Starting phenix.real_space_refine on Thu Sep 26 07:26:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/09_2024/6qq6_4619.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/09_2024/6qq6_4619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/09_2024/6qq6_4619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/09_2024/6qq6_4619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/09_2024/6qq6_4619.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/09_2024/6qq6_4619.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 P 3 5.49 5 S 46 5.16 5 C 8019 2.51 5 N 1991 2.21 5 O 2056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12123 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5872 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 743, 5862 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 707} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 743, 5862 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 707} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 6041 Chain: "B" Number of atoms: 5872 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 743, 5862 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 707} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 743, 5862 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 707} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 6041 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 130 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'LOP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'LMT': 2, 'LOP': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 224 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 224 " occ=0.50 residue: pdb=" N AHIS B 224 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 224 " occ=0.50 Time building chain proxies: 12.67, per 1000 atoms: 1.05 Number of scatterers: 12123 At special positions: 0 Unit cell: (118.65, 74.55, 103.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 6 26.01 Ca 2 19.99 S 46 16.00 P 3 15.00 O 2056 8.00 N 1991 7.00 C 8019 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 2.6 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 3 sheets defined 67.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 4 through 32 removed outlier: 3.559A pdb=" N PHE A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.588A pdb=" N LEU A 69 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.883A pdb=" N LEU A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 127 removed outlier: 4.155A pdb=" N ALA A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 removed outlier: 3.988A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 200 removed outlier: 3.977A pdb=" N HIS A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 254 removed outlier: 3.722A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 304 removed outlier: 3.762A pdb=" N VAL A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.566A pdb=" N VAL A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 355 removed outlier: 3.880A pdb=" N ALA A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Proline residue: A 352 - end of helix removed outlier: 3.804A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 390 Processing helix chain 'A' and resid 394 through 398 removed outlier: 3.683A pdb=" N ASN A 398 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 435 removed outlier: 3.924A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 490 through 498 removed outlier: 3.967A pdb=" N GLU A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 526 through 531 removed outlier: 4.066A pdb=" N GLY A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.897A pdb=" N THR A 535 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 536 " --> pdb=" O PRO A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 558 removed outlier: 3.647A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 578 removed outlier: 3.590A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR A 578 " --> pdb=" O TRP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 removed outlier: 7.108A pdb=" N TRP A 582 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 585 " --> pdb=" O TRP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 removed outlier: 3.579A pdb=" N VAL A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 625 through 635 removed outlier: 3.542A pdb=" N HIS A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.584A pdb=" N LEU A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.582A pdb=" N ILE A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.608A pdb=" N ILE A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 704 removed outlier: 3.740A pdb=" N ARG A 703 " --> pdb=" O MET A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 removed outlier: 3.506A pdb=" N GLN A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 719 removed outlier: 3.574A pdb=" N ARG A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 742 removed outlier: 4.729A pdb=" N VAL A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 32 removed outlier: 3.551A pdb=" N PHE B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 28 " --> pdb=" O PHE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.581A pdb=" N LEU B 69 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 removed outlier: 3.826A pdb=" N LEU B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 127 removed outlier: 4.164A pdb=" N ALA B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 160 removed outlier: 3.967A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 200 removed outlier: 3.976A pdb=" N HIS B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 254 removed outlier: 3.733A pdb=" N LEU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 304 removed outlier: 3.761A pdb=" N VAL B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.553A pdb=" N VAL B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 355 removed outlier: 3.881A pdb=" N ALA B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Proline residue: B 352 - end of helix removed outlier: 3.806A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 390 Processing helix chain 'B' and resid 394 through 398 removed outlier: 3.695A pdb=" N ASN B 398 " --> pdb=" O PRO B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 435 removed outlier: 3.928A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 498 through 508 Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 526 through 531 removed outlier: 4.065A pdb=" N GLY B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.899A pdb=" N THR B 535 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 536 " --> pdb=" O PRO B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 558 removed outlier: 3.644A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 removed outlier: 4.057A pdb=" N LEU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.932A pdb=" N GLU B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 603 removed outlier: 3.516A pdb=" N VAL B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 597 " --> pdb=" O PHE B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 610 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 625 through 635 removed outlier: 3.547A pdb=" N HIS B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 635 " --> pdb=" O HIS B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 651 removed outlier: 3.589A pdb=" N LEU B 647 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 649 " --> pdb=" O PHE B 645 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 681 removed outlier: 3.940A pdb=" N LEU B 671 " --> pdb=" O ALA B 667 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 673 " --> pdb=" O TRP B 669 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.599A pdb=" N ILE B 686 " --> pdb=" O SER B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 704 removed outlier: 3.515A pdb=" N ALA B 702 " --> pdb=" O GLY B 698 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 703 " --> pdb=" O MET B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 709 removed outlier: 3.550A pdb=" N GLN B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 719 removed outlier: 3.627A pdb=" N ARG B 717 " --> pdb=" O LEU B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 742 removed outlier: 4.669A pdb=" N VAL B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 4.018A pdb=" N PHE A 49 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41 removed outlier: 4.015A pdb=" N PHE B 49 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 611 hydrogen bonds defined for protein. 1764 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: 3.82 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 3747 1.35 - 1.53: 7671 1.53 - 1.70: 992 1.70 - 1.88: 88 1.88 - 2.05: 16 Bond restraints: 12514 Sorted by residual: bond pdb=" C1B LMT B 807 " pdb=" O5B LMT B 807 " ideal model delta sigma weight residual 1.393 1.508 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C1B LMT B 808 " pdb=" O5B LMT B 808 " ideal model delta sigma weight residual 1.393 1.506 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" C1' LMT B 807 " pdb=" O5' LMT B 807 " ideal model delta sigma weight residual 1.408 1.499 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C1' LMT B 808 " pdb=" O5' LMT B 808 " ideal model delta sigma weight residual 1.408 1.493 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C24 LOP B 806 " pdb=" O6 LOP B 806 " ideal model delta sigma weight residual 1.325 1.401 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 12509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 16369 2.27 - 4.55: 552 4.55 - 6.82: 134 6.82 - 9.10: 39 9.10 - 11.37: 15 Bond angle restraints: 17109 Sorted by residual: angle pdb=" N ILE B 712 " pdb=" CA ILE B 712 " pdb=" C ILE B 712 " ideal model delta sigma weight residual 112.96 106.66 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" C ILE A 712 " ideal model delta sigma weight residual 112.96 106.69 6.27 1.00e+00 1.00e+00 3.93e+01 angle pdb=" N GLU A 572 " pdb=" CA GLU A 572 " pdb=" C GLU A 572 " ideal model delta sigma weight residual 111.14 104.83 6.31 1.08e+00 8.57e-01 3.41e+01 angle pdb=" CA PHE A 536 " pdb=" C PHE A 536 " pdb=" N HIS A 537 " ideal model delta sigma weight residual 118.59 127.92 -9.33 1.63e+00 3.76e-01 3.28e+01 angle pdb=" N ARG B 579 " pdb=" CA ARG B 579 " pdb=" C ARG B 579 " ideal model delta sigma weight residual 111.36 117.57 -6.21 1.09e+00 8.42e-01 3.25e+01 ... (remaining 17104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 6525 22.36 - 44.71: 442 44.71 - 67.07: 81 67.07 - 89.43: 16 89.43 - 111.79: 14 Dihedral angle restraints: 7078 sinusoidal: 2846 harmonic: 4232 Sorted by residual: dihedral pdb=" CA ASN A 214 " pdb=" C ASN A 214 " pdb=" N TRP A 215 " pdb=" CA TRP A 215 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ASN B 214 " pdb=" C ASN B 214 " pdb=" N TRP B 215 " pdb=" CA TRP B 215 " ideal model delta harmonic sigma weight residual -180.00 -154.51 -25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA TYR B 652 " pdb=" C TYR B 652 " pdb=" N ILE B 653 " pdb=" CA ILE B 653 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 7075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1510 0.066 - 0.133: 256 0.133 - 0.199: 31 0.199 - 0.266: 5 0.266 - 0.332: 5 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA ILE B 392 " pdb=" N ILE B 392 " pdb=" C ILE B 392 " pdb=" CB ILE B 392 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE A 620 " pdb=" CA ILE A 620 " pdb=" CG1 ILE A 620 " pdb=" CG2 ILE A 620 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB ILE B 620 " pdb=" CA ILE B 620 " pdb=" CG1 ILE B 620 " pdb=" CG2 ILE B 620 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1804 not shown) Planarity restraints: 2113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 179 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C THR A 179 " -0.042 2.00e-02 2.50e+03 pdb=" O THR A 179 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 180 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP B 588 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO B 589 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 588 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO A 589 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " -0.032 5.00e-02 4.00e+02 ... (remaining 2110 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 89 2.52 - 3.11: 8141 3.11 - 3.71: 19849 3.71 - 4.30: 28771 4.30 - 4.90: 48210 Nonbonded interactions: 105060 Sorted by model distance: nonbonded pdb=" O ASP A 162 " pdb=" OD1 ASP A 162 " model vdw 1.924 3.040 nonbonded pdb=" NE2 HIS B 538 " pdb="FE FE B 803 " model vdw 1.988 2.340 nonbonded pdb=" NE2 HIS A 538 " pdb="FE FE A 803 " model vdw 1.989 2.340 nonbonded pdb=" NE2 HIS B 631 " pdb="FE HEM B 801 " model vdw 1.996 3.080 nonbonded pdb=" NE2 HIS A 631 " pdb="FE HEM A 801 " model vdw 1.996 3.080 ... (remaining 105055 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 1 through 223 or resid 225 through 743 or resid 801 throug \ h 804 or (resid 805 and (name C1 or name C10 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C2 or name C20 or name C24 or name C25 or name C26 or name C27 or name C28 or n \ ame C29 or name C3 or name C30 or name C4 or name C5 or name C6 or name C7 or na \ me C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name \ O5 or name O6 or name O7 or name O8 or name P1 )))) selection = (chain 'B' and (resid 1 through 223 or resid 225 through 743 or resid 801 throug \ h 804 or (resid 805 and (name C1 or name C10 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C2 or name C20 or name C24 or name C25 or name C26 or name C27 or name C28 or n \ ame C29 or name C3 or name C30 or name C4 or name C5 or name C6 or name C7 or na \ me C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name \ O5 or name O6 or name O7 or name O8 or name P1 )))) } 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: 0.380 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: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 37.010 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.007 0.115 12514 Z= 0.410 Angle : 1.076 11.372 17109 Z= 0.544 Chirality : 0.055 0.332 1807 Planarity : 0.007 0.059 2113 Dihedral : 16.787 111.787 4390 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.08 (0.15), residues: 1488 helix: -3.17 (0.11), residues: 988 sheet: None (None), residues: 0 loop : -3.43 (0.21), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 215 HIS 0.007 0.002 HIS B 537 PHE 0.022 0.002 PHE A 635 TYR 0.019 0.002 TYR A 468 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3616 (ptp) cc_final: 0.2964 (ttp) REVERT: A 718 TRP cc_start: 0.6828 (t60) cc_final: 0.6101 (t60) REVERT: B 1 MET cc_start: 0.3557 (ptp) cc_final: 0.3099 (ptp) REVERT: B 355 ASN cc_start: 0.8773 (t0) cc_final: 0.8303 (t0) REVERT: B 430 MET cc_start: 0.8193 (mmm) cc_final: 0.7888 (tpt) REVERT: B 718 TRP cc_start: 0.6139 (t60) cc_final: 0.5721 (t60) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2554 time to fit residues: 79.4312 Evaluate side-chains 158 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 130 ASN A 224 HIS A A 355 ASN A 398 ASN B 68 GLN B 130 ASN B 214 ASN B 355 ASN B 398 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12514 Z= 0.223 Angle : 0.670 8.671 17109 Z= 0.329 Chirality : 0.042 0.313 1807 Planarity : 0.005 0.051 2113 Dihedral : 11.612 86.547 1874 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.03 % Allowed : 9.36 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.20), residues: 1488 helix: -1.42 (0.15), residues: 1000 sheet: None (None), residues: 0 loop : -2.69 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 215 HIS 0.005 0.001 HIS B 537 PHE 0.015 0.001 PHE B 635 TYR 0.019 0.002 TYR B 108 ARG 0.014 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3558 (ptp) cc_final: 0.2905 (ttp) REVERT: A 280 ARG cc_start: 0.7291 (mtm110) cc_final: 0.6855 (mtm110) REVERT: A 320 GLN cc_start: 0.7750 (pt0) cc_final: 0.7064 (mp10) REVERT: A 494 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7578 (tm-30) REVERT: A 708 MET cc_start: 0.8370 (mmt) cc_final: 0.8132 (tpt) REVERT: A 718 TRP cc_start: 0.6856 (t60) cc_final: 0.6222 (t60) REVERT: B 1 MET cc_start: 0.3352 (ptp) cc_final: 0.2802 (ptp) REVERT: B 355 ASN cc_start: 0.8870 (t0) cc_final: 0.8355 (t0) REVERT: B 430 MET cc_start: 0.8580 (mmm) cc_final: 0.8227 (tpt) REVERT: B 494 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7816 (tm-30) REVERT: B 610 MET cc_start: 0.7391 (ttp) cc_final: 0.7185 (ttp) REVERT: B 718 TRP cc_start: 0.6318 (t60) cc_final: 0.5903 (t60) outliers start: 12 outliers final: 4 residues processed: 173 average time/residue: 0.2841 time to fit residues: 71.8046 Evaluate side-chains 152 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS A 355 ASN B 68 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12514 Z= 0.279 Angle : 0.704 14.875 17109 Z= 0.340 Chirality : 0.043 0.248 1807 Planarity : 0.005 0.064 2113 Dihedral : 10.358 82.973 1874 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.20 % Allowed : 10.91 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1488 helix: -0.81 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 215 HIS 0.005 0.001 HIS B 631 PHE 0.017 0.001 PHE B 635 TYR 0.019 0.002 TYR B 406 ARG 0.006 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.187 Fit side-chains REVERT: A 1 MET cc_start: 0.3386 (ptp) cc_final: 0.2772 (ttp) REVERT: A 39 GLU cc_start: 0.6722 (mm-30) cc_final: 0.6509 (mm-30) REVERT: A 67 MET cc_start: 0.8755 (mtt) cc_final: 0.8532 (mtt) REVERT: A 280 ARG cc_start: 0.7442 (mtm110) cc_final: 0.6882 (mtm110) REVERT: A 320 GLN cc_start: 0.8001 (pt0) cc_final: 0.7339 (mp10) REVERT: A 494 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 718 TRP cc_start: 0.6834 (t60) cc_final: 0.6176 (t60) REVERT: B 1 MET cc_start: 0.3438 (ptp) cc_final: 0.2868 (ptp) REVERT: B 355 ASN cc_start: 0.8894 (t0) cc_final: 0.8455 (t0) REVERT: B 401 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8248 (pp) REVERT: B 430 MET cc_start: 0.8651 (mmm) cc_final: 0.8349 (tpt) REVERT: B 460 LEU cc_start: 0.8769 (mp) cc_final: 0.8569 (mt) REVERT: B 494 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 591 MET cc_start: 0.8024 (mtp) cc_final: 0.7711 (mtt) REVERT: B 610 MET cc_start: 0.7841 (ttp) cc_final: 0.7573 (ttp) REVERT: B 680 PHE cc_start: 0.8853 (m-80) cc_final: 0.8650 (m-80) REVERT: B 718 TRP cc_start: 0.6431 (t60) cc_final: 0.6055 (t60) outliers start: 14 outliers final: 11 residues processed: 158 average time/residue: 0.2387 time to fit residues: 55.1476 Evaluate side-chains 151 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 708 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12514 Z= 0.200 Angle : 0.626 9.087 17109 Z= 0.303 Chirality : 0.041 0.280 1807 Planarity : 0.004 0.045 2113 Dihedral : 9.685 79.854 1874 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.37 % Allowed : 12.11 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1488 helix: -0.39 (0.17), residues: 1000 sheet: None (None), residues: 0 loop : -2.05 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 215 HIS 0.003 0.001 HIS B 486 PHE 0.013 0.001 PHE B 194 TYR 0.035 0.002 TYR B 406 ARG 0.005 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.277 Fit side-chains REVERT: A 1 MET cc_start: 0.3448 (ptp) cc_final: 0.2742 (ttp) REVERT: A 32 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7736 (mm-40) REVERT: A 67 MET cc_start: 0.8768 (mtt) cc_final: 0.8536 (mtt) REVERT: A 280 ARG cc_start: 0.7436 (mtm110) cc_final: 0.6950 (mtm110) REVERT: A 320 GLN cc_start: 0.8011 (pt0) cc_final: 0.7395 (mp10) REVERT: A 718 TRP cc_start: 0.6829 (t60) cc_final: 0.6235 (t60) REVERT: B 1 MET cc_start: 0.3379 (ptp) cc_final: 0.2809 (ptp) REVERT: B 355 ASN cc_start: 0.8831 (t0) cc_final: 0.8413 (t0) REVERT: B 515 MET cc_start: 0.7507 (mmp) cc_final: 0.6706 (mtm) REVERT: B 591 MET cc_start: 0.8016 (mtp) cc_final: 0.7716 (mtt) REVERT: B 610 MET cc_start: 0.7746 (ttp) cc_final: 0.7445 (ttp) REVERT: B 680 PHE cc_start: 0.8799 (m-80) cc_final: 0.8531 (m-80) REVERT: B 718 TRP cc_start: 0.6427 (t60) cc_final: 0.6054 (t60) outliers start: 16 outliers final: 9 residues processed: 153 average time/residue: 0.2376 time to fit residues: 53.5595 Evaluate side-chains 145 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 646 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 214 ASN ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12514 Z= 0.242 Angle : 0.644 10.393 17109 Z= 0.311 Chirality : 0.042 0.212 1807 Planarity : 0.004 0.046 2113 Dihedral : 9.349 78.414 1874 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.86 % Allowed : 12.29 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1488 helix: -0.24 (0.17), residues: 1012 sheet: None (None), residues: 0 loop : -1.85 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 215 HIS 0.004 0.001 HIS B 486 PHE 0.015 0.001 PHE B 194 TYR 0.017 0.002 TYR B 406 ARG 0.005 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 1.214 Fit side-chains REVERT: A 1 MET cc_start: 0.3530 (ptp) cc_final: 0.2716 (ttp) REVERT: A 67 MET cc_start: 0.8791 (mtt) cc_final: 0.8527 (mtt) REVERT: A 280 ARG cc_start: 0.7386 (mtm110) cc_final: 0.6879 (mtm110) REVERT: A 320 GLN cc_start: 0.8074 (pt0) cc_final: 0.7481 (mp10) REVERT: A 445 LYS cc_start: 0.6274 (ptmt) cc_final: 0.5092 (mmtm) REVERT: A 574 TRP cc_start: 0.7879 (t60) cc_final: 0.7675 (t60) REVERT: A 601 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8138 (tmm) REVERT: A 718 TRP cc_start: 0.6878 (t60) cc_final: 0.6236 (t60) REVERT: B 1 MET cc_start: 0.3532 (ptp) cc_final: 0.2969 (ptp) REVERT: B 32 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7773 (mt0) REVERT: B 355 ASN cc_start: 0.8846 (t0) cc_final: 0.8451 (t0) REVERT: B 515 MET cc_start: 0.7519 (mmp) cc_final: 0.6718 (mtm) REVERT: B 591 MET cc_start: 0.8021 (mtp) cc_final: 0.7744 (mtt) REVERT: B 610 MET cc_start: 0.7792 (ttp) cc_final: 0.7502 (ttp) REVERT: B 680 PHE cc_start: 0.8855 (m-80) cc_final: 0.8573 (m-80) REVERT: B 718 TRP cc_start: 0.6499 (t60) cc_final: 0.6152 (t60) outliers start: 10 outliers final: 7 residues processed: 152 average time/residue: 0.2483 time to fit residues: 55.3046 Evaluate side-chains 139 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN B 224 HIS A ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12514 Z= 0.281 Angle : 0.658 10.971 17109 Z= 0.318 Chirality : 0.043 0.183 1807 Planarity : 0.004 0.048 2113 Dihedral : 9.227 77.309 1874 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.29 % Allowed : 12.71 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1488 helix: -0.13 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -1.86 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 215 HIS 0.004 0.001 HIS A 537 PHE 0.016 0.001 PHE B 194 TYR 0.016 0.002 TYR B 406 ARG 0.006 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3511 (ptp) cc_final: 0.3022 (ptp) REVERT: A 280 ARG cc_start: 0.7428 (mtm110) cc_final: 0.6925 (mtm110) REVERT: A 320 GLN cc_start: 0.8116 (pt0) cc_final: 0.7522 (mp10) REVERT: A 445 LYS cc_start: 0.6184 (ptmt) cc_final: 0.5008 (mmtm) REVERT: A 574 TRP cc_start: 0.7903 (t60) cc_final: 0.7689 (t60) REVERT: A 601 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8189 (tmm) REVERT: A 718 TRP cc_start: 0.6877 (t60) cc_final: 0.6277 (t60) REVERT: B 1 MET cc_start: 0.3586 (ptp) cc_final: 0.3036 (ptp) REVERT: B 355 ASN cc_start: 0.8867 (t0) cc_final: 0.8449 (t0) REVERT: B 515 MET cc_start: 0.7533 (mmp) cc_final: 0.6740 (mtm) REVERT: B 591 MET cc_start: 0.8009 (mtp) cc_final: 0.7732 (mtt) REVERT: B 610 MET cc_start: 0.7846 (ttp) cc_final: 0.7548 (ttp) REVERT: B 673 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8366 (tp) REVERT: B 680 PHE cc_start: 0.8832 (m-80) cc_final: 0.8536 (m-80) REVERT: B 718 TRP cc_start: 0.6525 (t60) cc_final: 0.6217 (t60) outliers start: 15 outliers final: 12 residues processed: 146 average time/residue: 0.2571 time to fit residues: 53.8257 Evaluate side-chains 147 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12514 Z= 0.235 Angle : 0.624 9.247 17109 Z= 0.303 Chirality : 0.041 0.204 1807 Planarity : 0.004 0.046 2113 Dihedral : 9.068 78.279 1874 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.20 % Allowed : 13.23 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1488 helix: 0.02 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.68 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 215 HIS 0.004 0.001 HIS A 537 PHE 0.014 0.001 PHE B 194 TYR 0.016 0.002 TYR B 108 ARG 0.006 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3499 (ptp) cc_final: 0.3008 (ptp) REVERT: A 280 ARG cc_start: 0.7411 (mtm110) cc_final: 0.6919 (mtm110) REVERT: A 320 GLN cc_start: 0.8149 (pt0) cc_final: 0.7560 (mp10) REVERT: A 445 LYS cc_start: 0.6182 (ptmt) cc_final: 0.5044 (mmtm) REVERT: A 601 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8248 (tmm) REVERT: A 718 TRP cc_start: 0.6876 (t60) cc_final: 0.6284 (t60) REVERT: B 1 MET cc_start: 0.3607 (ptp) cc_final: 0.3056 (ptp) REVERT: B 355 ASN cc_start: 0.8743 (t0) cc_final: 0.8355 (t0) REVERT: B 445 LYS cc_start: 0.6603 (ptmt) cc_final: 0.5487 (mmtm) REVERT: B 515 MET cc_start: 0.7526 (mmp) cc_final: 0.6740 (mtm) REVERT: B 591 MET cc_start: 0.7992 (mtp) cc_final: 0.7719 (mtt) REVERT: B 610 MET cc_start: 0.7811 (ttp) cc_final: 0.7508 (ttp) REVERT: B 718 TRP cc_start: 0.6479 (t60) cc_final: 0.6168 (t60) outliers start: 14 outliers final: 10 residues processed: 152 average time/residue: 0.2587 time to fit residues: 57.1799 Evaluate side-chains 145 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 708 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.0370 chunk 85 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12514 Z= 0.171 Angle : 0.594 8.514 17109 Z= 0.288 Chirality : 0.039 0.195 1807 Planarity : 0.004 0.043 2113 Dihedral : 8.822 80.598 1874 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.29 % Allowed : 13.40 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1488 helix: 0.25 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -1.64 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 215 HIS 0.004 0.001 HIS A 537 PHE 0.013 0.001 PHE A 24 TYR 0.014 0.001 TYR B 108 ARG 0.010 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3443 (ptp) cc_final: 0.2957 (ptp) REVERT: A 280 ARG cc_start: 0.7329 (mtm110) cc_final: 0.7015 (mtm110) REVERT: A 320 GLN cc_start: 0.8122 (pt0) cc_final: 0.7550 (mp10) REVERT: A 445 LYS cc_start: 0.6156 (ptmt) cc_final: 0.4995 (mmtm) REVERT: A 601 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8165 (tmm) REVERT: A 718 TRP cc_start: 0.6815 (t60) cc_final: 0.6207 (t60) REVERT: B 1 MET cc_start: 0.3595 (ptp) cc_final: 0.3054 (ptp) REVERT: B 32 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7848 (tt0) REVERT: B 355 ASN cc_start: 0.8701 (t0) cc_final: 0.8340 (t0) REVERT: B 515 MET cc_start: 0.7510 (mmp) cc_final: 0.6729 (mtm) REVERT: B 591 MET cc_start: 0.7992 (mtp) cc_final: 0.7737 (mtt) REVERT: B 610 MET cc_start: 0.7729 (ttp) cc_final: 0.7411 (ttp) REVERT: B 718 TRP cc_start: 0.6470 (t60) cc_final: 0.6163 (t60) outliers start: 15 outliers final: 13 residues processed: 160 average time/residue: 0.2486 time to fit residues: 57.5004 Evaluate side-chains 154 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 68 GLN B 214 ASN B 305 HIS ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12514 Z= 0.230 Angle : 0.619 9.351 17109 Z= 0.300 Chirality : 0.041 0.192 1807 Planarity : 0.004 0.043 2113 Dihedral : 8.810 79.537 1874 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.29 % Allowed : 13.66 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1488 helix: 0.25 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.54 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 215 HIS 0.004 0.001 HIS A 537 PHE 0.014 0.001 PHE A 24 TYR 0.018 0.002 TYR B 406 ARG 0.008 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3456 (ptp) cc_final: 0.2970 (ptp) REVERT: A 5 ARG cc_start: 0.7278 (mtp85) cc_final: 0.7005 (ttm-80) REVERT: A 280 ARG cc_start: 0.7347 (mtm110) cc_final: 0.7020 (mtm110) REVERT: A 320 GLN cc_start: 0.8182 (pt0) cc_final: 0.7622 (mp10) REVERT: A 445 LYS cc_start: 0.6180 (ptmt) cc_final: 0.5066 (mmtm) REVERT: A 718 TRP cc_start: 0.6833 (t60) cc_final: 0.6273 (t60) REVERT: B 1 MET cc_start: 0.3428 (ptp) cc_final: 0.2871 (ptp) REVERT: B 355 ASN cc_start: 0.8714 (t0) cc_final: 0.8368 (t0) REVERT: B 445 LYS cc_start: 0.6680 (ptmt) cc_final: 0.5561 (mmtm) REVERT: B 515 MET cc_start: 0.7535 (mmp) cc_final: 0.6735 (mtm) REVERT: B 591 MET cc_start: 0.7996 (mtp) cc_final: 0.7731 (mtt) REVERT: B 610 MET cc_start: 0.7789 (ttp) cc_final: 0.7491 (ttp) REVERT: B 718 TRP cc_start: 0.6477 (t60) cc_final: 0.6174 (t60) outliers start: 15 outliers final: 14 residues processed: 153 average time/residue: 0.2587 time to fit residues: 57.5263 Evaluate side-chains 149 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12514 Z= 0.186 Angle : 0.601 8.252 17109 Z= 0.291 Chirality : 0.040 0.179 1807 Planarity : 0.004 0.043 2113 Dihedral : 8.686 80.252 1874 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.20 % Allowed : 13.66 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1488 helix: 0.42 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.57 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 215 HIS 0.004 0.001 HIS A 537 PHE 0.014 0.001 PHE A 24 TYR 0.016 0.001 TYR B 406 ARG 0.010 0.000 ARG A 358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3436 (ptp) cc_final: 0.2945 (ptp) REVERT: A 5 ARG cc_start: 0.7290 (mtp85) cc_final: 0.7025 (ttm-80) REVERT: A 280 ARG cc_start: 0.7328 (mtm110) cc_final: 0.6922 (mtm110) REVERT: A 320 GLN cc_start: 0.8145 (pt0) cc_final: 0.7584 (mp10) REVERT: A 398 ASN cc_start: 0.8519 (t0) cc_final: 0.8254 (t0) REVERT: A 445 LYS cc_start: 0.6177 (ptmt) cc_final: 0.5067 (mmtm) REVERT: A 718 TRP cc_start: 0.6824 (t60) cc_final: 0.6273 (t60) REVERT: B 1 MET cc_start: 0.3445 (ptp) cc_final: 0.2905 (ptp) REVERT: B 32 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7840 (tt0) REVERT: B 355 ASN cc_start: 0.8700 (t0) cc_final: 0.8357 (t0) REVERT: B 445 LYS cc_start: 0.6689 (ptmt) cc_final: 0.5577 (mmtm) REVERT: B 515 MET cc_start: 0.7518 (mmp) cc_final: 0.6727 (mtm) REVERT: B 591 MET cc_start: 0.8002 (mtp) cc_final: 0.7744 (mtt) REVERT: B 610 MET cc_start: 0.7748 (ttp) cc_final: 0.7445 (ttp) REVERT: B 718 TRP cc_start: 0.6476 (t60) cc_final: 0.6175 (t60) outliers start: 14 outliers final: 13 residues processed: 152 average time/residue: 0.2688 time to fit residues: 58.5086 Evaluate side-chains 153 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 214 ASN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.095121 restraints weight = 35247.967| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.04 r_work: 0.2801 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.082 | | 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) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12514 Z= 0.174 Angle : 0.592 8.154 17109 Z= 0.287 Chirality : 0.040 0.172 1807 Planarity : 0.004 0.043 2113 Dihedral : 8.568 81.541 1874 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.03 % Allowed : 13.92 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.23), residues: 1488 helix: 0.52 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.56 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 215 HIS 0.004 0.001 HIS A 537 PHE 0.014 0.001 PHE A 24 TYR 0.014 0.001 TYR B 406 ARG 0.006 0.000 ARG A 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2491.88 seconds wall clock time: 45 minutes 7.05 seconds (2707.05 seconds total)