ CA or name C or name O or name CB )) or resid 524 through 536 or (resid 537 and \ (name N or name CA or name C or name O or name CB )) or resid 538 through 560 o \ r (resid 561 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 62 through 568 or (resid 569 through 570 and (name N or name CA or name C or nam \ e O or name CB )) or resid 571 through 573 or (resid 574 and (name N or name CA \ or name C or name O or name CB )) or resid 575 through 580 or (resid 581 and (na \ me N or name CA or name C or name O or name CB )) or resid 582 or (resid 589 thr \ ough 602 and (name N or name CA or name C or name O or name CB )) or resid 603 t \ hrough 612 or (resid 613 through 615 and (name N or name CA or name C or name O \ or name CB )) or resid 616 through 617 or resid 641 or (resid 642 through 650 an \ d (name N or name CA or name C or name O or name CB )) or resid 651 or resid 656 \ through 657 or (resid 658 and (name N or name CA or name C or name O or name CB \ )) or resid 659 through 660 or (resid 661 and (name N or name CA or name C or n \ ame O or name CB )) or resid 662 through 663 or (resid 664 and (name N or name C \ A or name C or name O or name CB )) or resid 665 through 667 or (resid 668 and ( \ name N or name CA or name C or name O or name CB )) or resid 669 through 671 or \ resid 701)) selection = (chain 'F' and ((resid 380 and (name N or name CA or name C or name O or name CB \ )) or resid 381 or (resid 382 and (name N or name CA or name C or name O or nam \ e CB )) or resid 383 through 391 or (resid 392 through 394 and (name N or name C \ A or name C or name O or name CB )) or resid 395 through 401 or (resid 402 and ( \ name N or name CA or name C or name O or name CB )) or resid 403 through 414 or \ (resid 415 and (name N or name CA or name C or name O or name CB )) or resid 416 \ through 418 or resid 434 or (resid 435 and (name N or name CA or name C or name \ O or name CB )) or resid 436 through 507 or (resid 508 through 509 and (name N \ or name CA or name C or name O or name CB )) or resid 510 or (resid 511 and (nam \ e N or name CA or name C or name O or name CB )) or resid 512 or (resid 513 and \ (name N or name CA or name C or name O or name CB )) or resid 514 or (resid 515 \ and (name N or name CA or name C or name O or name CB )) or resid 516 through 51 \ 7 or (resid 518 through 519 and (name N or name CA or name C or name O or name C \ B )) or resid 520 through 522 or (resid 523 and (name N or name CA or name C or \ name O or name CB )) or resid 524 through 528 or (resid 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 535 or (resid 536 thro \ ugh 537 and (name N or name CA or name C or name O or name CB )) or resid 538 th \ rough 552 or (resid 553 through 555 and (name N or name CA or name C or name O o \ r name CB )) or resid 556 through 560 or (resid 561 and (name N or name CA or na \ me C or name O or name CB )) or resid 562 through 613 or (resid 614 through 615 \ and (name N or name CA or name C or name O or name CB )) or resid 616 through 65 \ 7 or (resid 658 and (name N or name CA or name C or name O or name CB )) or resi \ d 659 through 667 or (resid 668 and (name N or name CA or name C or name O or na \ me CB )) or resid 669 through 671 or resid 701)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.002 0.031 13664 Z= 0.088 Angle : 0.487 6.771 18576 Z= 0.246 Chirality : 0.046 0.307 2162 Planarity : 0.003 0.031 2376 Dihedral : 11.845 157.994 5147 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.29 % Allowed : 2.61 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.21), residues: 1742 helix: 2.55 (0.19), residues: 848 sheet: 1.76 (0.38), residues: 192 loop : 0.98 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 556 TYR 0.006 0.001 TYR C 564 PHE 0.006 0.001 PHE D 440 TRP 0.003 0.000 TRP B 474 HIS 0.001 0.000 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00177 (13664) covalent geometry : angle 0.48688 (18576) hydrogen bonds : bond 0.17005 ( 643) hydrogen bonds : angle 5.83343 ( 1836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 264 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: C 481 MET cc_start: 0.8964 (mmm) cc_final: 0.8759 (mmm) REVERT: C 524 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8158 (t80) REVERT: D 524 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8383 (t80) REVERT: E 586 CYS cc_start: 0.5232 (p) cc_final: 0.4836 (p) REVERT: F 380 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 390 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8191 (mm-30) REVERT: A 473 LYS cc_start: 0.8233 (pttt) cc_final: 0.7983 (ptmt) REVERT: A 540 LEU cc_start: 0.8798 (tp) cc_final: 0.8591 (tt) outliers start: 4 outliers final: 1 residues processed: 268 average time/residue: 0.1235 time to fit residues: 47.3830 Evaluate side-chains 167 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain F residue 529 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.0060 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 HIS B 599 GLN B 665 ASN C 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064574 restraints weight = 36740.162| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.27 r_work: 0.2848 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13664 Z= 0.122 Angle : 0.569 7.798 18576 Z= 0.287 Chirality : 0.041 0.141 2162 Planarity : 0.004 0.041 2376 Dihedral : 11.464 160.001 2066 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.16 % Allowed : 8.11 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.20), residues: 1742 helix: 2.24 (0.18), residues: 890 sheet: 1.78 (0.37), residues: 188 loop : 0.83 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 547 TYR 0.023 0.001 TYR A 564 PHE 0.027 0.002 PHE A 670 TRP 0.040 0.001 TRP A 400 HIS 0.003 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00263 (13664) covalent geometry : angle 0.56881 (18576) hydrogen bonds : bond 0.04090 ( 643) hydrogen bonds : angle 4.62969 ( 1836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.578 Fit side-chains REVERT: B 386 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9153 (mm) REVERT: B 399 ASN cc_start: 0.8049 (p0) cc_final: 0.7765 (p0) REVERT: B 579 ASN cc_start: 0.9076 (m-40) cc_final: 0.8807 (m110) REVERT: C 524 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8598 (t80) REVERT: D 524 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8745 (t80) REVERT: E 385 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8087 (tm-30) REVERT: E 586 CYS cc_start: 0.5679 (p) cc_final: 0.5430 (p) REVERT: F 380 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7076 (tm-30) REVERT: F 493 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7353 (tm-30) REVERT: F 529 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6110 (t0) REVERT: A 390 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8273 (mm-30) REVERT: A 473 LYS cc_start: 0.8169 (pttt) cc_final: 0.7847 (ptmt) REVERT: A 608 MET cc_start: 0.8842 (mmm) cc_final: 0.8601 (mmm) outliers start: 16 outliers final: 4 residues processed: 193 average time/residue: 0.1146 time to fit residues: 32.8306 Evaluate side-chains 159 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain F residue 529 ASP Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 69 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 94 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 142 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 chunk 172 optimal weight: 40.0000 chunk 111 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 85 optimal weight: 0.0040 chunk 93 optimal weight: 0.0270 overall best weight: 3.1254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.086273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.061753 restraints weight = 36804.223| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.28 r_work: 0.2792 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13664 Z= 0.167 Angle : 0.563 10.109 18576 Z= 0.285 Chirality : 0.042 0.138 2162 Planarity : 0.004 0.047 2376 Dihedral : 11.484 169.184 2066 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.52 % Allowed : 8.98 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.20), residues: 1742 helix: 1.98 (0.18), residues: 897 sheet: 1.57 (0.37), residues: 198 loop : 0.76 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 547 TYR 0.020 0.001 TYR A 564 PHE 0.016 0.002 PHE A 408 TRP 0.041 0.001 TRP A 400 HIS 0.002 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00392 (13664) covalent geometry : angle 0.56289 (18576) hydrogen bonds : bond 0.04089 ( 643) hydrogen bonds : angle 4.52522 ( 1836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.561 Fit side-chains REVERT: B 386 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9172 (mm) REVERT: B 399 ASN cc_start: 0.8056 (p0) cc_final: 0.7715 (p0) REVERT: B 579 ASN cc_start: 0.9162 (m-40) cc_final: 0.8915 (m110) REVERT: C 524 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8609 (t80) REVERT: D 524 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8607 (t80) REVERT: E 385 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8251 (tm-30) REVERT: E 586 CYS cc_start: 0.5519 (p) cc_final: 0.5267 (p) REVERT: F 493 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7450 (tm-30) REVERT: F 529 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6166 (m-30) REVERT: F 564 TYR cc_start: 0.8963 (t80) cc_final: 0.8751 (t80) REVERT: A 390 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8342 (mm-30) REVERT: A 473 LYS cc_start: 0.8198 (pttt) cc_final: 0.7873 (ptmt) outliers start: 21 outliers final: 10 residues processed: 172 average time/residue: 0.1195 time to fit residues: 30.4478 Evaluate side-chains 161 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 579 ASN Chi-restraints excluded: chain F residue 529 ASP Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.087396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063116 restraints weight = 36614.042| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.28 r_work: 0.2821 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13664 Z= 0.109 Angle : 0.520 9.572 18576 Z= 0.258 Chirality : 0.040 0.176 2162 Planarity : 0.004 0.044 2376 Dihedral : 11.197 173.897 2066 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.52 % Allowed : 9.20 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.20), residues: 1742 helix: 2.02 (0.18), residues: 896 sheet: 1.68 (0.37), residues: 193 loop : 0.70 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.021 0.001 TYR A 564 PHE 0.017 0.001 PHE F 462 TRP 0.023 0.001 TRP A 400 HIS 0.001 0.000 HIS E 514 Details of bonding type rmsd covalent geometry : bond 0.00248 (13664) covalent geometry : angle 0.52018 (18576) hydrogen bonds : bond 0.03157 ( 643) hydrogen bonds : angle 4.21950 ( 1836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.561 Fit side-chains REVERT: B 380 GLU cc_start: 0.8253 (pm20) cc_final: 0.8041 (pm20) REVERT: B 386 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9190 (mm) REVERT: B 399 ASN cc_start: 0.8089 (p0) cc_final: 0.7699 (p0) REVERT: B 579 ASN cc_start: 0.9185 (m-40) cc_final: 0.8915 (m110) REVERT: C 383 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.9010 (mmm) REVERT: C 524 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8548 (t80) REVERT: C 538 ARG cc_start: 0.8503 (mmp80) cc_final: 0.8232 (mmp-170) REVERT: C 658 LYS cc_start: 0.9206 (mmmt) cc_final: 0.8797 (mmmt) REVERT: D 524 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8646 (t80) REVERT: E 385 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8168 (tm-30) REVERT: E 586 CYS cc_start: 0.5698 (p) cc_final: 0.5423 (p) REVERT: F 383 MET cc_start: 0.8295 (tpp) cc_final: 0.8020 (tpp) REVERT: F 501 GLN cc_start: 0.8624 (mp10) cc_final: 0.8359 (mp10) REVERT: F 529 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6116 (m-30) REVERT: A 390 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8378 (mm-30) outliers start: 21 outliers final: 10 residues processed: 170 average time/residue: 0.1167 time to fit residues: 29.5039 Evaluate side-chains 160 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain E residue 500 ASP Chi-restraints excluded: chain F residue 511 ASP Chi-restraints excluded: chain F residue 529 ASP Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.086822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.062463 restraints weight = 36817.414| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.27 r_work: 0.2804 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13664 Z= 0.124 Angle : 0.526 10.519 18576 Z= 0.260 Chirality : 0.040 0.151 2162 Planarity : 0.004 0.045 2376 Dihedral : 11.105 179.723 2066 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.81 % Allowed : 9.78 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.20), residues: 1742 helix: 2.00 (0.18), residues: 899 sheet: 1.69 (0.37), residues: 193 loop : 0.67 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.006 0.001 TYR F 564 PHE 0.020 0.001 PHE F 462 TRP 0.018 0.001 TRP A 400 HIS 0.001 0.000 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00288 (13664) covalent geometry : angle 0.52649 (18576) hydrogen bonds : bond 0.03295 ( 643) hydrogen bonds : angle 4.18236 ( 1836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.559 Fit side-chains REVERT: B 380 GLU cc_start: 0.8284 (pm20) cc_final: 0.8062 (pm20) REVERT: B 386 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9202 (mm) REVERT: B 399 ASN cc_start: 0.8102 (p0) cc_final: 0.7687 (p0) REVERT: B 579 ASN cc_start: 0.9192 (m-40) cc_final: 0.8925 (m110) REVERT: C 383 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8959 (mmm) REVERT: C 524 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8543 (t80) REVERT: C 538 ARG cc_start: 0.8549 (mmp80) cc_final: 0.8183 (mmp-170) REVERT: D 524 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8601 (t80) REVERT: E 385 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 586 CYS cc_start: 0.5635 (p) cc_final: 0.5384 (p) REVERT: F 529 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6133 (m-30) REVERT: A 390 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 608 MET cc_start: 0.8650 (mmm) cc_final: 0.8282 (mmm) outliers start: 25 outliers final: 15 residues processed: 166 average time/residue: 0.1159 time to fit residues: 28.6609 Evaluate side-chains 162 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain E residue 500 ASP Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain F residue 511 ASP Chi-restraints excluded: chain F residue 529 ASP Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 149 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 126 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN F 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.084954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.060368 restraints weight = 36868.755| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.27 r_work: 0.2761 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13664 Z= 0.186 Angle : 0.569 9.289 18576 Z= 0.286 Chirality : 0.042 0.147 2162 Planarity : 0.004 0.054 2376 Dihedral : 11.234 167.989 2066 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.84 % Favored : 98.10 % Rotamer: Outliers : 1.88 % Allowed : 9.99 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.20), residues: 1742 helix: 1.92 (0.18), residues: 897 sheet: 1.48 (0.37), residues: 201 loop : 0.61 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.022 0.001 TYR A 564 PHE 0.026 0.002 PHE F 462 TRP 0.017 0.001 TRP A 400 HIS 0.002 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00440 (13664) covalent geometry : angle 0.56897 (18576) hydrogen bonds : bond 0.04034 ( 643) hydrogen bonds : angle 4.37301 ( 1836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: B 382 LYS cc_start: 0.9042 (tppt) cc_final: 0.8825 (tppt) REVERT: B 386 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9165 (mm) REVERT: B 399 ASN cc_start: 0.8126 (p0) cc_final: 0.7680 (p0) REVERT: C 385 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8519 (mm-30) REVERT: C 524 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8603 (t80) REVERT: C 538 ARG cc_start: 0.8624 (mmp80) cc_final: 0.8277 (mmp-170) REVERT: D 524 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8615 (t80) REVERT: E 385 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8342 (tm-30) REVERT: F 501 GLN cc_start: 0.8644 (mp10) cc_final: 0.8394 (mp10) REVERT: F 529 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6382 (m-30) REVERT: A 389 ASN cc_start: 0.7924 (p0) cc_final: 0.7482 (p0) REVERT: A 390 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8304 (mm-30) outliers start: 26 outliers final: 15 residues processed: 164 average time/residue: 0.1132 time to fit residues: 27.4803 Evaluate side-chains 162 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain D residue 579 ASN Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain F residue 511 ASP Chi-restraints excluded: chain F residue 529 ASP Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 170 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 646 ASN F 514 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.084863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.060382 restraints weight = 36746.685| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.26 r_work: 0.2759 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13664 Z= 0.182 Angle : 0.576 11.557 18576 Z= 0.285 Chirality : 0.041 0.151 2162 Planarity : 0.004 0.060 2376 Dihedral : 11.120 157.415 2066 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.78 % Favored : 98.16 % Rotamer: Outliers : 1.81 % Allowed : 10.64 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.20), residues: 1742 helix: 1.86 (0.17), residues: 902 sheet: 1.59 (0.37), residues: 197 loop : 0.52 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.009 0.001 TYR D 564 PHE 0.022 0.002 PHE F 462 TRP 0.019 0.001 TRP A 400 HIS 0.002 0.001 HIS F 514 Details of bonding type rmsd covalent geometry : bond 0.00430 (13664) covalent geometry : angle 0.57605 (18576) hydrogen bonds : bond 0.03812 ( 643) hydrogen bonds : angle 4.33588 ( 1836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: B 382 LYS cc_start: 0.9082 (tppt) cc_final: 0.8861 (tppt) REVERT: B 386 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9163 (mm) REVERT: B 399 ASN cc_start: 0.8049 (p0) cc_final: 0.7638 (p0) REVERT: C 385 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8616 (mm-30) REVERT: C 524 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8587 (t80) REVERT: C 538 ARG cc_start: 0.8594 (mmp80) cc_final: 0.8314 (mmp-170) REVERT: D 524 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8628 (t80) REVERT: E 385 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8398 (tm-30) REVERT: F 529 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6456 (m-30) REVERT: A 389 ASN cc_start: 0.7902 (p0) cc_final: 0.7453 (p0) REVERT: A 390 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8317 (mm-30) REVERT: A 500 ASP cc_start: 0.8464 (t0) cc_final: 0.8262 (t0) outliers start: 25 outliers final: 12 residues processed: 164 average time/residue: 0.1173 time to fit residues: 28.6147 Evaluate side-chains 157 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain F residue 529 ASP Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 123 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 147 optimal weight: 0.1980 chunk 85 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 514 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.086160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.061722 restraints weight = 36410.919| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.25 r_work: 0.2791 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13664 Z= 0.117 Angle : 0.563 11.137 18576 Z= 0.273 Chirality : 0.040 0.164 2162 Planarity : 0.004 0.055 2376 Dihedral : 10.783 151.048 2066 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.78 % Favored : 98.16 % Rotamer: Outliers : 1.59 % Allowed : 10.86 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.21), residues: 1742 helix: 2.09 (0.18), residues: 889 sheet: 1.66 (0.37), residues: 193 loop : 0.64 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 547 TYR 0.005 0.001 TYR D 564 PHE 0.018 0.001 PHE F 462 TRP 0.016 0.001 TRP A 400 HIS 0.002 0.001 HIS F 514 Details of bonding type rmsd covalent geometry : bond 0.00273 (13664) covalent geometry : angle 0.56331 (18576) hydrogen bonds : bond 0.03159 ( 643) hydrogen bonds : angle 4.14387 ( 1836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.590 Fit side-chains REVERT: B 382 LYS cc_start: 0.9067 (tppt) cc_final: 0.8857 (tppt) REVERT: B 386 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9143 (mm) REVERT: B 399 ASN cc_start: 0.8057 (p0) cc_final: 0.7625 (p0) REVERT: C 385 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8616 (mm-30) REVERT: C 524 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8561 (t80) REVERT: D 524 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8663 (t80) REVERT: E 385 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8340 (tm-30) REVERT: F 493 GLN cc_start: 0.8594 (tp40) cc_final: 0.8351 (tp-100) REVERT: F 501 GLN cc_start: 0.8646 (mp10) cc_final: 0.8367 (mp10) REVERT: F 529 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6320 (m-30) REVERT: A 389 ASN cc_start: 0.7910 (p0) cc_final: 0.7455 (p0) REVERT: A 390 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 608 MET cc_start: 0.8721 (mmm) cc_final: 0.8388 (mmm) outliers start: 22 outliers final: 13 residues processed: 158 average time/residue: 0.1211 time to fit residues: 28.5160 Evaluate side-chains 156 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain F residue 529 ASP Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 95 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.083784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.059287 restraints weight = 37042.632| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.24 r_work: 0.2735 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13664 Z= 0.231 Angle : 0.627 11.017 18576 Z= 0.314 Chirality : 0.043 0.184 2162 Planarity : 0.005 0.064 2376 Dihedral : 11.141 141.380 2066 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 1.45 % Allowed : 10.93 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.21), residues: 1742 helix: 1.91 (0.17), residues: 884 sheet: 1.44 (0.37), residues: 201 loop : 0.46 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 547 TYR 0.011 0.001 TYR C 564 PHE 0.024 0.002 PHE F 462 TRP 0.018 0.001 TRP A 400 HIS 0.002 0.001 HIS F 514 Details of bonding type rmsd covalent geometry : bond 0.00543 (13664) covalent geometry : angle 0.62679 (18576) hydrogen bonds : bond 0.04384 ( 643) hydrogen bonds : angle 4.47377 ( 1836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: B 382 LYS cc_start: 0.9138 (tppt) cc_final: 0.8894 (tppt) REVERT: B 386 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9096 (mm) REVERT: B 399 ASN cc_start: 0.8055 (p0) cc_final: 0.7633 (p0) REVERT: C 385 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8630 (mm-30) REVERT: C 524 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8625 (t80) REVERT: D 524 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8633 (t80) REVERT: E 385 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8440 (tm-30) REVERT: F 501 GLN cc_start: 0.8700 (mp10) cc_final: 0.8484 (mp10) REVERT: F 514 HIS cc_start: 0.8230 (m-70) cc_final: 0.7969 (m170) REVERT: F 529 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6536 (m-30) REVERT: A 389 ASN cc_start: 0.7837 (p0) cc_final: 0.7381 (p0) REVERT: A 390 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 608 MET cc_start: 0.8797 (mmm) cc_final: 0.8443 (mmm) outliers start: 20 outliers final: 13 residues processed: 154 average time/residue: 0.1180 time to fit residues: 27.5258 Evaluate side-chains 150 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain D residue 579 ASN Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain F residue 529 ASP Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 128 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 56 optimal weight: 0.0570 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.084751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.060289 restraints weight = 36668.995| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.27 r_work: 0.2754 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13664 Z= 0.169 Angle : 0.603 11.848 18576 Z= 0.296 Chirality : 0.041 0.189 2162 Planarity : 0.004 0.063 2376 Dihedral : 10.912 135.769 2066 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 1.30 % Allowed : 11.59 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.21), residues: 1742 helix: 1.98 (0.18), residues: 886 sheet: 1.46 (0.37), residues: 201 loop : 0.44 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 423 TYR 0.009 0.001 TYR C 564 PHE 0.023 0.001 PHE F 462 TRP 0.018 0.001 TRP A 400 HIS 0.002 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00399 (13664) covalent geometry : angle 0.60308 (18576) hydrogen bonds : bond 0.03702 ( 643) hydrogen bonds : angle 4.30815 ( 1836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: B 382 LYS cc_start: 0.9097 (tppt) cc_final: 0.8854 (tppt) REVERT: B 386 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9071 (mm) REVERT: B 399 ASN cc_start: 0.8057 (p0) cc_final: 0.7664 (p0) REVERT: C 385 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8627 (mm-30) REVERT: C 524 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8573 (t80) REVERT: D 524 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8682 (t80) REVERT: E 385 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8439 (tm-30) REVERT: E 524 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8578 (t80) REVERT: E 585 GLN cc_start: 0.7865 (pp30) cc_final: 0.7577 (pp30) REVERT: F 501 GLN cc_start: 0.8693 (mp10) cc_final: 0.8471 (mp10) REVERT: F 529 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6586 (m-30) REVERT: A 383 MET cc_start: 0.8637 (ttm) cc_final: 0.8373 (tmm) REVERT: A 389 ASN cc_start: 0.7837 (p0) cc_final: 0.7377 (p0) REVERT: A 390 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8329 (mm-30) REVERT: A 608 MET cc_start: 0.8791 (mmm) cc_final: 0.8441 (mmm) outliers start: 18 outliers final: 12 residues processed: 151 average time/residue: 0.1135 time to fit residues: 26.0523 Evaluate side-chains 152 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain E residue 524 PHE Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain F residue 529 ASP Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 57 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.084356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.059513 restraints weight = 36705.330| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.28 r_work: 0.2746 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13664 Z= 0.186 Angle : 0.610 11.599 18576 Z= 0.301 Chirality : 0.042 0.189 2162 Planarity : 0.004 0.065 2376 Dihedral : 10.891 139.723 2066 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.82 % Rotamer: Outliers : 1.38 % Allowed : 11.51 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.21), residues: 1742 helix: 1.92 (0.17), residues: 884 sheet: 1.48 (0.37), residues: 201 loop : 0.40 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.009 0.001 TYR C 564 PHE 0.024 0.002 PHE F 462 TRP 0.018 0.001 TRP A 400 HIS 0.002 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00440 (13664) covalent geometry : angle 0.61020 (18576) hydrogen bonds : bond 0.03923 ( 643) hydrogen bonds : angle 4.35744 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.34 seconds wall clock time: 60 minutes 58.40 seconds (3658.40 seconds total)