Starting phenix.real_space_refine on Thu Jul 2 19:58:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wi6_32526/07_2026/7wi6_32526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi6_32526/07_2026/7wi6_32526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wi6_32526/07_2026/7wi6_32526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi6_32526/07_2026/7wi6_32526.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wi6_32526/07_2026/7wi6_32526.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wi6_32526/07_2026/7wi6_32526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wi6_32526/07_2026/7wi6_32526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi6_32526/07_2026/7wi6_32526.map" } resolution = 3.71 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 104 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6206 2.51 5 N 1638 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9696 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 4808 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 232} Link IDs: {'PTRANS': 28, 'TRANS': 694} Chain breaks: 6 Unresolved non-hydrogen bonds: 945 Unresolved non-hydrogen angles: 1197 Unresolved non-hydrogen dihedrals: 794 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'ARG:plan': 21, 'GLU:plan': 30, 'ASP:plan': 28, 'ASN:plan1': 13, 'TYR:plan': 12, 'PHE:plan': 11, 'GLN:plan1': 12, 'HIS:plan': 4, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 608 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B Time building chain proxies: 3.45, per 1000 atoms: 0.36 Number of scatterers: 9696 At special positions: 0 Unit cell: (95.95, 97.97, 181.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1786 8.00 N 1638 7.00 C 6206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 373 " distance=2.02 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 513 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 546 " distance=2.04 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 373 " distance=2.02 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 513 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 546 " distance=2.04 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 562 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 902 " - " ASN A 209 " " NAG B 902 " - " ASN B 209 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 265.9 milliseconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 32.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 65 through 80 removed outlier: 4.073A pdb=" N ALA A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 removed outlier: 4.508A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.568A pdb=" N SER A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 removed outlier: 4.748A pdb=" N GLU A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN A 232 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG A 235 " --> pdb=" O GLN A 232 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU A 236 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.929A pdb=" N ASP A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 399 through 409 removed outlier: 4.383A pdb=" N HIS A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 removed outlier: 3.925A pdb=" N LYS A 423 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.950A pdb=" N ASP A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 577 through 588 removed outlier: 3.864A pdb=" N VAL A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 598 removed outlier: 3.623A pdb=" N VAL A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 615 through 625 removed outlier: 4.243A pdb=" N GLY A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 624 " --> pdb=" O PHE A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 632 removed outlier: 5.996A pdb=" N THR A 629 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 631 " --> pdb=" O MET A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 646 removed outlier: 3.681A pdb=" N ARG A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.773A pdb=" N THR A 661 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS A 662 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR A 663 " --> pdb=" O LEU A 660 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 664 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS A 665 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.820A pdb=" N LEU A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 699 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.529A pdb=" N ILE A 746 " --> pdb=" O TYR A 743 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 747 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 776 removed outlier: 3.606A pdb=" N MET A 775 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR A 776 " --> pdb=" O PHE A 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 772 through 776' Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 786 through 792 removed outlier: 4.046A pdb=" N TYR A 790 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 802 removed outlier: 4.078A pdb=" N THR A 802 " --> pdb=" O VAL A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 816 through 820 removed outlier: 3.649A pdb=" N PHE A 819 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 820 " --> pdb=" O CYS A 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 816 through 820' Processing helix chain 'B' and resid 65 through 80 removed outlier: 4.074A pdb=" N ALA B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 4.508A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.569A pdb=" N SER B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 4.749A pdb=" N GLU B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN B 232 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ARG B 235 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 236 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 238 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.928A pdb=" N ASP B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 399 through 409 removed outlier: 4.383A pdb=" N HIS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 423 removed outlier: 3.924A pdb=" N LYS B 423 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.951A pdb=" N ASP B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 577 through 588 removed outlier: 3.864A pdb=" N VAL B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 removed outlier: 3.622A pdb=" N VAL B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 608 Processing helix chain 'B' and resid 615 through 625 removed outlier: 4.244A pdb=" N GLY B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 624 " --> pdb=" O PHE B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 632 removed outlier: 5.996A pdb=" N THR B 629 " --> pdb=" O TYR B 626 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 631 " --> pdb=" O MET B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 646 removed outlier: 3.681A pdb=" N ARG B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 657 through 665 removed outlier: 3.774A pdb=" N THR B 661 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS B 662 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR B 663 " --> pdb=" O LEU B 660 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN B 664 " --> pdb=" O THR B 661 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS B 665 " --> pdb=" O LYS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 699 removed outlier: 3.820A pdb=" N LEU B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 709 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.528A pdb=" N ILE B 746 " --> pdb=" O TYR B 743 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 747 " --> pdb=" O ASP B 744 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 748 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 776 removed outlier: 3.606A pdb=" N MET B 775 " --> pdb=" O GLY B 772 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR B 776 " --> pdb=" O PHE B 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 772 through 776' Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 786 through 792 removed outlier: 4.046A pdb=" N TYR B 790 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 792 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 802 removed outlier: 4.078A pdb=" N THR B 802 " --> pdb=" O VAL B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 811 Processing helix chain 'B' and resid 816 through 820 removed outlier: 3.649A pdb=" N PHE B 819 " --> pdb=" O GLY B 816 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA B 820 " --> pdb=" O CYS B 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 816 through 820' Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 3.710A pdb=" N ILE A 33 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 39 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N HIS A 94 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 41 " --> pdb=" O HIS A 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU A 96 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY A 43 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE A 146 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY A 42 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 218 removed outlier: 5.946A pdb=" N VAL A 213 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR A 243 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 245 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 247 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 274 removed outlier: 3.779A pdb=" N VAL A 272 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP A 297 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N LEU A 323 " --> pdb=" O TRP A 297 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA A 299 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N LEU A 325 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 484 through 485 removed outlier: 3.744A pdb=" N HIS A 485 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.367A pdb=" N THR A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 718 through 720 Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.710A pdb=" N ILE B 33 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 39 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N HIS B 94 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 41 " --> pdb=" O HIS B 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU B 96 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY B 43 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE B 146 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY B 42 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 212 through 218 removed outlier: 5.947A pdb=" N VAL B 213 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 243 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 245 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 247 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 271 through 274 removed outlier: 3.777A pdb=" N VAL B 272 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP B 297 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LEU B 323 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA B 299 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N LEU B 325 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 484 through 485 removed outlier: 3.744A pdb=" N HIS B 485 " --> pdb=" O SER B 491 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.368A pdb=" N THR B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 718 through 720 210 hydrogen bonds defined for protein. 516 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: 1.00 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2487 1.33 - 1.45: 2165 1.45 - 1.58: 5148 1.58 - 1.70: 2 1.70 - 1.82: 84 Bond restraints: 9886 Sorted by residual: bond pdb=" CAT Z99 B 901 " pdb=" OAP Z99 B 901 " ideal model delta sigma weight residual 1.364 1.492 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" CAT Z99 A 901 " pdb=" OAP Z99 A 901 " ideal model delta sigma weight residual 1.364 1.492 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" CAS Z99 A 901 " pdb=" OAP Z99 A 901 " ideal model delta sigma weight residual 1.369 1.494 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" CAS Z99 B 901 " pdb=" OAP Z99 B 901 " ideal model delta sigma weight residual 1.369 1.493 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C LEU B 340 " pdb=" N ASN B 341 " ideal model delta sigma weight residual 1.331 1.264 0.067 2.07e-02 2.33e+03 1.04e+01 ... (remaining 9881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 12511 1.69 - 3.38: 856 3.38 - 5.07: 161 5.07 - 6.76: 26 6.76 - 8.45: 26 Bond angle restraints: 13580 Sorted by residual: angle pdb=" N ILE A 155 " pdb=" CA ILE A 155 " pdb=" C ILE A 155 " ideal model delta sigma weight residual 113.20 105.06 8.14 9.60e-01 1.09e+00 7.20e+01 angle pdb=" N ILE B 155 " pdb=" CA ILE B 155 " pdb=" C ILE B 155 " ideal model delta sigma weight residual 113.20 105.10 8.10 9.60e-01 1.09e+00 7.12e+01 angle pdb=" C GLY A 713 " pdb=" N THR A 714 " pdb=" CA THR A 714 " ideal model delta sigma weight residual 122.46 128.34 -5.88 1.41e+00 5.03e-01 1.74e+01 angle pdb=" C GLY B 713 " pdb=" N THR B 714 " pdb=" CA THR B 714 " ideal model delta sigma weight residual 122.46 128.25 -5.79 1.41e+00 5.03e-01 1.69e+01 angle pdb=" N VAL B 701 " pdb=" CA VAL B 701 " pdb=" C VAL B 701 " ideal model delta sigma weight residual 113.20 109.32 3.88 9.60e-01 1.09e+00 1.63e+01 ... (remaining 13575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 5130 16.63 - 33.26: 514 33.26 - 49.89: 106 49.89 - 66.52: 16 66.52 - 83.15: 10 Dihedral angle restraints: 5776 sinusoidal: 1570 harmonic: 4206 Sorted by residual: dihedral pdb=" CB CYS B 513 " pdb=" SG CYS B 513 " pdb=" SG CYS B 531 " pdb=" CB CYS B 531 " ideal model delta sinusoidal sigma weight residual -86.00 -169.15 83.15 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS A 513 " pdb=" SG CYS A 513 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual -86.00 -169.13 83.13 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS B 534 " pdb=" SG CYS B 534 " pdb=" SG CYS B 546 " pdb=" CB CYS B 546 " ideal model delta sinusoidal sigma weight residual 93.00 170.72 -77.72 1 1.00e+01 1.00e-02 7.56e+01 ... (remaining 5773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1410 0.077 - 0.153: 250 0.153 - 0.230: 14 0.230 - 0.307: 8 0.307 - 0.383: 6 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CAW Z99 B 901 " pdb=" CAN Z99 B 901 " pdb=" CAU Z99 B 901 " pdb=" CAV Z99 B 901 " both_signs ideal model delta sigma weight residual False 2.61 2.23 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CAW Z99 A 901 " pdb=" CAN Z99 A 901 " pdb=" CAU Z99 A 901 " pdb=" CAV Z99 A 901 " both_signs ideal model delta sigma weight residual False 2.61 2.23 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CAY Z99 B 901 " pdb=" CAN Z99 B 901 " pdb=" CAR Z99 B 901 " pdb=" CAZ Z99 B 901 " both_signs ideal model delta sigma weight residual False -2.97 -2.62 -0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 1685 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 146 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C ILE B 146 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE B 146 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY B 147 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 146 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C ILE A 146 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 146 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY A 147 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 390 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C ILE A 390 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE A 390 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 391 " -0.014 2.00e-02 2.50e+03 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3322 2.81 - 3.33: 8182 3.33 - 3.86: 14819 3.86 - 4.38: 15446 4.38 - 4.90: 26121 Nonbonded interactions: 67890 Sorted by model distance: nonbonded pdb=" OE1 GLN B 165 " pdb=" OH TYR B 186 " model vdw 2.290 3.040 nonbonded pdb=" OE1 GLN A 165 " pdb=" OH TYR A 186 " model vdw 2.290 3.040 nonbonded pdb=" O SER B 179 " pdb=" OG SER B 179 " model vdw 2.295 3.040 nonbonded pdb=" O SER A 179 " pdb=" OG SER A 179 " model vdw 2.295 3.040 nonbonded pdb=" O THR A 296 " pdb=" OG1 THR A 296 " model vdw 2.298 3.040 ... (remaining 67885 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.009 0.128 9902 Z= 0.418 Angle : 1.035 11.779 13614 Z= 0.558 Chirality : 0.063 0.383 1688 Planarity : 0.006 0.056 1736 Dihedral : 14.548 78.703 3002 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 1.54 % Allowed : 14.10 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -6.21 (0.16), residues: 1418 helix: -4.83 (0.09), residues: 512 sheet: -3.65 (0.35), residues: 154 loop : -3.75 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 183 TYR 0.021 0.002 TYR A 434 PHE 0.025 0.002 PHE B 456 TRP 0.019 0.003 TRP B 297 HIS 0.007 0.002 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00916 / 0.42 ( 9886) covalent geometry : angle 1.01700 / 0.55 (13580) SS BOND : bond 0.00601 / 0.45 ( 14) SS BOND : angle 2.10475 / 1.52 ( 28) hydrogen bonds : bond 0.29210 / 20.46 ( 210) hydrogen bonds : angle 11.16083 / 7.66 ( 516) link_NAG-ASN : bond 0.00603 / 0.30 ( 2) link_NAG-ASN : angle 8.43257 / 4.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.370 Fit side-chains REVERT: A 266 LYS cc_start: 0.8849 (mptt) cc_final: 0.8628 (mptt) REVERT: B 266 LYS cc_start: 0.8826 (mptt) cc_final: 0.8600 (mptt) REVERT: B 754 TYR cc_start: 0.6736 (t80) cc_final: 0.5443 (t80) outliers start: 12 outliers final: 4 residues processed: 110 average time/residue: 0.0735 time to fit residues: 12.0472 Evaluate side-chains 87 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 747 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 156 GLN A 386 GLN B 108 GLN B 156 GLN B 386 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.158767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.101140 restraints weight = 17548.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.103775 restraints weight = 9462.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105504 restraints weight = 6477.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.106608 restraints weight = 5145.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107099 restraints weight = 4465.442| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9902 Z= 0.118 Angle : 0.631 7.938 13614 Z= 0.339 Chirality : 0.042 0.162 1688 Planarity : 0.004 0.037 1736 Dihedral : 7.739 65.642 1514 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 1.67 % Allowed : 21.41 % Favored : 76.92 % 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: -5.52 (0.18), residues: 1418 helix: -4.14 (0.13), residues: 500 sheet: -3.35 (0.37), residues: 154 loop : -3.44 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 162 TYR 0.019 0.001 TYR B 434 PHE 0.010 0.001 PHE A 620 TRP 0.013 0.001 TRP A 297 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9886) covalent geometry : angle 0.61780 / 0.34 (13580) SS BOND : bond 0.00323 / 0.25 ( 14) SS BOND : angle 1.49066 / 1.03 ( 28) hydrogen bonds : bond 0.03778 / 2.50 ( 210) hydrogen bonds : angle 6.33021 / 4.41 ( 516) link_NAG-ASN : bond 0.00264 / 0.13 ( 2) link_NAG-ASN : angle 5.35937 / 2.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.291 Fit side-chains REVERT: A 340 LEU cc_start: 0.9471 (mm) cc_final: 0.9270 (mm) REVERT: A 355 TRP cc_start: 0.8998 (t-100) cc_final: 0.8156 (t-100) REVERT: A 391 MET cc_start: 0.8361 (tmm) cc_final: 0.8117 (tmm) REVERT: B 355 TRP cc_start: 0.8974 (t-100) cc_final: 0.8120 (t-100) REVERT: B 391 MET cc_start: 0.8368 (tmm) cc_final: 0.8121 (tmm) REVERT: B 754 TYR cc_start: 0.6422 (t80) cc_final: 0.5052 (t80) outliers start: 13 outliers final: 7 residues processed: 102 average time/residue: 0.0702 time to fit residues: 11.1708 Evaluate side-chains 81 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 0.2980 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 86 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 HIS B 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.159483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.100473 restraints weight = 17130.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103148 restraints weight = 9261.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104911 restraints weight = 6346.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106042 restraints weight = 5050.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106603 restraints weight = 4387.362| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9902 Z= 0.100 Angle : 0.571 6.875 13614 Z= 0.304 Chirality : 0.042 0.161 1688 Planarity : 0.004 0.033 1736 Dihedral : 6.788 63.802 1510 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.82 % Allowed : 23.33 % Favored : 73.85 % 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: -4.98 (0.19), residues: 1418 helix: -3.59 (0.16), residues: 500 sheet: -3.01 (0.39), residues: 132 loop : -3.23 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 162 TYR 0.016 0.001 TYR B 434 PHE 0.007 0.001 PHE B 632 TRP 0.011 0.001 TRP A 529 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9886) covalent geometry : angle 0.55951 / 0.30 (13580) SS BOND : bond 0.00468 / 0.37 ( 14) SS BOND : angle 1.39978 / 0.99 ( 28) hydrogen bonds : bond 0.03499 / 2.35 ( 210) hydrogen bonds : angle 5.43007 / 3.77 ( 516) link_NAG-ASN : bond 0.00403 / 0.20 ( 2) link_NAG-ASN : angle 4.67458 / 2.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.330 Fit side-chains REVERT: A 355 TRP cc_start: 0.8994 (t-100) cc_final: 0.8180 (t-100) REVERT: B 355 TRP cc_start: 0.8995 (t-100) cc_final: 0.8177 (t-100) outliers start: 22 outliers final: 11 residues processed: 108 average time/residue: 0.0661 time to fit residues: 11.3601 Evaluate side-chains 83 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 0.3980 chunk 76 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 119 optimal weight: 40.0000 chunk 125 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.154081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094304 restraints weight = 17592.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096751 restraints weight = 9751.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098338 restraints weight = 6858.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099370 restraints weight = 5541.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100008 restraints weight = 4856.459| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9902 Z= 0.209 Angle : 0.645 8.724 13614 Z= 0.333 Chirality : 0.046 0.283 1688 Planarity : 0.004 0.039 1736 Dihedral : 7.151 63.875 1510 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 3.85 % Allowed : 25.26 % Favored : 70.90 % 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: -4.62 (0.20), residues: 1418 helix: -3.32 (0.18), residues: 498 sheet: -2.96 (0.40), residues: 132 loop : -2.97 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 282 TYR 0.024 0.001 TYR B 434 PHE 0.015 0.002 PHE B 456 TRP 0.011 0.002 TRP B 297 HIS 0.003 0.002 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 9886) covalent geometry : angle 0.63477 / 0.33 (13580) SS BOND : bond 0.00317 / 0.23 ( 14) SS BOND : angle 1.41759 / 1.02 ( 28) hydrogen bonds : bond 0.03692 / 2.47 ( 210) hydrogen bonds : angle 5.45445 / 3.81 ( 516) link_NAG-ASN : bond 0.00178 / 0.09 ( 2) link_NAG-ASN : angle 4.63856 / 2.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.228 Fit side-chains outliers start: 30 outliers final: 24 residues processed: 107 average time/residue: 0.0598 time to fit residues: 10.4289 Evaluate side-chains 99 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 116 optimal weight: 40.0000 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 40.0000 chunk 93 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.156368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.098067 restraints weight = 17734.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.100503 restraints weight = 9752.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.102061 restraints weight = 6817.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.103114 restraints weight = 5496.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.103727 restraints weight = 4808.755| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9902 Z= 0.171 Angle : 0.603 6.887 13614 Z= 0.313 Chirality : 0.044 0.217 1688 Planarity : 0.004 0.040 1736 Dihedral : 6.948 64.391 1510 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 4.87 % Allowed : 24.36 % Favored : 70.77 % 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: -4.37 (0.21), residues: 1418 helix: -3.12 (0.19), residues: 498 sheet: -2.94 (0.40), residues: 132 loop : -2.79 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.021 0.001 TYR B 434 PHE 0.012 0.001 PHE B 456 TRP 0.012 0.001 TRP A 297 HIS 0.004 0.002 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9886) covalent geometry : angle 0.59364 / 0.31 (13580) SS BOND : bond 0.00321 / 0.24 ( 14) SS BOND : angle 1.30346 / 0.93 ( 28) hydrogen bonds : bond 0.03304 / 2.19 ( 210) hydrogen bonds : angle 5.21361 / 3.64 ( 516) link_NAG-ASN : bond 0.00402 / 0.20 ( 2) link_NAG-ASN : angle 4.54557 / 2.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.363 Fit side-chains REVERT: A 393 VAL cc_start: 0.6825 (OUTLIER) cc_final: 0.6491 (p) REVERT: A 402 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7470 (m-70) REVERT: B 402 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.7478 (m-70) outliers start: 38 outliers final: 30 residues processed: 113 average time/residue: 0.0619 time to fit residues: 11.4719 Evaluate side-chains 110 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.0060 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 78 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 overall best weight: 0.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.167152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.107989 restraints weight = 17210.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.110750 restraints weight = 9344.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.112524 restraints weight = 6489.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.113607 restraints weight = 5198.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.114180 restraints weight = 4559.362| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9902 Z= 0.097 Angle : 0.549 7.089 13614 Z= 0.285 Chirality : 0.042 0.157 1688 Planarity : 0.004 0.037 1736 Dihedral : 6.408 63.093 1510 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.82 % Allowed : 26.54 % Favored : 70.64 % 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: -4.14 (0.21), residues: 1418 helix: -2.89 (0.20), residues: 498 sheet: -2.77 (0.39), residues: 146 loop : -2.66 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.017 0.001 TYR A 434 PHE 0.007 0.001 PHE B 295 TRP 0.012 0.001 TRP A 529 HIS 0.002 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 9886) covalent geometry : angle 0.53933 / 0.28 (13580) SS BOND : bond 0.00317 / 0.24 ( 14) SS BOND : angle 1.09602 / 0.77 ( 28) hydrogen bonds : bond 0.02659 / 1.76 ( 210) hydrogen bonds : angle 4.75477 / 3.32 ( 516) link_NAG-ASN : bond 0.00575 / 0.29 ( 2) link_NAG-ASN : angle 4.38959 / 2.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.373 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 104 average time/residue: 0.0686 time to fit residues: 11.3987 Evaluate side-chains 96 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 732 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 0.2980 chunk 122 optimal weight: 0.1980 chunk 73 optimal weight: 0.0980 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 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 = 0.4284 r_free = 0.4284 target = 0.165023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105411 restraints weight = 17339.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108036 restraints weight = 9564.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.109772 restraints weight = 6718.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110868 restraints weight = 5413.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.111420 restraints weight = 4760.659| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9902 Z= 0.135 Angle : 0.563 7.336 13614 Z= 0.290 Chirality : 0.043 0.201 1688 Planarity : 0.004 0.039 1736 Dihedral : 6.458 62.662 1510 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.49 % Allowed : 25.00 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.90 (0.22), residues: 1418 helix: -2.80 (0.20), residues: 502 sheet: -2.56 (0.41), residues: 146 loop : -2.45 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.016 0.001 TYR B 434 PHE 0.009 0.001 PHE B 456 TRP 0.011 0.001 TRP B 529 HIS 0.003 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9886) covalent geometry : angle 0.55429 / 0.29 (13580) SS BOND : bond 0.00312 / 0.23 ( 14) SS BOND : angle 1.12992 / 0.81 ( 28) hydrogen bonds : bond 0.02847 / 1.90 ( 210) hydrogen bonds : angle 4.74386 / 3.31 ( 516) link_NAG-ASN : bond 0.00415 / 0.21 ( 2) link_NAG-ASN : angle 4.27109 / 2.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.404 Fit side-chains outliers start: 35 outliers final: 25 residues processed: 116 average time/residue: 0.0709 time to fit residues: 13.2260 Evaluate side-chains 103 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 732 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 76 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.0070 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 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 = 0.4223 r_free = 0.4223 target = 0.162336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116181 restraints weight = 17340.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.110679 restraints weight = 13547.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.111798 restraints weight = 14450.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.112286 restraints weight = 8856.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.114019 restraints weight = 7643.717| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9902 Z= 0.112 Angle : 0.544 7.302 13614 Z= 0.281 Chirality : 0.042 0.201 1688 Planarity : 0.004 0.037 1736 Dihedral : 6.291 62.887 1510 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.59 % Allowed : 26.15 % Favored : 70.26 % 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: -3.79 (0.22), residues: 1418 helix: -2.69 (0.20), residues: 514 sheet: -2.49 (0.42), residues: 146 loop : -2.38 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.023 0.001 TYR B 434 PHE 0.007 0.001 PHE B 456 TRP 0.011 0.001 TRP B 529 HIS 0.002 0.001 HIS B 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 9886) covalent geometry : angle 0.53535 / 0.28 (13580) SS BOND : bond 0.00306 / 0.23 ( 14) SS BOND : angle 1.04119 / 0.75 ( 28) hydrogen bonds : bond 0.02650 / 1.76 ( 210) hydrogen bonds : angle 4.58095 / 3.21 ( 516) link_NAG-ASN : bond 0.00504 / 0.25 ( 2) link_NAG-ASN : angle 4.27300 / 2.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.384 Fit side-chains REVERT: B 434 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7541 (p90) outliers start: 28 outliers final: 20 residues processed: 108 average time/residue: 0.0697 time to fit residues: 12.1456 Evaluate side-chains 102 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 732 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 142 optimal weight: 8.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 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 = 0.4228 r_free = 0.4228 target = 0.162529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.103356 restraints weight = 17163.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105684 restraints weight = 10164.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.107229 restraints weight = 7406.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.108269 restraints weight = 6078.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108768 restraints weight = 5363.633| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9902 Z= 0.109 Angle : 0.545 7.467 13614 Z= 0.281 Chirality : 0.042 0.176 1688 Planarity : 0.003 0.038 1736 Dihedral : 6.200 62.338 1510 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.59 % Allowed : 25.64 % Favored : 70.77 % 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: -3.81 (0.22), residues: 1418 helix: -2.66 (0.20), residues: 526 sheet: -2.38 (0.43), residues: 146 loop : -2.45 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.026 0.001 TYR A 434 PHE 0.009 0.001 PHE A 789 TRP 0.010 0.001 TRP B 529 HIS 0.002 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9886) covalent geometry : angle 0.53652 / 0.28 (13580) SS BOND : bond 0.00283 / 0.21 ( 14) SS BOND : angle 1.09948 / 0.78 ( 28) hydrogen bonds : bond 0.02600 / 1.75 ( 210) hydrogen bonds : angle 4.47061 / 3.12 ( 516) link_NAG-ASN : bond 0.00490 / 0.25 ( 2) link_NAG-ASN : angle 4.19610 / 2.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.280 Fit side-chains REVERT: A 434 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7578 (p90) REVERT: B 662 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7875 (pptt) outliers start: 28 outliers final: 25 residues processed: 108 average time/residue: 0.0677 time to fit residues: 11.8566 Evaluate side-chains 106 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 732 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 133 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 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 = 0.4229 r_free = 0.4229 target = 0.162749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.103463 restraints weight = 17228.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.105958 restraints weight = 10000.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107584 restraints weight = 7156.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108464 restraints weight = 5827.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.109228 restraints weight = 5173.612| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9902 Z= 0.107 Angle : 0.540 7.250 13614 Z= 0.277 Chirality : 0.042 0.181 1688 Planarity : 0.003 0.038 1736 Dihedral : 6.101 62.151 1510 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 3.72 % Allowed : 25.38 % Favored : 70.90 % 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: -3.72 (0.22), residues: 1418 helix: -2.56 (0.21), residues: 526 sheet: -2.38 (0.43), residues: 146 loop : -2.40 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 162 TYR 0.021 0.001 TYR A 434 PHE 0.007 0.001 PHE B 295 TRP 0.010 0.001 TRP B 529 HIS 0.002 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 9886) covalent geometry : angle 0.53072 / 0.27 (13580) SS BOND : bond 0.00276 / 0.20 ( 14) SS BOND : angle 1.22336 / 0.85 ( 28) hydrogen bonds : bond 0.02549 / 1.71 ( 210) hydrogen bonds : angle 4.38138 / 3.07 ( 516) link_NAG-ASN : bond 0.00481 / 0.24 ( 2) link_NAG-ASN : angle 4.19450 / 2.25 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.274 Fit side-chains REVERT: B 662 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7871 (pptt) outliers start: 29 outliers final: 25 residues processed: 110 average time/residue: 0.0558 time to fit residues: 9.9821 Evaluate side-chains 107 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 732 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 125 optimal weight: 0.0980 chunk 101 optimal weight: 0.0170 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 53 optimal weight: 0.0170 chunk 83 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.1656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.166375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.112849 restraints weight = 17217.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.109640 restraints weight = 11747.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.111650 restraints weight = 9856.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112030 restraints weight = 7417.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.112269 restraints weight = 6670.933| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9902 Z= 0.080 Angle : 0.519 7.437 13614 Z= 0.267 Chirality : 0.041 0.156 1688 Planarity : 0.003 0.037 1736 Dihedral : 5.673 61.098 1510 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.08 % Allowed : 26.41 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.48 (0.22), residues: 1418 helix: -2.39 (0.22), residues: 514 sheet: -2.31 (0.43), residues: 146 loop : -2.23 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 162 TYR 0.017 0.001 TYR A 434 PHE 0.007 0.001 PHE A 333 TRP 0.009 0.001 TRP B 529 HIS 0.002 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.08 ( 9886) covalent geometry : angle 0.51040 / 0.27 (13580) SS BOND : bond 0.00292 / 0.21 ( 14) SS BOND : angle 1.07416 / 0.74 ( 28) hydrogen bonds : bond 0.02152 / 1.44 ( 210) hydrogen bonds : angle 4.18090 / 2.92 ( 516) link_NAG-ASN : bond 0.00570 / 0.29 ( 2) link_NAG-ASN : angle 4.12872 / 2.23 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1698.65 seconds wall clock time: 29 minutes 52.13 seconds (1792.13 seconds total)