Starting phenix.real_space_refine on Thu Jul 2 21:06:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wih_32530/07_2026/7wih_32530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wih_32530/07_2026/7wih_32530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wih_32530/07_2026/7wih_32530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wih_32530/07_2026/7wih_32530.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wih_32530/07_2026/7wih_32530.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wih_32530/07_2026/7wih_32530.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wih_32530/07_2026/7wih_32530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wih_32530/07_2026/7wih_32530.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 6320 2.51 5 N 1740 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10002 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 4963 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PTRANS': 28, 'TRANS': 712} Chain breaks: 4 Unresolved non-hydrogen bonds: 953 Unresolved non-hydrogen angles: 1211 Unresolved non-hydrogen dihedrals: 815 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLU:plan': 27, 'ASP:plan': 14, 'ARG:plan': 21, 'GLN:plan1': 10, 'TYR:plan': 15, 'HIS:plan': 4, 'ASN:plan1': 9, 'PHE:plan': 16, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 588 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'CWY': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B Time building chain proxies: 3.67, per 1000 atoms: 0.37 Number of scatterers: 10002 At special positions: 0 Unit cell: (104.442, 84.162, 179.478, 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 1876 8.00 N 1740 7.00 C 6320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 527 " distance=2.04 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 373 " distance=2.03 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 A 641 " - pdb=" SG CYS A 730 " distance=2.04 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 Simple disulfide: pdb=" SG CYS B 641 " - pdb=" SG CYS B 730 " distance=2.04 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 901 " - " ASN A 209 " " NAG B 901 " - " ASN B 209 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 389.4 milliseconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2800 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 34.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 65 through 78 removed outlier: 4.559A pdb=" N ALA A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 removed outlier: 3.508A pdb=" N ALA A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 4.017A pdb=" N GLN A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.721A pdb=" N SER A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 180 " --> pdb=" O LYS A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 194 through 203 removed outlier: 4.266A pdb=" N ALA A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 261 through 266 removed outlier: 4.074A pdb=" N LYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.719A pdb=" N LEU A 340 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 407 removed outlier: 3.744A pdb=" N TYR A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.546A pdb=" N CYS A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.518A pdb=" N ASN A 502 " --> pdb=" O TRP A 499 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 503 " --> pdb=" O SER A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 503' Processing helix chain 'A' and resid 578 through 586 removed outlier: 3.525A pdb=" N THR A 582 " --> pdb=" O ILE A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.227A pdb=" N THR A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 619 through 626 Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.508A pdb=" N ARG A 645 " --> pdb=" O CYS A 641 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 666 removed outlier: 3.897A pdb=" N ASN A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 696 Processing helix chain 'A' and resid 701 through 709 Processing helix chain 'A' and resid 733 through 750 removed outlier: 3.922A pdb=" N ASP A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU A 747 " --> pdb=" O TYR A 743 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 750 " --> pdb=" O ILE A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 766 through 783 removed outlier: 4.886A pdb=" N GLY A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 778 " --> pdb=" O THR A 774 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N CYS A 779 " --> pdb=" O MET A 775 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 789 Processing helix chain 'A' and resid 799 through 813 removed outlier: 3.681A pdb=" N MET A 803 " --> pdb=" O GLN A 799 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 804 " --> pdb=" O THR A 800 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 807 " --> pdb=" O MET A 803 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 808 " --> pdb=" O CYS A 804 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 809 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 810 " --> pdb=" O SER A 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 78 removed outlier: 4.560A pdb=" N ALA B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.508A pdb=" N ALA B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 removed outlier: 4.017A pdb=" N GLN B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.720A pdb=" N SER B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP B 180 " --> pdb=" O LYS B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 180' Processing helix chain 'B' and resid 194 through 203 removed outlier: 4.266A pdb=" N ALA B 200 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 261 through 266 removed outlier: 4.075A pdb=" N LYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.720A pdb=" N LEU B 340 " --> pdb=" O PHE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 407 removed outlier: 3.744A pdb=" N TYR B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.546A pdb=" N CYS B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 499 through 503 removed outlier: 3.518A pdb=" N ASN B 502 " --> pdb=" O TRP B 499 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 503 " --> pdb=" O SER B 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 503' Processing helix chain 'B' and resid 578 through 586 removed outlier: 3.524A pdb=" N THR B 582 " --> pdb=" O ILE B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 594 removed outlier: 4.226A pdb=" N THR B 591 " --> pdb=" O GLY B 587 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 599 Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 619 through 626 Processing helix chain 'B' and resid 640 through 652 removed outlier: 3.508A pdb=" N ARG B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 666 removed outlier: 3.896A pdb=" N ASN B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 696 Processing helix chain 'B' and resid 701 through 709 Processing helix chain 'B' and resid 733 through 750 removed outlier: 3.922A pdb=" N ASP B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 746 " --> pdb=" O THR B 742 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU B 747 " --> pdb=" O TYR B 743 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 750 " --> pdb=" O ILE B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 Processing helix chain 'B' and resid 766 through 783 removed outlier: 4.887A pdb=" N GLY B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 778 " --> pdb=" O THR B 774 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 789 Processing helix chain 'B' and resid 799 through 813 removed outlier: 3.683A pdb=" N MET B 803 " --> pdb=" O GLN B 799 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 804 " --> pdb=" O THR B 800 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 807 " --> pdb=" O MET B 803 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER B 808 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 809 " --> pdb=" O ILE B 805 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 810 " --> pdb=" O SER B 806 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 241 removed outlier: 6.352A pdb=" N CYS A 240 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR A 215 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 245 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241 removed outlier: 6.352A pdb=" N CYS A 240 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR A 215 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL A 271 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 272 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP A 297 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 553 through 555 Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 241 removed outlier: 6.352A pdb=" N CYS B 240 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR B 215 " --> pdb=" O CYS B 240 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 245 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 241 removed outlier: 6.352A pdb=" N CYS B 240 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR B 215 " --> pdb=" O CYS B 240 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL B 271 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 272 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP B 297 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AB4, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AB5, first strand: chain 'B' and resid 553 through 555 238 hydrogen bonds defined for protein. 672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1700 1.31 - 1.44: 2573 1.44 - 1.57: 5821 1.57 - 1.70: 4 1.70 - 1.83: 82 Bond restraints: 10180 Sorted by residual: bond pdb=" C CWY A 902 " pdb=" C7 CWY A 902 " ideal model delta sigma weight residual 1.537 1.315 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C CWY B 902 " pdb=" C7 CWY B 902 " ideal model delta sigma weight residual 1.537 1.316 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C1 CWY A 902 " pdb=" C3 CWY A 902 " ideal model delta sigma weight residual 1.533 1.355 0.178 2.00e-02 2.50e+03 7.94e+01 bond pdb=" C1 CWY B 902 " pdb=" C3 CWY B 902 " ideal model delta sigma weight residual 1.533 1.355 0.178 2.00e-02 2.50e+03 7.92e+01 bond pdb=" C8 CWY A 902 " pdb=" N1 CWY A 902 " ideal model delta sigma weight residual 1.342 1.461 -0.119 2.00e-02 2.50e+03 3.53e+01 ... (remaining 10175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.66: 13910 5.66 - 11.31: 50 11.31 - 16.97: 6 16.97 - 22.63: 0 22.63 - 28.28: 2 Bond angle restraints: 13968 Sorted by residual: angle pdb=" C4 CWY A 902 " pdb=" C6 CWY A 902 " pdb=" C7 CWY A 902 " ideal model delta sigma weight residual 116.66 144.94 -28.28 3.00e+00 1.11e-01 8.89e+01 angle pdb=" C4 CWY B 902 " pdb=" C6 CWY B 902 " pdb=" C7 CWY B 902 " ideal model delta sigma weight residual 116.66 144.92 -28.26 3.00e+00 1.11e-01 8.87e+01 angle pdb=" C TRP B 486 " pdb=" N ALA B 487 " pdb=" CA ALA B 487 " ideal model delta sigma weight residual 121.54 133.51 -11.97 1.91e+00 2.74e-01 3.93e+01 angle pdb=" C TRP A 486 " pdb=" N ALA A 487 " pdb=" CA ALA A 487 " ideal model delta sigma weight residual 121.54 133.49 -11.95 1.91e+00 2.74e-01 3.92e+01 angle pdb=" C VAL A 247 " pdb=" CA VAL A 247 " pdb=" CB VAL A 247 " ideal model delta sigma weight residual 110.70 116.28 -5.58 9.90e-01 1.02e+00 3.18e+01 ... (remaining 13963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5504 17.78 - 35.57: 437 35.57 - 53.35: 67 53.35 - 71.13: 14 71.13 - 88.91: 6 Dihedral angle restraints: 6028 sinusoidal: 1720 harmonic: 4308 Sorted by residual: dihedral pdb=" CB CYS A 240 " pdb=" SG CYS A 240 " pdb=" SG CYS A 527 " pdb=" CB CYS A 527 " ideal model delta sinusoidal sigma weight residual -86.00 -3.62 -82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS B 240 " pdb=" SG CYS B 240 " pdb=" SG CYS B 527 " pdb=" CB CYS B 527 " ideal model delta sinusoidal sigma weight residual -86.00 -3.63 -82.37 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS B 361 " pdb=" SG CYS B 361 " pdb=" SG CYS B 373 " pdb=" CB CYS B 373 " ideal model delta sinusoidal sigma weight residual -86.00 -143.20 57.20 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 6025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1698 0.165 - 0.329: 8 0.329 - 0.494: 2 0.494 - 0.659: 2 0.659 - 0.823: 2 Chirality restraints: 1712 Sorted by residual: chirality pdb=" C6 CWY A 902 " pdb=" C3 CWY A 902 " pdb=" C4 CWY A 902 " pdb=" C7 CWY A 902 " both_signs ideal model delta sigma weight residual True 2.64 1.81 0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C6 CWY B 902 " pdb=" C3 CWY B 902 " pdb=" C4 CWY B 902 " pdb=" C7 CWY B 902 " both_signs ideal model delta sigma weight residual True 2.64 1.82 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C3 CWY A 902 " pdb=" C1 CWY A 902 " pdb=" C4 CWY A 902 " pdb=" C6 CWY A 902 " both_signs ideal model delta sigma weight residual True 2.61 2.03 0.58 2.00e-01 2.50e+01 8.33e+00 ... (remaining 1709 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 247 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C VAL B 247 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL B 247 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY B 248 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 247 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C VAL A 247 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL A 247 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY A 248 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 637 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO B 638 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 638 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 638 " 0.035 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3429 2.83 - 3.35: 8448 3.35 - 3.87: 15395 3.87 - 4.38: 16830 4.38 - 4.90: 28536 Nonbonded interactions: 72638 Sorted by model distance: nonbonded pdb=" O SER A 250 " pdb=" OG SER A 250 " model vdw 2.318 3.040 nonbonded pdb=" O SER B 250 " pdb=" OG SER B 250 " model vdw 2.318 3.040 nonbonded pdb=" OG SER B 149 " pdb=" O2 CWY B 902 " model vdw 2.321 3.040 nonbonded pdb=" OG SER A 149 " pdb=" O2 CWY A 902 " model vdw 2.323 3.040 nonbonded pdb=" O SER B 100 " pdb=" OG SER B 100 " model vdw 2.327 3.040 ... (remaining 72633 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: 0.01 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=1.00 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.950 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.006 0.222 10198 Z= 0.316 Angle : 1.036 28.282 14006 Z= 0.544 Chirality : 0.064 0.823 1712 Planarity : 0.006 0.062 1826 Dihedral : 13.597 88.913 3180 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.81 % Favored : 88.92 % Rotamer: Outliers : 0.73 % Allowed : 7.56 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.08 (0.15), residues: 1462 helix: -4.83 (0.07), residues: 508 sheet: -4.23 (0.29), residues: 164 loop : -3.46 (0.18), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.012 0.001 TYR B 539 PHE 0.015 0.001 PHE B 45 TRP 0.015 0.002 TRP A 486 HIS 0.006 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.32 (10180) covalent geometry : angle 1.03282 / 0.54 (13968) SS BOND : bond 0.00407 / 0.25 ( 16) SS BOND : angle 0.69368 / 0.50 ( 32) hydrogen bonds : bond 0.31768 / 21.18 ( 234) hydrogen bonds : angle 10.77039 / 7.24 ( 672) link_NAG-ASN : bond 0.00406 / 0.21 ( 2) link_NAG-ASN : angle 4.15082 / 2.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 PHE cc_start: 0.8383 (m-10) cc_final: 0.7977 (m-80) REVERT: B 630 PHE cc_start: 0.8335 (m-10) cc_final: 0.7912 (m-80) outliers start: 6 outliers final: 0 residues processed: 143 average time/residue: 0.0679 time to fit residues: 14.7397 Evaluate side-chains 105 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN A 467 ASN B 80 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN B 467 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.230323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.165236 restraints weight = 15111.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.167458 restraints weight = 11225.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.168659 restraints weight = 9125.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.169876 restraints weight = 8002.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.170411 restraints weight = 7303.981| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10198 Z= 0.152 Angle : 0.669 9.252 14006 Z= 0.357 Chirality : 0.043 0.134 1712 Planarity : 0.005 0.052 1826 Dihedral : 7.065 85.365 1550 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.26 % Favored : 89.60 % Rotamer: Outliers : 2.44 % Allowed : 13.29 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.36 (0.17), residues: 1462 helix: -3.99 (0.13), residues: 526 sheet: -3.73 (0.33), residues: 168 loop : -3.20 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.009 0.001 TYR B 256 PHE 0.009 0.001 PHE B 471 TRP 0.011 0.001 TRP B 297 HIS 0.002 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (10180) covalent geometry : angle 0.66501 / 0.36 (13968) SS BOND : bond 0.00282 / 0.18 ( 16) SS BOND : angle 0.80889 / 0.53 ( 32) hydrogen bonds : bond 0.05049 / 3.28 ( 234) hydrogen bonds : angle 6.62617 / 4.44 ( 672) link_NAG-ASN : bond 0.00034 / 0.02 ( 2) link_NAG-ASN : angle 3.63189 / 1.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.313 Fit side-chains REVERT: A 194 ASP cc_start: 0.8025 (m-30) cc_final: 0.7812 (m-30) REVERT: A 260 ILE cc_start: 0.8496 (tp) cc_final: 0.8278 (tp) REVERT: A 630 PHE cc_start: 0.8451 (m-10) cc_final: 0.8038 (m-80) REVERT: B 194 ASP cc_start: 0.8019 (m-30) cc_final: 0.7801 (m-30) REVERT: B 630 PHE cc_start: 0.8407 (m-10) cc_final: 0.7981 (m-80) outliers start: 20 outliers final: 12 residues processed: 124 average time/residue: 0.0723 time to fit residues: 13.7812 Evaluate side-chains 116 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 78 optimal weight: 0.0170 chunk 37 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 82 optimal weight: 0.0000 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 63 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 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 = 0.4733 r_free = 0.4733 target = 0.227294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.170049 restraints weight = 14713.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.168136 restraints weight = 10916.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168048 restraints weight = 7979.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.168297 restraints weight = 7412.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.169006 restraints weight = 6749.068| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10198 Z= 0.111 Angle : 0.609 7.808 14006 Z= 0.324 Chirality : 0.042 0.139 1712 Planarity : 0.004 0.051 1826 Dihedral : 6.433 76.667 1550 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 2.56 % Allowed : 16.10 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.64 (0.19), residues: 1462 helix: -3.38 (0.16), residues: 532 sheet: -3.36 (0.36), residues: 170 loop : -2.76 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 189 TYR 0.020 0.001 TYR A 537 PHE 0.008 0.001 PHE B 295 TRP 0.020 0.002 TRP A 297 HIS 0.005 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10180) covalent geometry : angle 0.60555 / 0.32 (13968) SS BOND : bond 0.00224 / 0.14 ( 16) SS BOND : angle 0.71863 / 0.47 ( 32) hydrogen bonds : bond 0.04137 / 2.71 ( 234) hydrogen bonds : angle 5.72134 / 3.82 ( 672) link_NAG-ASN : bond 0.00186 / 0.09 ( 2) link_NAG-ASN : angle 2.93776 / 1.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 260 ILE cc_start: 0.8469 (tp) cc_final: 0.8269 (tp) REVERT: A 630 PHE cc_start: 0.8413 (m-10) cc_final: 0.8035 (m-80) REVERT: B 156 GLN cc_start: 0.7065 (tp-100) cc_final: 0.6698 (tp40) REVERT: B 630 PHE cc_start: 0.8348 (m-10) cc_final: 0.7978 (m-80) outliers start: 21 outliers final: 20 residues processed: 129 average time/residue: 0.0631 time to fit residues: 12.8252 Evaluate side-chains 123 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 660 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 5 optimal weight: 4.9990 chunk 142 optimal weight: 0.1980 chunk 65 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 50.0000 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 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 = 0.4727 r_free = 0.4727 target = 0.226774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159922 restraints weight = 14647.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.163081 restraints weight = 9729.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.165303 restraints weight = 7497.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.166502 restraints weight = 6382.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.167498 restraints weight = 5781.306| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10198 Z= 0.119 Angle : 0.592 7.758 14006 Z= 0.314 Chirality : 0.041 0.134 1712 Planarity : 0.004 0.050 1826 Dihedral : 6.056 67.016 1550 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 3.29 % Allowed : 18.17 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.20), residues: 1462 helix: -2.85 (0.18), residues: 552 sheet: -3.12 (0.39), residues: 170 loop : -2.70 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.011 0.001 TYR A 539 PHE 0.019 0.001 PHE A 598 TRP 0.025 0.002 TRP B 529 HIS 0.003 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10180) covalent geometry : angle 0.58945 / 0.31 (13968) SS BOND : bond 0.00195 / 0.12 ( 16) SS BOND : angle 0.63404 / 0.41 ( 32) hydrogen bonds : bond 0.03589 / 2.34 ( 234) hydrogen bonds : angle 5.31175 / 3.54 ( 672) link_NAG-ASN : bond 0.00119 / 0.06 ( 2) link_NAG-ASN : angle 2.70549 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.235 Fit side-chains REVERT: A 156 GLN cc_start: 0.7308 (mm-40) cc_final: 0.7090 (mt0) REVERT: A 194 ASP cc_start: 0.8140 (m-30) cc_final: 0.7852 (m-30) REVERT: A 630 PHE cc_start: 0.8505 (m-10) cc_final: 0.8066 (m-80) REVERT: B 630 PHE cc_start: 0.8500 (m-10) cc_final: 0.8055 (m-80) outliers start: 27 outliers final: 22 residues processed: 133 average time/residue: 0.0611 time to fit residues: 12.8053 Evaluate side-chains 134 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 485 HIS Chi-restraints excluded: chain B residue 518 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 128 optimal weight: 40.0000 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 101 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.212632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.153009 restraints weight = 14484.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.148725 restraints weight = 12857.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.149078 restraints weight = 11237.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149423 restraints weight = 10196.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.149640 restraints weight = 9344.971| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10198 Z= 0.138 Angle : 0.592 7.346 14006 Z= 0.312 Chirality : 0.042 0.132 1712 Planarity : 0.004 0.049 1826 Dihedral : 5.932 58.551 1550 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 3.78 % Allowed : 19.88 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.21), residues: 1462 helix: -2.53 (0.20), residues: 558 sheet: -2.96 (0.40), residues: 168 loop : -2.58 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.010 0.001 TYR B 539 PHE 0.012 0.001 PHE B 471 TRP 0.027 0.002 TRP B 529 HIS 0.003 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10180) covalent geometry : angle 0.58745 / 0.31 (13968) SS BOND : bond 0.00172 / 0.10 ( 16) SS BOND : angle 1.19205 / 0.73 ( 32) hydrogen bonds : bond 0.03468 / 2.27 ( 234) hydrogen bonds : angle 5.18770 / 3.46 ( 672) link_NAG-ASN : bond 0.00065 / 0.03 ( 2) link_NAG-ASN : angle 2.66748 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.334 Fit side-chains REVERT: A 104 TYR cc_start: 0.8006 (t80) cc_final: 0.7755 (t80) REVERT: A 156 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6914 (mt0) REVERT: A 194 ASP cc_start: 0.8149 (m-30) cc_final: 0.7825 (m-30) REVERT: A 630 PHE cc_start: 0.8261 (m-10) cc_final: 0.7910 (m-80) REVERT: B 104 TYR cc_start: 0.7981 (t80) cc_final: 0.7653 (t80) REVERT: B 194 ASP cc_start: 0.8141 (m-30) cc_final: 0.7835 (m-30) REVERT: B 630 PHE cc_start: 0.8232 (m-10) cc_final: 0.7902 (m-80) outliers start: 31 outliers final: 26 residues processed: 134 average time/residue: 0.0649 time to fit residues: 13.6477 Evaluate side-chains 140 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 485 HIS Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 660 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 147 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 141 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 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 = 0.4617 r_free = 0.4617 target = 0.212600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.156255 restraints weight = 14421.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.155583 restraints weight = 16793.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.157225 restraints weight = 16472.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.157481 restraints weight = 11493.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.157653 restraints weight = 10904.914| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10198 Z= 0.139 Angle : 0.593 7.000 14006 Z= 0.312 Chirality : 0.042 0.136 1712 Planarity : 0.004 0.046 1826 Dihedral : 5.798 53.917 1550 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 3.29 % Allowed : 21.46 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.21), residues: 1462 helix: -2.30 (0.20), residues: 558 sheet: -2.82 (0.39), residues: 180 loop : -2.54 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 465 TYR 0.008 0.001 TYR A 539 PHE 0.022 0.001 PHE B 598 TRP 0.029 0.002 TRP B 529 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10180) covalent geometry : angle 0.58897 / 0.31 (13968) SS BOND : bond 0.00190 / 0.12 ( 16) SS BOND : angle 1.01643 / 0.64 ( 32) hydrogen bonds : bond 0.03393 / 2.21 ( 234) hydrogen bonds : angle 5.00547 / 3.35 ( 672) link_NAG-ASN : bond 0.00089 / 0.04 ( 2) link_NAG-ASN : angle 2.63623 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.362 Fit side-chains REVERT: A 104 TYR cc_start: 0.8056 (t80) cc_final: 0.7746 (t80) REVERT: A 156 GLN cc_start: 0.7047 (mm-40) cc_final: 0.6767 (mt0) REVERT: A 194 ASP cc_start: 0.8230 (m-30) cc_final: 0.7879 (m-30) REVERT: A 630 PHE cc_start: 0.7943 (m-10) cc_final: 0.7718 (m-80) REVERT: B 104 TYR cc_start: 0.7995 (t80) cc_final: 0.7670 (t80) REVERT: B 194 ASP cc_start: 0.8254 (m-30) cc_final: 0.7903 (m-30) REVERT: B 630 PHE cc_start: 0.7922 (m-10) cc_final: 0.7695 (m-80) outliers start: 27 outliers final: 25 residues processed: 130 average time/residue: 0.0686 time to fit residues: 14.0795 Evaluate side-chains 134 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 485 HIS Chi-restraints excluded: chain B residue 518 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 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 = 0.4626 r_free = 0.4626 target = 0.213579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.157343 restraints weight = 14391.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.157238 restraints weight = 15732.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.158100 restraints weight = 14859.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.158450 restraints weight = 11028.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.158812 restraints weight = 10063.159| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10198 Z= 0.119 Angle : 0.578 6.358 14006 Z= 0.304 Chirality : 0.042 0.138 1712 Planarity : 0.004 0.051 1826 Dihedral : 5.576 59.585 1550 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 3.17 % Allowed : 22.80 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.21), residues: 1462 helix: -2.11 (0.21), residues: 558 sheet: -2.28 (0.43), residues: 160 loop : -2.47 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 206 TYR 0.008 0.001 TYR A 539 PHE 0.008 0.001 PHE A 295 TRP 0.032 0.002 TRP B 529 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10180) covalent geometry : angle 0.57483 / 0.30 (13968) SS BOND : bond 0.00167 / 0.10 ( 16) SS BOND : angle 0.85149 / 0.52 ( 32) hydrogen bonds : bond 0.03187 / 2.07 ( 234) hydrogen bonds : angle 4.86832 / 3.24 ( 672) link_NAG-ASN : bond 0.00036 / 0.02 ( 2) link_NAG-ASN : angle 2.59249 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.296 Fit side-chains REVERT: A 104 TYR cc_start: 0.8002 (t80) cc_final: 0.7724 (t80) REVERT: A 156 GLN cc_start: 0.6960 (mm-40) cc_final: 0.6725 (mt0) REVERT: A 194 ASP cc_start: 0.8160 (m-30) cc_final: 0.7832 (m-30) REVERT: A 391 MET cc_start: 0.7290 (tpp) cc_final: 0.7054 (ttm) REVERT: A 529 TRP cc_start: 0.7543 (p-90) cc_final: 0.7166 (p-90) REVERT: B 104 TYR cc_start: 0.7934 (t80) cc_final: 0.7703 (t80) REVERT: B 194 ASP cc_start: 0.8152 (m-30) cc_final: 0.7822 (m-30) outliers start: 26 outliers final: 22 residues processed: 128 average time/residue: 0.0685 time to fit residues: 13.7224 Evaluate side-chains 131 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 28 optimal weight: 0.0040 chunk 132 optimal weight: 7.9990 chunk 94 optimal weight: 0.1980 chunk 66 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 141 optimal weight: 0.4980 chunk 75 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.2370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 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 = 0.4755 r_free = 0.4755 target = 0.228929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.172632 restraints weight = 14539.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.168682 restraints weight = 10208.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.169130 restraints weight = 8047.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.170111 restraints weight = 7407.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.170345 restraints weight = 6873.817| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10198 Z= 0.092 Angle : 0.555 6.022 14006 Z= 0.293 Chirality : 0.041 0.134 1712 Planarity : 0.003 0.051 1826 Dihedral : 5.151 53.471 1550 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 2.56 % Allowed : 23.78 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.21), residues: 1462 helix: -1.95 (0.21), residues: 560 sheet: -2.17 (0.42), residues: 160 loop : -2.41 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.017 0.001 TYR A 537 PHE 0.016 0.001 PHE B 598 TRP 0.020 0.002 TRP A 554 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (10180) covalent geometry : angle 0.55287 / 0.29 (13968) SS BOND : bond 0.00145 / 0.09 ( 16) SS BOND : angle 0.81970 / 0.52 ( 32) hydrogen bonds : bond 0.02903 / 1.89 ( 234) hydrogen bonds : angle 4.60395 / 3.06 ( 672) link_NAG-ASN : bond 0.00193 / 0.10 ( 2) link_NAG-ASN : angle 2.20374 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.275 Fit side-chains REVERT: A 104 TYR cc_start: 0.7880 (t80) cc_final: 0.7634 (t80) REVERT: A 156 GLN cc_start: 0.6870 (mm-40) cc_final: 0.6646 (mt0) REVERT: A 194 ASP cc_start: 0.8221 (m-30) cc_final: 0.7864 (m-30) REVERT: B 104 TYR cc_start: 0.7834 (t80) cc_final: 0.7603 (t80) REVERT: B 194 ASP cc_start: 0.8196 (m-30) cc_final: 0.7831 (m-30) outliers start: 21 outliers final: 20 residues processed: 138 average time/residue: 0.0631 time to fit residues: 13.7531 Evaluate side-chains 136 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.213078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.157245 restraints weight = 14416.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.155797 restraints weight = 16566.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.157168 restraints weight = 14496.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.157154 restraints weight = 12518.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.157432 restraints weight = 10421.768| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10198 Z= 0.147 Angle : 0.590 5.983 14006 Z= 0.310 Chirality : 0.042 0.122 1712 Planarity : 0.003 0.050 1826 Dihedral : 5.364 57.154 1550 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 3.17 % Allowed : 23.41 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.21), residues: 1462 helix: -1.81 (0.22), residues: 556 sheet: -2.14 (0.43), residues: 160 loop : -2.40 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 335 TYR 0.007 0.001 TYR A 150 PHE 0.018 0.001 PHE A 598 TRP 0.020 0.002 TRP A 529 HIS 0.003 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10180) covalent geometry : angle 0.58774 / 0.31 (13968) SS BOND : bond 0.00167 / 0.10 ( 16) SS BOND : angle 0.76113 / 0.48 ( 32) hydrogen bonds : bond 0.03263 / 2.12 ( 234) hydrogen bonds : angle 4.72837 / 3.13 ( 672) link_NAG-ASN : bond 0.00018 / 0.01 ( 2) link_NAG-ASN : angle 2.43520 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.407 Fit side-chains REVERT: A 104 TYR cc_start: 0.8052 (t80) cc_final: 0.7804 (t80) REVERT: A 156 GLN cc_start: 0.6980 (mm-40) cc_final: 0.6736 (mt0) REVERT: A 194 ASP cc_start: 0.8243 (m-30) cc_final: 0.7891 (m-30) REVERT: B 104 TYR cc_start: 0.7962 (t80) cc_final: 0.7738 (t80) REVERT: B 194 ASP cc_start: 0.8225 (m-30) cc_final: 0.7860 (m-30) REVERT: B 270 ARG cc_start: 0.7168 (mmm-85) cc_final: 0.6875 (mtm180) outliers start: 26 outliers final: 21 residues processed: 134 average time/residue: 0.0657 time to fit residues: 13.7617 Evaluate side-chains 130 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 94 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 0.0070 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 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 = 0.4735 r_free = 0.4735 target = 0.227326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.169917 restraints weight = 14564.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.165404 restraints weight = 10003.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.165534 restraints weight = 7931.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.166265 restraints weight = 8186.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.166582 restraints weight = 6973.642| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10198 Z= 0.115 Angle : 0.574 6.689 14006 Z= 0.301 Chirality : 0.042 0.129 1712 Planarity : 0.003 0.050 1826 Dihedral : 5.178 52.541 1550 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 2.68 % Allowed : 24.02 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.21), residues: 1462 helix: -1.73 (0.22), residues: 556 sheet: -2.06 (0.43), residues: 160 loop : -2.33 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.007 0.001 TYR A 171 PHE 0.019 0.001 PHE B 598 TRP 0.021 0.002 TRP A 529 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10180) covalent geometry : angle 0.57134 / 0.30 (13968) SS BOND : bond 0.00158 / 0.10 ( 16) SS BOND : angle 0.75879 / 0.48 ( 32) hydrogen bonds : bond 0.03057 / 1.97 ( 234) hydrogen bonds : angle 4.61291 / 3.05 ( 672) link_NAG-ASN : bond 0.00133 / 0.07 ( 2) link_NAG-ASN : angle 2.25622 / 1.20 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.529 Fit side-chains REVERT: A 104 TYR cc_start: 0.7974 (t80) cc_final: 0.7713 (t80) REVERT: A 194 ASP cc_start: 0.8219 (m-30) cc_final: 0.7881 (m-30) REVERT: B 194 ASP cc_start: 0.8208 (m-30) cc_final: 0.7852 (m-30) REVERT: B 270 ARG cc_start: 0.7235 (mmm-85) cc_final: 0.6818 (mtm180) outliers start: 22 outliers final: 21 residues processed: 129 average time/residue: 0.0810 time to fit residues: 16.0968 Evaluate side-chains 131 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 115 optimal weight: 0.0870 chunk 94 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 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 = 0.4728 r_free = 0.4728 target = 0.226377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160888 restraints weight = 14624.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.162572 restraints weight = 10734.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.164099 restraints weight = 8658.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.164372 restraints weight = 8070.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.164629 restraints weight = 7211.696| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10198 Z= 0.128 Angle : 0.583 6.739 14006 Z= 0.306 Chirality : 0.042 0.122 1712 Planarity : 0.003 0.050 1826 Dihedral : 5.180 51.509 1550 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 3.17 % Allowed : 23.78 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.22), residues: 1462 helix: -1.73 (0.22), residues: 560 sheet: -2.06 (0.43), residues: 160 loop : -2.30 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.006 0.001 TYR B 431 PHE 0.019 0.001 PHE A 598 TRP 0.021 0.002 TRP A 529 HIS 0.003 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (10180) covalent geometry : angle 0.58035 / 0.31 (13968) SS BOND : bond 0.00155 / 0.09 ( 16) SS BOND : angle 0.74243 / 0.47 ( 32) hydrogen bonds : bond 0.03112 / 2.01 ( 234) hydrogen bonds : angle 4.62334 / 3.06 ( 672) link_NAG-ASN : bond 0.00071 / 0.04 ( 2) link_NAG-ASN : angle 2.29114 / 1.23 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.38 seconds wall clock time: 28 minutes 31.31 seconds (1711.31 seconds total)