Starting phenix.real_space_refine on Mon Jul 28 04:46:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wi6_32526/07_2025/7wi6_32526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi6_32526/07_2025/7wi6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wi6_32526/07_2025/7wi6_32526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi6_32526/07_2025/7wi6_32526.map" model { file = "/net/cci-nas-00/data/ceres_data/7wi6_32526/07_2025/7wi6_32526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi6_32526/07_2025/7wi6_32526.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 13, 'TRP:plan': 5, 'ASP:plan': 28, 'PHE:plan': 11, 'GLU:plan': 30, 'ARG:plan': 21} 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B Time building chain proxies: 9.52, per 1000 atoms: 0.98 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: 2.31 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.48 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: 2.88 Time building geometry restraints manager: 2.78 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 - 18.34: 5244 18.34 - 36.67: 488 36.67 - 55.01: 98 55.01 - 73.34: 12 73.34 - 91.68: 18 Dihedral angle restraints: 5860 sinusoidal: 1654 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 5857 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: 0.06 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.300 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 15.694 91.675 3086 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.003 TRP B 297 HIS 0.007 0.002 HIS B 498 PHE 0.025 0.002 PHE B 456 TYR 0.021 0.002 TYR A 434 ARG 0.005 0.001 ARG B 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 2) link_NAG-ASN : angle 8.43257 ( 6) hydrogen bonds : bond 0.29210 ( 210) hydrogen bonds : angle 11.16083 ( 516) SS BOND : bond 0.00601 ( 14) SS BOND : angle 2.10475 ( 28) covalent geometry : bond 0.00916 ( 9886) covalent geometry : angle 1.01700 (13580) *********************** 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 : 1.009 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: 0.1849 time to fit residues: 30.2490 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 : 1.134 ------------------------------------------------------------------------------- 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 121 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.0670 chunk 37 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 0.0010 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 overall best weight: 0.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4120 r_free = 0.4120 target = 0.156998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098054 restraints weight = 17286.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100556 restraints weight = 9514.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102252 restraints weight = 6649.050| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9902 Z= 0.118 Angle : 0.633 8.142 13614 Z= 0.341 Chirality : 0.042 0.165 1688 Planarity : 0.004 0.038 1736 Dihedral : 10.495 95.273 1598 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 1.79 % Allowed : 21.03 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.53 (0.18), residues: 1418 helix: -4.13 (0.13), residues: 496 sheet: -3.37 (0.37), residues: 154 loop : -3.47 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 297 HIS 0.003 0.001 HIS A 498 PHE 0.009 0.001 PHE B 620 TYR 0.018 0.001 TYR B 434 ARG 0.004 0.000 ARG A 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 2) link_NAG-ASN : angle 5.41128 ( 6) hydrogen bonds : bond 0.04092 ( 210) hydrogen bonds : angle 6.43444 ( 516) SS BOND : bond 0.00357 ( 14) SS BOND : angle 1.57830 ( 28) covalent geometry : bond 0.00262 ( 9886) covalent geometry : angle 0.61903 (13580) *********************** 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 105 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.024 Fit side-chains REVERT: A 340 LEU cc_start: 0.9505 (mm) cc_final: 0.9257 (mm) REVERT: A 355 TRP cc_start: 0.8990 (t-100) cc_final: 0.8146 (t-100) REVERT: A 391 MET cc_start: 0.8394 (tmm) cc_final: 0.8151 (tmm) REVERT: B 340 LEU cc_start: 0.9497 (mm) cc_final: 0.9258 (mm) REVERT: B 355 TRP cc_start: 0.8966 (t-100) cc_final: 0.8105 (t-100) REVERT: B 391 MET cc_start: 0.8387 (tmm) cc_final: 0.8144 (tmm) REVERT: B 754 TYR cc_start: 0.6482 (t80) cc_final: 0.5090 (t80) outliers start: 14 outliers final: 8 residues processed: 103 average time/residue: 0.1703 time to fit residues: 26.8979 Evaluate side-chains 81 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 747 LEU 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 95 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 48 optimal weight: 30.0000 chunk 126 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4053 r_free = 0.4053 target = 0.150944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.093491 restraints weight = 17736.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.095136 restraints weight = 10910.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095626 restraints weight = 7688.604| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 9902 Z= 0.297 Angle : 0.722 7.450 13614 Z= 0.380 Chirality : 0.048 0.249 1688 Planarity : 0.005 0.041 1736 Dihedral : 11.154 96.120 1596 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.39 % Favored : 85.61 % Rotamer: Outliers : 5.00 % Allowed : 21.79 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.19), residues: 1418 helix: -3.68 (0.16), residues: 524 sheet: -3.26 (0.41), residues: 126 loop : -3.22 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 297 HIS 0.005 0.002 HIS A 485 PHE 0.019 0.002 PHE B 456 TYR 0.024 0.002 TYR B 434 ARG 0.003 0.001 ARG B 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00029 ( 2) link_NAG-ASN : angle 5.18111 ( 6) hydrogen bonds : bond 0.04539 ( 210) hydrogen bonds : angle 6.22040 ( 516) SS BOND : bond 0.00368 ( 14) SS BOND : angle 1.71088 ( 28) covalent geometry : bond 0.00682 ( 9886) covalent geometry : angle 0.71071 (13580) *********************** 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 119 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 1.128 Fit side-chains REVERT: A 407 MET cc_start: 0.8160 (tpp) cc_final: 0.7520 (tpt) REVERT: A 628 MET cc_start: 0.6579 (tpt) cc_final: 0.6344 (tpt) REVERT: B 153 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8996 (p) REVERT: B 407 MET cc_start: 0.8104 (tpp) cc_final: 0.7480 (tpt) outliers start: 39 outliers final: 21 residues processed: 116 average time/residue: 0.1463 time to fit residues: 27.4487 Evaluate side-chains 94 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 174 THR Chi-restraints excluded: chain A residue 190 THR 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 747 LEU 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 153 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 393 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 86 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 0.0270 chunk 106 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN B 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.156268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097182 restraints weight = 17096.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099729 restraints weight = 9382.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.101353 restraints weight = 6504.076| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9902 Z= 0.116 Angle : 0.583 7.273 13614 Z= 0.310 Chirality : 0.042 0.168 1688 Planarity : 0.004 0.039 1736 Dihedral : 9.981 94.237 1596 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 3.72 % Allowed : 24.49 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.20), residues: 1418 helix: -3.35 (0.18), residues: 514 sheet: -3.04 (0.41), residues: 118 loop : -3.18 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 529 HIS 0.004 0.001 HIS B 498 PHE 0.008 0.001 PHE A 632 TYR 0.020 0.001 TYR A 434 ARG 0.006 0.000 ARG B 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 2) link_NAG-ASN : angle 4.66674 ( 6) hydrogen bonds : bond 0.03277 ( 210) hydrogen bonds : angle 5.42137 ( 516) SS BOND : bond 0.00355 ( 14) SS BOND : angle 1.38313 ( 28) covalent geometry : bond 0.00266 ( 9886) covalent geometry : angle 0.57206 (13580) *********************** 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 118 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 1.037 Fit side-chains REVERT: A 194 ASP cc_start: 0.8510 (m-30) cc_final: 0.8228 (m-30) REVERT: A 391 MET cc_start: 0.8453 (tmm) cc_final: 0.8221 (tmm) REVERT: A 407 MET cc_start: 0.7721 (tpp) cc_final: 0.7341 (tpt) REVERT: B 194 ASP cc_start: 0.8515 (m-30) cc_final: 0.8240 (m-30) REVERT: B 391 MET cc_start: 0.8419 (tmm) cc_final: 0.8195 (tmm) REVERT: B 407 MET cc_start: 0.7725 (tpp) cc_final: 0.7379 (tpt) outliers start: 29 outliers final: 20 residues processed: 115 average time/residue: 0.1529 time to fit residues: 27.8409 Evaluate side-chains 95 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 73 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 498 HIS 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 73 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 397 VAL Chi-restraints excluded: chain B residue 498 HIS 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 69 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 13 optimal weight: 0.0770 chunk 117 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 40.0000 chunk 130 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.156870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099274 restraints weight = 17513.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.101670 restraints weight = 9831.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.103250 restraints weight = 6925.874| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9902 Z= 0.146 Angle : 0.580 7.239 13614 Z= 0.304 Chirality : 0.043 0.146 1688 Planarity : 0.004 0.040 1736 Dihedral : 9.882 95.496 1594 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 4.62 % Allowed : 24.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.20), residues: 1418 helix: -3.18 (0.18), residues: 524 sheet: -2.51 (0.46), residues: 112 loop : -2.97 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 529 HIS 0.003 0.001 HIS A 485 PHE 0.010 0.001 PHE B 456 TYR 0.017 0.001 TYR B 434 ARG 0.005 0.000 ARG B 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 2) link_NAG-ASN : angle 4.44110 ( 6) hydrogen bonds : bond 0.03222 ( 210) hydrogen bonds : angle 5.18036 ( 516) SS BOND : bond 0.00335 ( 14) SS BOND : angle 1.27698 ( 28) covalent geometry : bond 0.00342 ( 9886) covalent geometry : angle 0.56984 (13580) *********************** 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: 36 poor density : 83 time to evaluate : 1.020 Fit side-chains REVERT: A 391 MET cc_start: 0.8508 (tmm) cc_final: 0.8240 (tmm) REVERT: A 402 HIS cc_start: 0.7770 (OUTLIER) cc_final: 0.7542 (m-70) REVERT: A 407 MET cc_start: 0.7852 (tpp) cc_final: 0.7204 (tpt) REVERT: B 391 MET cc_start: 0.8488 (tmm) cc_final: 0.8215 (tmm) REVERT: B 407 MET cc_start: 0.7891 (tpp) cc_final: 0.7296 (tpt) outliers start: 36 outliers final: 29 residues processed: 112 average time/residue: 0.1435 time to fit residues: 26.0402 Evaluate side-chains 110 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 73 LEU 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 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 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 73 LEU 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 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 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 108 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 76 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 142 optimal weight: 0.0570 chunk 80 optimal weight: 0.3980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 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 = 0.4321 r_free = 0.4321 target = 0.168534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.111706 restraints weight = 17156.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.112908 restraints weight = 11737.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114311 restraints weight = 7278.369| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2683 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= 0.089 Angle : 0.533 7.389 13614 Z= 0.280 Chirality : 0.041 0.171 1688 Planarity : 0.004 0.038 1736 Dihedral : 9.096 95.932 1594 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.56 % Allowed : 26.03 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.21), residues: 1418 helix: -2.91 (0.20), residues: 500 sheet: -2.45 (0.43), residues: 146 loop : -2.70 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 529 HIS 0.005 0.001 HIS A 498 PHE 0.007 0.001 PHE A 632 TYR 0.014 0.001 TYR B 434 ARG 0.006 0.000 ARG B 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 2) link_NAG-ASN : angle 4.30881 ( 6) hydrogen bonds : bond 0.02576 ( 210) hydrogen bonds : angle 4.72529 ( 516) SS BOND : bond 0.00349 ( 14) SS BOND : angle 1.09526 ( 28) covalent geometry : bond 0.00202 ( 9886) covalent geometry : angle 0.52352 (13580) *********************** 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 111 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.146 Fit side-chains REVERT: A 391 MET cc_start: 0.8435 (tmm) cc_final: 0.8131 (tmm) REVERT: A 407 MET cc_start: 0.7904 (tpp) cc_final: 0.7476 (tpt) REVERT: B 355 TRP cc_start: 0.9042 (t-100) cc_final: 0.8363 (t-100) REVERT: B 391 MET cc_start: 0.8433 (tmm) cc_final: 0.8144 (tmm) REVERT: B 407 MET cc_start: 0.7849 (tpp) cc_final: 0.7472 (tpt) REVERT: B 628 MET cc_start: 0.6759 (tpt) cc_final: 0.6456 (tpt) outliers start: 20 outliers final: 16 residues processed: 107 average time/residue: 0.2075 time to fit residues: 36.2373 Evaluate side-chains 95 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 141 LEU 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 732 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 141 LEU 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 386 GLN 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 29 optimal weight: 0.0470 chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 84 optimal weight: 0.3980 chunk 108 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.169551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.115967 restraints weight = 17281.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.113389 restraints weight = 12418.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.115382 restraints weight = 8938.402| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2963 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= 0.084 Angle : 0.527 7.159 13614 Z= 0.275 Chirality : 0.041 0.158 1688 Planarity : 0.003 0.037 1736 Dihedral : 8.836 97.862 1594 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.46 % Allowed : 26.15 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.21), residues: 1418 helix: -2.83 (0.19), residues: 516 sheet: -2.29 (0.44), residues: 146 loop : -2.61 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 529 HIS 0.001 0.000 HIS B 485 PHE 0.009 0.001 PHE A 789 TYR 0.010 0.001 TYR B 434 ARG 0.003 0.000 ARG B 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 2) link_NAG-ASN : angle 4.08818 ( 6) hydrogen bonds : bond 0.02383 ( 210) hydrogen bonds : angle 4.46780 ( 516) SS BOND : bond 0.00324 ( 14) SS BOND : angle 1.03711 ( 28) covalent geometry : bond 0.00196 ( 9886) covalent geometry : angle 0.51885 (13580) *********************** 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 116 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 1.046 Fit side-chains REVERT: A 391 MET cc_start: 0.8497 (tmm) cc_final: 0.8209 (tmm) REVERT: A 407 MET cc_start: 0.7832 (tpp) cc_final: 0.7285 (tpt) REVERT: B 355 TRP cc_start: 0.9060 (t-100) cc_final: 0.8411 (t-100) REVERT: B 391 MET cc_start: 0.8473 (tmm) cc_final: 0.8182 (tmm) REVERT: B 407 MET cc_start: 0.7857 (tpp) cc_final: 0.7320 (tpt) REVERT: B 628 MET cc_start: 0.7214 (tpt) cc_final: 0.6766 (tpt) outliers start: 27 outliers final: 20 residues processed: 115 average time/residue: 0.1812 time to fit residues: 33.5451 Evaluate side-chains 104 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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 732 VAL Chi-restraints excluded: chain B residue 33 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 732 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 24 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 112 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.163952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.119692 restraints weight = 17488.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116490 restraints weight = 17358.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.116730 restraints weight = 17415.528| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9902 Z= 0.106 Angle : 0.541 7.496 13614 Z= 0.278 Chirality : 0.042 0.143 1688 Planarity : 0.003 0.037 1736 Dihedral : 8.915 98.762 1594 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.82 % Allowed : 27.18 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.21), residues: 1418 helix: -2.69 (0.20), residues: 512 sheet: -2.31 (0.44), residues: 146 loop : -2.48 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 529 HIS 0.002 0.001 HIS B 498 PHE 0.007 0.001 PHE B 295 TYR 0.015 0.001 TYR B 434 ARG 0.004 0.000 ARG B 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 2) link_NAG-ASN : angle 4.12153 ( 6) hydrogen bonds : bond 0.02520 ( 210) hydrogen bonds : angle 4.41528 ( 516) SS BOND : bond 0.00301 ( 14) SS BOND : angle 1.08285 ( 28) covalent geometry : bond 0.00249 ( 9886) covalent geometry : angle 0.53272 (13580) *********************** 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 102 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.427 Fit side-chains REVERT: A 391 MET cc_start: 0.8638 (tmm) cc_final: 0.8295 (tmm) REVERT: A 407 MET cc_start: 0.7932 (tpp) cc_final: 0.7156 (tpt) REVERT: B 391 MET cc_start: 0.8558 (tmm) cc_final: 0.8201 (tmm) REVERT: B 407 MET cc_start: 0.7931 (tpp) cc_final: 0.7159 (tpt) REVERT: B 628 MET cc_start: 0.7512 (tpt) cc_final: 0.6958 (tpt) outliers start: 22 outliers final: 20 residues processed: 102 average time/residue: 0.1866 time to fit residues: 31.0157 Evaluate side-chains 99 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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 732 VAL Chi-restraints excluded: chain B residue 33 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 732 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 52 optimal weight: 0.0570 chunk 119 optimal weight: 9.9990 chunk 118 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.164775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.110653 restraints weight = 17164.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107957 restraints weight = 11773.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.109805 restraints weight = 9635.366| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9902 Z= 0.094 Angle : 0.524 6.252 13614 Z= 0.271 Chirality : 0.042 0.153 1688 Planarity : 0.003 0.037 1736 Dihedral : 8.752 98.985 1594 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.95 % Allowed : 27.05 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.22), residues: 1418 helix: -2.56 (0.20), residues: 524 sheet: -2.29 (0.44), residues: 146 loop : -2.44 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 529 HIS 0.002 0.001 HIS A 498 PHE 0.009 0.001 PHE A 789 TYR 0.011 0.001 TYR B 537 ARG 0.003 0.000 ARG B 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 2) link_NAG-ASN : angle 4.00020 ( 6) hydrogen bonds : bond 0.02337 ( 210) hydrogen bonds : angle 4.29888 ( 516) SS BOND : bond 0.00277 ( 14) SS BOND : angle 1.26564 ( 28) covalent geometry : bond 0.00220 ( 9886) covalent geometry : angle 0.51478 (13580) *********************** 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 107 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 1.847 Fit side-chains REVERT: A 407 MET cc_start: 0.7775 (tpp) cc_final: 0.7002 (tpt) REVERT: B 391 MET cc_start: 0.8603 (tmm) cc_final: 0.8339 (tmm) REVERT: B 407 MET cc_start: 0.7778 (tpp) cc_final: 0.7052 (tpt) REVERT: B 628 MET cc_start: 0.6849 (tpt) cc_final: 0.6373 (tpt) outliers start: 23 outliers final: 20 residues processed: 106 average time/residue: 0.2088 time to fit residues: 36.6321 Evaluate side-chains 100 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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 732 VAL Chi-restraints excluded: chain B residue 33 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 732 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4239 r_free = 0.4239 target = 0.163427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109120 restraints weight = 17374.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106958 restraints weight = 11673.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108095 restraints weight = 8572.375| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9902 Z= 0.116 Angle : 0.541 6.801 13614 Z= 0.277 Chirality : 0.043 0.148 1688 Planarity : 0.003 0.037 1736 Dihedral : 8.902 99.181 1594 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.69 % Allowed : 27.31 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.22), residues: 1418 helix: -2.46 (0.21), residues: 522 sheet: -2.35 (0.43), residues: 146 loop : -2.36 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 529 HIS 0.002 0.001 HIS A 498 PHE 0.007 0.001 PHE B 456 TYR 0.017 0.001 TYR A 434 ARG 0.003 0.000 ARG B 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 2) link_NAG-ASN : angle 3.98661 ( 6) hydrogen bonds : bond 0.02518 ( 210) hydrogen bonds : angle 4.31299 ( 516) SS BOND : bond 0.00276 ( 14) SS BOND : angle 1.10584 ( 28) covalent geometry : bond 0.00275 ( 9886) covalent geometry : angle 0.53315 (13580) ********************** 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 107 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.160 Fit side-chains REVERT: A 407 MET cc_start: 0.7815 (tpp) cc_final: 0.6992 (tpt) REVERT: B 407 MET cc_start: 0.7848 (tpp) cc_final: 0.6995 (tpt) REVERT: B 628 MET cc_start: 0.6834 (tpt) cc_final: 0.6334 (tpt) outliers start: 21 outliers final: 20 residues processed: 107 average time/residue: 0.1606 time to fit residues: 27.8503 Evaluate side-chains 100 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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 732 VAL Chi-restraints excluded: chain B residue 33 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 732 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 133 optimal weight: 0.0470 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4254 r_free = 0.4254 target = 0.164755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119398 restraints weight = 17248.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.113268 restraints weight = 14654.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.114903 restraints weight = 15033.797| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9902 Z= 0.096 Angle : 0.525 6.725 13614 Z= 0.270 Chirality : 0.042 0.141 1688 Planarity : 0.003 0.036 1736 Dihedral : 8.731 98.964 1594 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.56 % Allowed : 27.56 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.22), residues: 1418 helix: -2.35 (0.21), residues: 524 sheet: -2.36 (0.43), residues: 146 loop : -2.34 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 529 HIS 0.002 0.001 HIS B 498 PHE 0.009 0.001 PHE A 789 TYR 0.010 0.001 TYR B 434 ARG 0.003 0.000 ARG B 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 2) link_NAG-ASN : angle 3.98404 ( 6) hydrogen bonds : bond 0.02337 ( 210) hydrogen bonds : angle 4.21426 ( 516) SS BOND : bond 0.00276 ( 14) SS BOND : angle 1.09465 ( 28) covalent geometry : bond 0.00227 ( 9886) covalent geometry : angle 0.51616 (13580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3381.11 seconds wall clock time: 61 minutes 25.78 seconds (3685.78 seconds total)