Starting phenix.real_space_refine on Fri Feb 14 14:23:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_32530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_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_32530/02_2025/7wih_32530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_32530.map" model { file = "/net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_32530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wih_32530/02_2025/7wih_32530.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 10, 'ASP:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 9, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 21} 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B Time building chain proxies: 9.97, per 1000 atoms: 1.00 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=8, 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 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: 2.23 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.28 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: 3.29 Time building geometry restraints manager: 2.61 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: 5540 17.78 - 35.57: 450 35.57 - 53.35: 81 53.35 - 71.13: 26 71.13 - 88.91: 11 Dihedral angle restraints: 6108 sinusoidal: 1800 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 A 361 " pdb=" SG CYS A 361 " pdb=" SG CYS A 373 " pdb=" CB CYS A 373 " ideal model delta sinusoidal sigma weight residual -86.00 -143.16 57.16 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CA ALA B 487 " pdb=" C ALA B 487 " pdb=" N GLU B 488 " pdb=" CA GLU B 488 " ideal model delta harmonic sigma weight residual 180.00 149.10 30.90 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 6105 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: 2.02 - 2.60: 106 2.60 - 3.17: 7824 3.17 - 3.75: 14827 3.75 - 4.32: 19164 4.32 - 4.90: 30741 Nonbonded interactions: 72662 Sorted by model distance: nonbonded pdb=" SG CYS B 361 " pdb=" SG CYS B 373 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS B 412 " pdb=" SG CYS B 419 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 509 " pdb=" SG CYS B 528 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 549 " pdb=" SG CYS B 562 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS B 513 " pdb=" SG CYS B 531 " model vdw 2.033 3.760 ... (remaining 72657 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: 0.08 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 29.230 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 10180 Z= 0.469 Angle : 1.033 28.282 13968 Z= 0.544 Chirality : 0.064 0.823 1712 Planarity : 0.006 0.062 1826 Dihedral : 14.904 88.913 3284 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.08 (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 TRP 0.015 0.002 TRP A 486 HIS 0.006 0.001 HIS B 94 PHE 0.015 0.001 PHE B 45 TYR 0.012 0.001 TYR B 539 ARG 0.002 0.000 ARG A 253 *********************** 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 : 1.134 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: 0.1974 time to fit residues: 41.6273 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 : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4697 r_free = 0.4697 target = 0.217260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.163422 restraints weight = 14283.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.159813 restraints weight = 14016.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.162042 restraints weight = 11057.132| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10180 Z= 0.279 Angle : 0.693 9.649 13968 Z= 0.369 Chirality : 0.044 0.142 1712 Planarity : 0.005 0.052 1826 Dihedral : 9.650 84.093 1654 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.01 % Favored : 88.85 % Rotamer: Outliers : 2.56 % Allowed : 13.29 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.36 (0.17), residues: 1462 helix: -3.97 (0.13), residues: 524 sheet: -3.70 (0.34), residues: 168 loop : -3.24 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 297 HIS 0.003 0.001 HIS A 485 PHE 0.014 0.001 PHE B 471 TYR 0.010 0.002 TYR A 466 ARG 0.002 0.000 ARG A 183 *********************** 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 130 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 ASP cc_start: 0.8101 (m-30) cc_final: 0.7862 (m-30) REVERT: A 204 ILE cc_start: 0.8941 (tp) cc_final: 0.8641 (tp) REVERT: A 630 PHE cc_start: 0.8039 (m-10) cc_final: 0.7789 (m-80) REVERT: B 194 ASP cc_start: 0.8093 (m-30) cc_final: 0.7877 (m-30) REVERT: B 204 ILE cc_start: 0.8895 (tp) cc_final: 0.8577 (tp) REVERT: B 630 PHE cc_start: 0.7983 (m-10) cc_final: 0.7714 (m-80) outliers start: 21 outliers final: 13 residues processed: 124 average time/residue: 0.1832 time to fit residues: 34.6893 Evaluate side-chains 114 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE 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 B residue 79 ILE Chi-restraints excluded: chain B residue 174 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 30 optimal weight: 0.0270 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 0.0770 chunk 57 optimal weight: 0.0870 overall best weight: 0.8378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4606 r_free = 0.4606 target = 0.203133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.150261 restraints weight = 14311.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.144115 restraints weight = 9915.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.144514 restraints weight = 9013.814| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10180 Z= 0.224 Angle : 0.630 8.336 13968 Z= 0.335 Chirality : 0.043 0.151 1712 Planarity : 0.004 0.051 1826 Dihedral : 8.820 81.975 1654 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.60 % Favored : 89.26 % Rotamer: Outliers : 2.68 % Allowed : 15.00 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.19), residues: 1462 helix: -3.34 (0.16), residues: 550 sheet: -3.38 (0.37), residues: 168 loop : -2.98 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 529 HIS 0.004 0.001 HIS B 94 PHE 0.011 0.001 PHE A 471 TYR 0.009 0.001 TYR B 171 ARG 0.002 0.000 ARG A 335 *********************** 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 136 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.100 Fit side-chains REVERT: A 104 TYR cc_start: 0.8111 (t80) cc_final: 0.7797 (t80) REVERT: A 194 ASP cc_start: 0.8235 (m-30) cc_final: 0.7966 (m-30) REVERT: A 204 ILE cc_start: 0.8882 (tp) cc_final: 0.8589 (tp) REVERT: A 630 PHE cc_start: 0.8413 (m-10) cc_final: 0.8040 (m-80) REVERT: B 104 TYR cc_start: 0.8082 (t80) cc_final: 0.7765 (t80) REVERT: B 194 ASP cc_start: 0.8244 (m-30) cc_final: 0.7994 (m-30) REVERT: B 204 ILE cc_start: 0.8879 (tp) cc_final: 0.8588 (tp) REVERT: B 630 PHE cc_start: 0.8392 (m-10) cc_final: 0.8016 (m-80) outliers start: 22 outliers final: 20 residues processed: 127 average time/residue: 0.1763 time to fit residues: 34.6782 Evaluate side-chains 130 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 518 MET 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 101 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 61 optimal weight: 0.0170 chunk 30 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4642 r_free = 0.4642 target = 0.216576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.151022 restraints weight = 14516.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.153849 restraints weight = 9693.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154184 restraints weight = 7610.624| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10180 Z= 0.194 Angle : 0.606 7.990 13968 Z= 0.321 Chirality : 0.042 0.148 1712 Planarity : 0.004 0.050 1826 Dihedral : 8.203 81.517 1654 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 3.05 % Allowed : 17.68 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.20), residues: 1462 helix: -2.80 (0.19), residues: 548 sheet: -3.10 (0.38), residues: 168 loop : -2.79 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 529 HIS 0.004 0.001 HIS B 94 PHE 0.019 0.001 PHE A 598 TYR 0.011 0.001 TYR A 539 ARG 0.001 0.000 ARG A 183 *********************** 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 140 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.035 Fit side-chains REVERT: A 104 TYR cc_start: 0.8097 (t80) cc_final: 0.7620 (t80) REVERT: A 194 ASP cc_start: 0.8231 (m-30) cc_final: 0.7928 (m-30) REVERT: A 204 ILE cc_start: 0.8837 (tp) cc_final: 0.8537 (tp) REVERT: A 630 PHE cc_start: 0.8510 (m-10) cc_final: 0.8092 (m-80) REVERT: B 104 TYR cc_start: 0.8094 (t80) cc_final: 0.7646 (t80) REVERT: B 194 ASP cc_start: 0.8215 (m-30) cc_final: 0.7961 (m-30) REVERT: B 204 ILE cc_start: 0.8840 (tp) cc_final: 0.8539 (tp) REVERT: B 630 PHE cc_start: 0.8512 (m-10) cc_final: 0.8060 (m-80) outliers start: 25 outliers final: 19 residues processed: 131 average time/residue: 0.1645 time to fit residues: 33.7083 Evaluate side-chains 129 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 527 CYS Chi-restraints excluded: chain B residue 44 LEU 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 518 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 125 optimal weight: 20.0000 chunk 93 optimal weight: 0.0470 chunk 36 optimal weight: 0.8980 chunk 113 optimal weight: 0.4980 chunk 134 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4636 r_free = 0.4636 target = 0.208231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.153231 restraints weight = 14238.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.148640 restraints weight = 11042.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.148999 restraints weight = 9050.469| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10180 Z= 0.172 Angle : 0.578 7.157 13968 Z= 0.306 Chirality : 0.042 0.140 1712 Planarity : 0.004 0.049 1826 Dihedral : 7.720 82.538 1654 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 3.90 % Allowed : 18.41 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.20), residues: 1462 helix: -2.49 (0.20), residues: 552 sheet: -2.97 (0.39), residues: 170 loop : -2.68 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 529 HIS 0.004 0.001 HIS A 94 PHE 0.009 0.001 PHE A 295 TYR 0.010 0.001 TYR A 539 ARG 0.002 0.000 ARG A 335 *********************** 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 146 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.087 Fit side-chains REVERT: A 104 TYR cc_start: 0.8135 (t80) cc_final: 0.7725 (t80) REVERT: A 194 ASP cc_start: 0.8153 (m-30) cc_final: 0.7833 (m-30) REVERT: A 630 PHE cc_start: 0.8447 (m-10) cc_final: 0.8040 (m-80) REVERT: B 104 TYR cc_start: 0.8106 (t80) cc_final: 0.7676 (t80) REVERT: B 194 ASP cc_start: 0.8150 (m-30) cc_final: 0.7825 (m-30) REVERT: B 630 PHE cc_start: 0.8428 (m-10) cc_final: 0.8010 (m-80) outliers start: 32 outliers final: 28 residues processed: 133 average time/residue: 0.1722 time to fit residues: 35.3609 Evaluate side-chains 134 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 182 SER 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 300 SER Chi-restraints excluded: chain A residue 323 LEU 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 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 182 SER 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 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 Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 115 optimal weight: 0.0870 chunk 101 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 0.0370 chunk 73 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4637 r_free = 0.4637 target = 0.215662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.156059 restraints weight = 14640.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.152932 restraints weight = 10060.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.152182 restraints weight = 8558.804| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10180 Z= 0.238 Angle : 0.605 7.411 13968 Z= 0.318 Chirality : 0.043 0.137 1712 Planarity : 0.004 0.048 1826 Dihedral : 7.972 84.962 1654 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 3.78 % Allowed : 20.49 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.21), residues: 1462 helix: -2.26 (0.21), residues: 558 sheet: -2.87 (0.39), residues: 168 loop : -2.61 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 529 HIS 0.003 0.001 HIS A 94 PHE 0.022 0.001 PHE B 598 TYR 0.008 0.001 TYR A 539 ARG 0.003 0.000 ARG B 206 *********************** 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 139 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.089 Fit side-chains REVERT: A 104 TYR cc_start: 0.8163 (t80) cc_final: 0.7761 (t80) REVERT: A 194 ASP cc_start: 0.8321 (m-30) cc_final: 0.7971 (m-30) REVERT: A 630 PHE cc_start: 0.8614 (m-10) cc_final: 0.8162 (m-80) REVERT: B 104 TYR cc_start: 0.8162 (t80) cc_final: 0.7776 (t80) REVERT: B 194 ASP cc_start: 0.8314 (m-30) cc_final: 0.7938 (m-30) REVERT: B 630 PHE cc_start: 0.8593 (m-10) cc_final: 0.8137 (m-80) outliers start: 31 outliers final: 28 residues processed: 129 average time/residue: 0.1662 time to fit residues: 33.1054 Evaluate side-chains 135 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 300 SER 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 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 300 SER 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 Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 660 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 106 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4622 r_free = 0.4622 target = 0.204696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.146176 restraints weight = 14270.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.147012 restraints weight = 9827.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.146635 restraints weight = 8248.136| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10180 Z= 0.202 Angle : 0.592 6.684 13968 Z= 0.311 Chirality : 0.042 0.142 1712 Planarity : 0.004 0.048 1826 Dihedral : 7.852 88.096 1654 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 4.27 % Allowed : 21.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.21), residues: 1462 helix: -2.08 (0.21), residues: 556 sheet: -2.41 (0.43), residues: 150 loop : -2.56 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 529 HIS 0.003 0.001 HIS A 94 PHE 0.009 0.001 PHE B 295 TYR 0.007 0.001 TYR A 539 ARG 0.003 0.000 ARG A 206 *********************** 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 143 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.144 Fit side-chains REVERT: A 104 TYR cc_start: 0.8118 (t80) cc_final: 0.7729 (t80) REVERT: A 194 ASP cc_start: 0.8225 (m-30) cc_final: 0.7878 (m-30) REVERT: A 630 PHE cc_start: 0.8554 (m-10) cc_final: 0.8113 (m-80) REVERT: B 104 TYR cc_start: 0.8119 (t80) cc_final: 0.7739 (t80) REVERT: B 194 ASP cc_start: 0.8208 (m-30) cc_final: 0.7840 (m-30) REVERT: B 630 PHE cc_start: 0.8538 (m-10) cc_final: 0.8156 (m-80) outliers start: 35 outliers final: 28 residues processed: 133 average time/residue: 0.1728 time to fit residues: 35.5545 Evaluate side-chains 133 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 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 225 THR Chi-restraints excluded: chain A residue 300 SER 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 518 MET Chi-restraints excluded: chain B residue 35 ILE 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 300 SER Chi-restraints excluded: chain B residue 323 LEU 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 527 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 141 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 134 optimal weight: 20.0000 chunk 80 optimal weight: 0.0670 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 overall best weight: 1.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.212578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.148742 restraints weight = 14744.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.149221 restraints weight = 11121.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.149680 restraints weight = 7920.741| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10180 Z= 0.360 Angle : 0.656 6.926 13968 Z= 0.343 Chirality : 0.045 0.137 1712 Planarity : 0.004 0.048 1826 Dihedral : 8.528 87.632 1654 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 4.39 % Allowed : 21.95 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.21), residues: 1462 helix: -2.05 (0.21), residues: 558 sheet: -2.38 (0.43), residues: 148 loop : -2.59 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 529 HIS 0.003 0.001 HIS B 94 PHE 0.021 0.002 PHE A 598 TYR 0.019 0.002 TYR A 537 ARG 0.002 0.000 ARG A 206 *********************** 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 140 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 1.092 Fit side-chains REVERT: A 104 TYR cc_start: 0.8310 (t80) cc_final: 0.7943 (t80) REVERT: A 194 ASP cc_start: 0.8267 (m-30) cc_final: 0.7930 (m-30) REVERT: A 630 PHE cc_start: 0.8503 (m-10) cc_final: 0.8082 (m-80) REVERT: B 104 TYR cc_start: 0.8309 (t80) cc_final: 0.7950 (t80) REVERT: B 194 ASP cc_start: 0.8254 (m-30) cc_final: 0.7927 (m-30) REVERT: B 529 TRP cc_start: 0.7712 (p-90) cc_final: 0.7221 (p-90) REVERT: B 630 PHE cc_start: 0.8509 (m-10) cc_final: 0.8146 (m-80) outliers start: 36 outliers final: 32 residues processed: 128 average time/residue: 0.1718 time to fit residues: 34.2789 Evaluate side-chains 135 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE 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 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 35 ILE 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 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 300 SER 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 Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 771 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4637 r_free = 0.4637 target = 0.215709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.148624 restraints weight = 14593.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151339 restraints weight = 9853.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.153310 restraints weight = 7728.258| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10180 Z= 0.222 Angle : 0.602 6.407 13968 Z= 0.316 Chirality : 0.043 0.149 1712 Planarity : 0.004 0.048 1826 Dihedral : 7.925 82.861 1654 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 3.66 % Allowed : 22.44 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.21), residues: 1462 helix: -1.91 (0.22), residues: 554 sheet: -2.28 (0.43), residues: 148 loop : -2.48 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 554 HIS 0.003 0.001 HIS A 94 PHE 0.010 0.001 PHE B 295 TYR 0.007 0.001 TYR B 171 ARG 0.003 0.000 ARG A 335 *********************** 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 135 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.977 Fit side-chains REVERT: A 104 TYR cc_start: 0.8215 (t80) cc_final: 0.7837 (t80) REVERT: A 194 ASP cc_start: 0.8218 (m-30) cc_final: 0.7901 (m-30) REVERT: A 630 PHE cc_start: 0.8692 (m-10) cc_final: 0.8293 (m-80) REVERT: B 104 TYR cc_start: 0.8222 (t80) cc_final: 0.7848 (t80) REVERT: B 194 ASP cc_start: 0.8215 (m-30) cc_final: 0.7881 (m-30) REVERT: B 529 TRP cc_start: 0.7599 (p-90) cc_final: 0.7141 (p-90) REVERT: B 630 PHE cc_start: 0.8656 (m-10) cc_final: 0.8252 (m-80) outliers start: 30 outliers final: 29 residues processed: 127 average time/residue: 0.1871 time to fit residues: 36.5586 Evaluate side-chains 130 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE 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 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 327 SER 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 B residue 35 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 174 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 300 SER Chi-restraints excluded: chain B residue 323 LEU 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 485 HIS Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 147 optimal weight: 0.0670 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.205819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.152419 restraints weight = 14287.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.146198 restraints weight = 9925.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.146113 restraints weight = 9893.215| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10180 Z= 0.168 Angle : 0.581 6.458 13968 Z= 0.305 Chirality : 0.042 0.141 1712 Planarity : 0.004 0.048 1826 Dihedral : 7.355 76.864 1654 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 3.29 % Allowed : 23.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.21), residues: 1462 helix: -1.85 (0.21), residues: 564 sheet: -2.19 (0.43), residues: 160 loop : -2.39 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 529 HIS 0.003 0.001 HIS B 94 PHE 0.018 0.001 PHE A 598 TYR 0.021 0.001 TYR A 537 ARG 0.002 0.000 ARG A 270 ********************** 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 136 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 1.087 Fit side-chains REVERT: A 104 TYR cc_start: 0.8164 (t80) cc_final: 0.7842 (t80) REVERT: A 194 ASP cc_start: 0.8184 (m-30) cc_final: 0.7852 (m-30) REVERT: A 630 PHE cc_start: 0.8460 (m-10) cc_final: 0.8163 (m-10) REVERT: B 104 TYR cc_start: 0.8174 (t80) cc_final: 0.7857 (t80) REVERT: B 194 ASP cc_start: 0.8185 (m-30) cc_final: 0.7863 (m-30) REVERT: B 529 TRP cc_start: 0.7519 (p-90) cc_final: 0.7257 (p-90) REVERT: B 630 PHE cc_start: 0.8434 (m-10) cc_final: 0.8094 (m-80) outliers start: 27 outliers final: 22 residues processed: 125 average time/residue: 0.1660 time to fit residues: 31.9708 Evaluate side-chains 128 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 174 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 B residue 44 LEU Chi-restraints excluded: chain B residue 174 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 245 GLU 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 518 MET Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.0670 chunk 138 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 32 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 147 optimal weight: 0.2980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4720 r_free = 0.4720 target = 0.225650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.159162 restraints weight = 14535.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.161966 restraints weight = 9967.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.163976 restraints weight = 7878.284| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10180 Z= 0.185 Angle : 0.584 6.200 13968 Z= 0.306 Chirality : 0.042 0.134 1712 Planarity : 0.003 0.049 1826 Dihedral : 7.265 74.095 1654 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 3.29 % Allowed : 23.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.22), residues: 1462 helix: -1.78 (0.22), residues: 560 sheet: -2.14 (0.43), residues: 160 loop : -2.36 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 554 HIS 0.003 0.001 HIS B 94 PHE 0.010 0.001 PHE B 295 TYR 0.006 0.001 TYR B 431 ARG 0.002 0.000 ARG B 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3166.82 seconds wall clock time: 57 minutes 22.59 seconds (3442.59 seconds total)