Starting phenix.real_space_refine on Sat Sep 12 00:14:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qq6_4619/09_2026/6qq6_4619.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qq6_4619/09_2026/6qq6_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 { model { file = "/net/cci-nas-00/data/ceres_data/6qq6_4619/09_2026/6qq6_4619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qq6_4619/09_2026/6qq6_4619.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6qq6_4619/09_2026/6qq6_4619.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qq6_4619/09_2026/6qq6_4619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qq6_4619/09_2026/6qq6_4619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qq6_4619/09_2026/6qq6_4619.map" } resolution = 3.3 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= 0.013 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): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 3.86, per 1000 atoms: 0.32 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: 0.73 Conformation dependent library (CDL) restraints added in 834.7 milliseconds 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: 0.29 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: 1.52 Time building geometry restraints manager: 0.96 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 - 16.63: 6094 16.63 - 33.26: 659 33.26 - 49.89: 141 49.89 - 66.52: 43 66.52 - 83.15: 11 Dihedral angle restraints: 6948 sinusoidal: 2716 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 6945 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 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 C \ 24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or nam \ e C30 or name C4 or name C5 or name C6 or name C7 or name 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 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 C \ 24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or nam \ e C30 or name C4 or name C5 or name C6 or name C7 or name 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: 0.520 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.630 Find NCS groups from input model: 0.170 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.270 12518 Z= 0.304 Angle : 1.076 11.372 17109 Z= 0.544 Chirality : 0.055 0.332 1807 Planarity : 0.007 0.059 2113 Dihedral : 15.093 83.146 4260 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG B 328 TYR 0.019 0.002 TYR A 468 PHE 0.022 0.002 PHE A 635 TRP 0.024 0.002 TRP A 215 HIS 0.007 0.002 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.30 (12514) covalent geometry : angle 1.07581 / 0.54 (17109) hydrogen bonds : bond 0.15790 / 9.99 ( 611) hydrogen bonds : angle 6.99370 / 4.98 ( 1764) Misc. bond : bond 0.25504 / 12.74 ( 4) *********************** 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 to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3616 (ptp) cc_final: 0.2965 (ttp) REVERT: A 718 TRP cc_start: 0.6828 (t60) cc_final: 0.6101 (t60) REVERT: B 1 MET cc_start: 0.3558 (ptp) cc_final: 0.3098 (ptp) REVERT: B 355 ASN cc_start: 0.8773 (t0) cc_final: 0.8304 (t0) REVERT: B 430 MET cc_start: 0.8193 (mmm) cc_final: 0.7889 (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: 0.1096 time to fit residues: 34.5694 Evaluate side-chains 159 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.096223 restraints weight = 27831.077| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.48 r_work: 0.2846 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.223 12518 Z= 0.138 Angle : 0.657 8.663 17109 Z= 0.325 Chirality : 0.041 0.163 1807 Planarity : 0.005 0.050 2113 Dihedral : 10.071 86.163 1744 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.03 % Allowed : 9.19 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.91 (0.19), residues: 1488 helix: -1.45 (0.15), residues: 1000 sheet: None (None), residues: 0 loop : -2.71 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 280 TYR 0.017 0.002 TYR B 108 PHE 0.014 0.001 PHE B 635 TRP 0.023 0.001 TRP B 215 HIS 0.006 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (12514) covalent geometry : angle 0.65670 / 0.32 (17109) hydrogen bonds : bond 0.03909 / 2.58 ( 611) hydrogen bonds : angle 4.73270 / 3.36 ( 1764) Misc. bond : bond 0.17964 / 9.10 ( 4) *********************** 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 187 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3398 (ptp) cc_final: 0.2761 (ttp) REVERT: A 231 MET cc_start: 0.7662 (mmm) cc_final: 0.7176 (ttt) REVERT: A 280 ARG cc_start: 0.7484 (mtm110) cc_final: 0.6983 (mtm110) REVERT: A 320 GLN cc_start: 0.7918 (pt0) cc_final: 0.7274 (mp10) REVERT: A 445 LYS cc_start: 0.6269 (ptmt) cc_final: 0.6059 (ptmt) REVERT: A 494 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7778 (tm-30) REVERT: A 708 MET cc_start: 0.8625 (mmt) cc_final: 0.8389 (tpt) REVERT: A 718 TRP cc_start: 0.7410 (t60) cc_final: 0.6499 (t60) REVERT: B 1 MET cc_start: 0.3145 (ptp) cc_final: 0.2610 (ptp) REVERT: B 231 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7255 (ttp) REVERT: B 355 ASN cc_start: 0.9077 (t0) cc_final: 0.8553 (t0) REVERT: B 430 MET cc_start: 0.8624 (mmm) cc_final: 0.8243 (tpt) REVERT: B 652 TYR cc_start: 0.8141 (m-80) cc_final: 0.7862 (m-80) REVERT: B 718 TRP cc_start: 0.6916 (t60) cc_final: 0.6210 (t60) outliers start: 12 outliers final: 3 residues processed: 180 average time/residue: 0.0962 time to fit residues: 25.6397 Evaluate side-chains 156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 238 VAL 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 14 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 0.0470 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 146 optimal weight: 0.0030 chunk 7 optimal weight: 0.6980 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 HIS A 355 ASN B 68 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.099787 restraints weight = 36549.249| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.91 r_work: 0.2832 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 12518 Z= 0.115 Angle : 0.611 8.607 17109 Z= 0.300 Chirality : 0.039 0.182 1807 Planarity : 0.004 0.064 2113 Dihedral : 9.609 86.530 1744 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.03 % Allowed : 10.74 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.89 (0.21), residues: 1488 helix: -0.67 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 432 TYR 0.021 0.001 TYR B 406 PHE 0.012 0.001 PHE B 635 TRP 0.022 0.001 TRP B 215 HIS 0.005 0.001 HIS B 692 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (12514) covalent geometry : angle 0.61078 / 0.30 (17109) hydrogen bonds : bond 0.03406 / 2.26 ( 611) hydrogen bonds : angle 4.37694 / 3.11 ( 1764) Misc. bond : bond 0.16376 / 8.26 ( 4) *********************** 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 174 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3224 (ptp) cc_final: 0.2564 (ttp) REVERT: A 39 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6476 (mm-30) REVERT: A 280 ARG cc_start: 0.7536 (mtm110) cc_final: 0.6927 (mtm110) REVERT: A 320 GLN cc_start: 0.8006 (pt0) cc_final: 0.7400 (mp10) REVERT: A 701 TYR cc_start: 0.8921 (t80) cc_final: 0.8706 (t80) REVERT: A 708 MET cc_start: 0.8518 (mmt) cc_final: 0.8288 (tpt) REVERT: A 718 TRP cc_start: 0.7428 (t60) cc_final: 0.6493 (t60) REVERT: B 1 MET cc_start: 0.3152 (ptp) cc_final: 0.2712 (ptp) REVERT: B 355 ASN cc_start: 0.9124 (t0) cc_final: 0.8670 (t0) REVERT: B 430 MET cc_start: 0.8593 (mmm) cc_final: 0.8222 (tpt) REVERT: B 591 MET cc_start: 0.8553 (mtp) cc_final: 0.8310 (ttm) REVERT: B 652 TYR cc_start: 0.8134 (m-80) cc_final: 0.7855 (m-80) REVERT: B 718 TRP cc_start: 0.6964 (t60) cc_final: 0.6236 (t60) outliers start: 12 outliers final: 8 residues processed: 168 average time/residue: 0.0987 time to fit residues: 24.8550 Evaluate side-chains 157 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 302 PHE 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 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 147 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 GLN B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.096370 restraints weight = 35713.570| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.00 r_work: 0.2821 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 12518 Z= 0.136 Angle : 0.618 8.621 17109 Z= 0.301 Chirality : 0.040 0.210 1807 Planarity : 0.004 0.052 2113 Dihedral : 9.335 84.161 1744 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.03 % Allowed : 11.68 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.39 (0.22), residues: 1488 helix: -0.33 (0.17), residues: 1006 sheet: None (None), residues: 0 loop : -2.03 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 432 TYR 0.031 0.002 TYR B 406 PHE 0.013 0.001 PHE B 194 TRP 0.020 0.001 TRP B 215 HIS 0.003 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (12514) covalent geometry : angle 0.61796 / 0.30 (17109) hydrogen bonds : bond 0.03386 / 2.25 ( 611) hydrogen bonds : angle 4.18302 / 2.98 ( 1764) Misc. bond : bond 0.15740 / 7.96 ( 4) *********************** 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 169 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.264 Fit side-chains REVERT: A 1 MET cc_start: 0.3231 (ptp) cc_final: 0.2535 (ttp) REVERT: A 280 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7185 (mtm110) REVERT: A 320 GLN cc_start: 0.8171 (pt0) cc_final: 0.7579 (mp10) REVERT: A 445 LYS cc_start: 0.6155 (ptmt) cc_final: 0.4858 (mmtm) REVERT: A 718 TRP cc_start: 0.7501 (t60) cc_final: 0.6574 (t60) REVERT: B 1 MET cc_start: 0.3018 (ptp) cc_final: 0.2467 (ptp) REVERT: B 355 ASN cc_start: 0.9165 (t0) cc_final: 0.8734 (t0) REVERT: B 401 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7918 (pp) REVERT: B 515 MET cc_start: 0.7971 (mmp) cc_final: 0.6890 (mtm) REVERT: B 591 MET cc_start: 0.8580 (mtp) cc_final: 0.8326 (mtt) REVERT: B 601 MET cc_start: 0.8963 (ttp) cc_final: 0.8715 (tmm) REVERT: B 652 TYR cc_start: 0.8190 (m-80) cc_final: 0.7938 (m-80) REVERT: B 718 TRP cc_start: 0.7041 (t60) cc_final: 0.6337 (t60) outliers start: 12 outliers final: 6 residues processed: 165 average time/residue: 0.0979 time to fit residues: 23.6499 Evaluate side-chains 157 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 B residue 141 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 0.0570 chunk 114 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 chunk 137 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099386 restraints weight = 35136.178| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.00 r_work: 0.2851 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 12518 Z= 0.105 Angle : 0.587 10.420 17109 Z= 0.284 Chirality : 0.039 0.182 1807 Planarity : 0.004 0.044 2113 Dihedral : 8.829 81.208 1744 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.60 % Allowed : 12.80 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.23), residues: 1488 helix: 0.09 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -1.91 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 432 TYR 0.016 0.001 TYR B 406 PHE 0.011 0.001 PHE A 461 TRP 0.020 0.001 TRP A 215 HIS 0.004 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 (12514) covalent geometry : angle 0.58727 / 0.28 (17109) hydrogen bonds : bond 0.03139 / 2.10 ( 611) hydrogen bonds : angle 4.06476 / 2.89 ( 1764) Misc. bond : bond 0.11802 / 5.89 ( 4) *********************** 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 170 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3283 (ptp) cc_final: 0.2422 (ttp) REVERT: A 67 MET cc_start: 0.8753 (mtt) cc_final: 0.8495 (mtt) REVERT: A 280 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7128 (mtm110) REVERT: A 320 GLN cc_start: 0.8129 (pt0) cc_final: 0.7556 (mp10) REVERT: A 445 LYS cc_start: 0.6243 (ptmt) cc_final: 0.4900 (mmtm) REVERT: A 601 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8361 (tmm) REVERT: A 708 MET cc_start: 0.8247 (mmt) cc_final: 0.7829 (tpt) REVERT: A 718 TRP cc_start: 0.7432 (t60) cc_final: 0.6515 (t60) REVERT: B 1 MET cc_start: 0.3099 (ptp) cc_final: 0.2566 (ptp) REVERT: B 401 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7883 (pp) REVERT: B 477 MET cc_start: 0.7918 (ttp) cc_final: 0.7642 (tmm) REVERT: B 515 MET cc_start: 0.7970 (mmp) cc_final: 0.6856 (mtm) REVERT: B 591 MET cc_start: 0.8524 (mtp) cc_final: 0.8293 (mtt) REVERT: B 601 MET cc_start: 0.8962 (ttp) cc_final: 0.8728 (tmm) REVERT: B 718 TRP cc_start: 0.7005 (t60) cc_final: 0.6299 (t60) outliers start: 7 outliers final: 5 residues processed: 167 average time/residue: 0.0974 time to fit residues: 24.0237 Evaluate side-chains 153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 401 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 97 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 GLN B 305 HIS ** 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 = 0.3477 r_free = 0.3477 target = 0.133347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.097245 restraints weight = 27182.720| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.62 r_work: 0.2846 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 12518 Z= 0.130 Angle : 0.615 10.892 17109 Z= 0.294 Chirality : 0.040 0.207 1807 Planarity : 0.004 0.044 2113 Dihedral : 8.588 80.398 1744 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.77 % Allowed : 13.40 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.23), residues: 1488 helix: 0.19 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.77 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 432 TYR 0.024 0.002 TYR B 406 PHE 0.013 0.001 PHE B 194 TRP 0.017 0.001 TRP B 215 HIS 0.003 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (12514) covalent geometry : angle 0.61464 / 0.29 (17109) hydrogen bonds : bond 0.03320 / 2.20 ( 611) hydrogen bonds : angle 4.04932 / 2.87 ( 1764) Misc. bond : bond 0.14524 / 7.29 ( 4) *********************** 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 163 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.436 Fit side-chains REVERT: A 1 MET cc_start: 0.3561 (ptp) cc_final: 0.2700 (ttp) REVERT: A 280 ARG cc_start: 0.7692 (mtm110) cc_final: 0.7103 (mtm110) REVERT: A 320 GLN cc_start: 0.8248 (pt0) cc_final: 0.7505 (mp10) REVERT: A 445 LYS cc_start: 0.6284 (ptmt) cc_final: 0.5063 (mmtm) REVERT: A 601 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8191 (tmm) REVERT: A 718 TRP cc_start: 0.7442 (t60) cc_final: 0.6534 (t60) REVERT: B 1 MET cc_start: 0.3241 (ptp) cc_final: 0.2704 (ptp) REVERT: B 355 ASN cc_start: 0.9014 (t0) cc_final: 0.8655 (t0) REVERT: B 401 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7833 (pp) REVERT: B 515 MET cc_start: 0.7891 (mmp) cc_final: 0.6799 (mtm) REVERT: B 591 MET cc_start: 0.8544 (mtp) cc_final: 0.8301 (mtt) REVERT: B 718 TRP cc_start: 0.7048 (t60) cc_final: 0.6362 (t60) outliers start: 9 outliers final: 6 residues processed: 160 average time/residue: 0.0982 time to fit residues: 23.2233 Evaluate side-chains 153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 401 LEU Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 0.0030 chunk 5 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 0.0570 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.096867 restraints weight = 25955.686| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.41 r_work: 0.2816 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 12518 Z= 0.161 Angle : 0.642 10.807 17109 Z= 0.309 Chirality : 0.041 0.186 1807 Planarity : 0.004 0.045 2113 Dihedral : 8.586 78.602 1744 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.29 % Allowed : 13.32 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.66 (0.23), residues: 1488 helix: 0.17 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -1.60 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 358 TYR 0.022 0.002 TYR B 406 PHE 0.014 0.001 PHE A 24 TRP 0.018 0.001 TRP A 215 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (12514) covalent geometry : angle 0.64187 / 0.31 (17109) hydrogen bonds : bond 0.03534 / 2.33 ( 611) hydrogen bonds : angle 4.09127 / 2.90 ( 1764) Misc. bond : bond 0.17119 / 8.62 ( 4) *********************** 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 158 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3486 (ptp) cc_final: 0.2971 (ptp) REVERT: A 320 GLN cc_start: 0.8337 (pt0) cc_final: 0.7780 (mp10) REVERT: A 445 LYS cc_start: 0.6320 (ptmt) cc_final: 0.4966 (mmtm) REVERT: A 601 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8438 (tmm) REVERT: A 718 TRP cc_start: 0.7475 (t60) cc_final: 0.6644 (t60) REVERT: B 1 MET cc_start: 0.3168 (ptp) cc_final: 0.2622 (ptp) REVERT: B 355 ASN cc_start: 0.9002 (t0) cc_final: 0.8612 (t0) REVERT: B 515 MET cc_start: 0.7920 (mmp) cc_final: 0.6840 (mtm) REVERT: B 591 MET cc_start: 0.8572 (mtp) cc_final: 0.8337 (mtt) REVERT: B 718 TRP cc_start: 0.7179 (t60) cc_final: 0.6486 (t60) outliers start: 15 outliers final: 9 residues processed: 153 average time/residue: 0.1149 time to fit residues: 26.1326 Evaluate side-chains 143 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 389 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 673 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 132 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 305 HIS ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.098259 restraints weight = 31363.784| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.86 r_work: 0.2814 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 12518 Z= 0.128 Angle : 0.606 10.517 17109 Z= 0.292 Chirality : 0.040 0.187 1807 Planarity : 0.004 0.045 2113 Dihedral : 8.368 79.390 1744 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.69 % Allowed : 14.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.23), residues: 1488 helix: 0.39 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -1.66 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 358 TYR 0.013 0.001 TYR A 127 PHE 0.013 0.001 PHE B 194 TRP 0.021 0.001 TRP B 215 HIS 0.004 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (12514) covalent geometry : angle 0.60610 / 0.29 (17109) hydrogen bonds : bond 0.03332 / 2.21 ( 611) hydrogen bonds : angle 4.04534 / 2.87 ( 1764) Misc. bond : bond 0.14931 / 7.46 ( 4) *********************** 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 150 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.447 Fit side-chains REVERT: A 1 MET cc_start: 0.3393 (ptp) cc_final: 0.2873 (ptp) REVERT: A 280 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7183 (mtm110) REVERT: A 320 GLN cc_start: 0.8353 (pt0) cc_final: 0.7743 (mp10) REVERT: A 445 LYS cc_start: 0.6313 (ptmt) cc_final: 0.4980 (mmtm) REVERT: A 601 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8439 (tmm) REVERT: A 718 TRP cc_start: 0.7526 (t60) cc_final: 0.6655 (t60) REVERT: B 1 MET cc_start: 0.3151 (ptp) cc_final: 0.2605 (ptp) REVERT: B 355 ASN cc_start: 0.8992 (t0) cc_final: 0.8590 (t0) REVERT: B 515 MET cc_start: 0.7997 (mmp) cc_final: 0.6890 (mtm) REVERT: B 591 MET cc_start: 0.8574 (mtp) cc_final: 0.8363 (mtt) REVERT: B 718 TRP cc_start: 0.7224 (t60) cc_final: 0.6550 (t60) outliers start: 8 outliers final: 7 residues processed: 148 average time/residue: 0.1213 time to fit residues: 26.3010 Evaluate side-chains 142 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 673 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 110 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.103833 restraints weight = 21862.003| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.07 r_work: 0.2841 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 12518 Z= 0.138 Angle : 0.618 10.469 17109 Z= 0.297 Chirality : 0.041 0.203 1807 Planarity : 0.004 0.045 2113 Dihedral : 8.297 79.823 1744 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.03 % Allowed : 14.09 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.41 (0.23), residues: 1488 helix: 0.42 (0.17), residues: 992 sheet: None (None), residues: 0 loop : -1.61 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 358 TYR 0.014 0.002 TYR B 468 PHE 0.013 0.001 PHE B 194 TRP 0.020 0.001 TRP B 215 HIS 0.004 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (12514) covalent geometry : angle 0.61846 / 0.30 (17109) hydrogen bonds : bond 0.03379 / 2.23 ( 611) hydrogen bonds : angle 4.02347 / 2.85 ( 1764) Misc. bond : bond 0.15720 / 7.88 ( 4) *********************** 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 150 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.403 Fit side-chains REVERT: A 1 MET cc_start: 0.3340 (ptp) cc_final: 0.2836 (ptp) REVERT: A 5 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6904 (ttm-80) REVERT: A 280 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7072 (mtm110) REVERT: A 320 GLN cc_start: 0.8367 (pt0) cc_final: 0.7761 (mp10) REVERT: A 445 LYS cc_start: 0.6299 (ptmt) cc_final: 0.4977 (mmtm) REVERT: A 601 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8491 (tmm) REVERT: A 718 TRP cc_start: 0.7418 (t60) cc_final: 0.6587 (t60) REVERT: B 1 MET cc_start: 0.3153 (ptp) cc_final: 0.2607 (ptp) REVERT: B 355 ASN cc_start: 0.8963 (t0) cc_final: 0.8573 (t0) REVERT: B 445 LYS cc_start: 0.6534 (ptmt) cc_final: 0.5284 (mmtm) REVERT: B 515 MET cc_start: 0.7984 (mmp) cc_final: 0.6879 (mtm) REVERT: B 591 MET cc_start: 0.8512 (mtp) cc_final: 0.8298 (mtt) REVERT: B 718 TRP cc_start: 0.7142 (t60) cc_final: 0.6498 (t60) outliers start: 12 outliers final: 11 residues processed: 147 average time/residue: 0.1255 time to fit residues: 26.9526 Evaluate side-chains 143 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 208 SER 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 673 LEU 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 494 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 103 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 105 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 GLN ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108914 restraints weight = 26483.657| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.31 r_work: 0.2881 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 12518 Z= 0.109 Angle : 0.588 10.413 17109 Z= 0.283 Chirality : 0.039 0.186 1807 Planarity : 0.004 0.043 2113 Dihedral : 8.110 81.993 1744 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.86 % Allowed : 14.35 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1488 helix: 0.62 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -1.56 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 358 TYR 0.013 0.001 TYR A 127 PHE 0.012 0.001 PHE A 461 TRP 0.023 0.001 TRP B 215 HIS 0.004 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (12514) covalent geometry : angle 0.58840 / 0.28 (17109) hydrogen bonds : bond 0.03142 / 2.10 ( 611) hydrogen bonds : angle 3.95251 / 2.80 ( 1764) Misc. bond : bond 0.12044 / 5.96 ( 4) ********************** 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 149 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.445 Fit side-chains REVERT: A 1 MET cc_start: 0.3313 (ptp) cc_final: 0.2816 (ptp) REVERT: A 5 ARG cc_start: 0.7084 (mtp85) cc_final: 0.6856 (ttm-80) REVERT: A 280 ARG cc_start: 0.7597 (mtm110) cc_final: 0.7034 (mtm110) REVERT: A 320 GLN cc_start: 0.8349 (pt0) cc_final: 0.7832 (mp10) REVERT: A 445 LYS cc_start: 0.6289 (ptmt) cc_final: 0.5025 (mmtm) REVERT: A 601 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8414 (tmm) REVERT: A 718 TRP cc_start: 0.7401 (t60) cc_final: 0.6545 (t60) REVERT: B 1 MET cc_start: 0.3273 (ptp) cc_final: 0.2753 (ptp) REVERT: B 355 ASN cc_start: 0.8926 (t0) cc_final: 0.8553 (t0) REVERT: B 515 MET cc_start: 0.7906 (mmp) cc_final: 0.6833 (mtm) REVERT: B 718 TRP cc_start: 0.7136 (t60) cc_final: 0.6501 (t60) outliers start: 10 outliers final: 9 residues processed: 147 average time/residue: 0.1217 time to fit residues: 26.0771 Evaluate side-chains 143 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR 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 673 LEU 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 494 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 103 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 94 optimal weight: 8.9990 chunk 145 optimal weight: 0.0470 chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 305 HIS ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103575 restraints weight = 34978.753| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.70 r_work: 0.2827 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 12518 Z= 0.123 Angle : 0.602 9.074 17109 Z= 0.289 Chirality : 0.040 0.196 1807 Planarity : 0.004 0.044 2113 Dihedral : 8.094 82.687 1744 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.95 % Allowed : 14.18 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.14 (0.23), residues: 1488 helix: 0.66 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -1.57 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.013 0.001 TYR B 638 PHE 0.012 0.001 PHE A 461 TRP 0.020 0.001 TRP B 215 HIS 0.004 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 (12514) covalent geometry : angle 0.60193 / 0.29 (17109) hydrogen bonds : bond 0.03237 / 2.15 ( 611) hydrogen bonds : angle 3.95842 / 2.81 ( 1764) Misc. bond : bond 0.13735 / 6.85 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.57 seconds wall clock time: 45 minutes 4.75 seconds (2704.75 seconds total)