Starting phenix.real_space_refine on Sun Dec 29 08:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y69_33638/12_2024/7y69_33638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y69_33638/12_2024/7y69_33638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y69_33638/12_2024/7y69_33638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y69_33638/12_2024/7y69_33638.map" model { file = "/net/cci-nas-00/data/ceres_data/7y69_33638/12_2024/7y69_33638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y69_33638/12_2024/7y69_33638.cif" } resolution = 3.21 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 62 5.16 5 C 6532 2.51 5 N 1640 2.21 5 O 1854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10090 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4946 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 615} Chain breaks: 3 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, E, F Time building chain proxies: 9.65, per 1000 atoms: 0.96 Number of scatterers: 10090 At special positions: 0 Unit cell: (105.002, 79.0225, 134.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 62 16.00 O 1854 8.00 N 1640 7.00 C 6532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 570 " distance=2.04 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 787 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 902 " - " ASN A 27 " " NAG A 903 " - " ASN A 141 " " NAG A 904 " - " ASN A 123 " " NAG B 902 " - " ASN B 27 " " NAG B 903 " - " ASN B 141 " " NAG B 904 " - " ASN B 123 " " NAG C 1 " - " ASN A 54 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN B 54 " " NAG F 1 " - " ASN B 165 " Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 568 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 568 " 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 46.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.618A pdb=" N GLY A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 303 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 479 removed outlier: 3.974A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Proline residue: A 463 - end of helix removed outlier: 3.514A pdb=" N THR A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 506 through 533 removed outlier: 3.769A pdb=" N ILE A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 564 removed outlier: 4.498A pdb=" N PHE A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 562 " --> pdb=" O MET A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 570 removed outlier: 3.543A pdb=" N VAL A 569 " --> pdb=" O CYS A 566 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 570 " --> pdb=" O TYR A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 570' Processing helix chain 'A' and resid 577 through 597 removed outlier: 4.152A pdb=" N PHE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 626 removed outlier: 3.536A pdb=" N TYR A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 652 removed outlier: 3.616A pdb=" N THR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 710 removed outlier: 3.545A pdb=" N VAL A 693 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 698 " --> pdb=" O MET A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.864A pdb=" N ALA A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 721 " --> pdb=" O TYR A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 769 removed outlier: 3.851A pdb=" N CYS A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 769 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 782 Processing helix chain 'A' and resid 794 through 817 removed outlier: 3.820A pdb=" N PHE A 801 " --> pdb=" O ASP A 797 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A 804 " --> pdb=" O HIS A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.618A pdb=" N GLY B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B 303 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 479 removed outlier: 3.975A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Proline residue: B 463 - end of helix removed outlier: 3.514A pdb=" N THR B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 506 through 533 removed outlier: 3.769A pdb=" N ILE B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 564 removed outlier: 4.497A pdb=" N PHE B 550 " --> pdb=" O HIS B 546 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 562 " --> pdb=" O MET B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.543A pdb=" N VAL B 569 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 570 " --> pdb=" O TYR B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 570' Processing helix chain 'B' and resid 577 through 597 removed outlier: 4.151A pdb=" N PHE B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 626 removed outlier: 3.536A pdb=" N TYR B 607 " --> pdb=" O ASN B 603 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 652 removed outlier: 3.616A pdb=" N THR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 710 removed outlier: 3.545A pdb=" N VAL B 693 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 698 " --> pdb=" O MET B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.863A pdb=" N ALA B 720 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 721 " --> pdb=" O TYR B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 769 removed outlier: 3.851A pdb=" N CYS B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 764 " --> pdb=" O GLY B 760 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 769 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 782 Processing helix chain 'B' and resid 794 through 817 removed outlier: 3.820A pdb=" N PHE B 801 " --> pdb=" O ASP B 797 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER B 804 " --> pdb=" O HIS B 800 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 32 removed outlier: 6.762A pdb=" N ASN A 27 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE A 50 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER A 29 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR A 52 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS A 31 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASN A 54 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU A 47 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR A 136 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 115 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.628A pdb=" N LYS A 106 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 165 removed outlier: 3.555A pdb=" N PHE A 164 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 281 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 176 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 32 removed outlier: 6.762A pdb=" N ASN B 27 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE B 50 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER B 29 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR B 52 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS B 31 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ASN B 54 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU B 47 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR B 136 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 111 through 115 Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.627A pdb=" N LYS B 106 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165 removed outlier: 3.555A pdb=" N PHE B 164 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 281 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 176 508 hydrogen bonds defined for protein. 1458 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: 3.27 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3075 1.34 - 1.46: 2074 1.46 - 1.58: 5067 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 10310 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" CA ASN B 502 " pdb=" C ASN B 502 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.34e-02 5.57e+03 1.29e+01 ... (remaining 10305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 13452 1.86 - 3.72: 501 3.72 - 5.58: 61 5.58 - 7.43: 11 7.43 - 9.29: 9 Bond angle restraints: 14034 Sorted by residual: angle pdb=" N PHE A 195 " pdb=" CA PHE A 195 " pdb=" C PHE A 195 " ideal model delta sigma weight residual 109.81 116.74 -6.93 2.21e+00 2.05e-01 9.82e+00 angle pdb=" N PHE B 195 " pdb=" CA PHE B 195 " pdb=" C PHE B 195 " ideal model delta sigma weight residual 109.81 116.74 -6.93 2.21e+00 2.05e-01 9.82e+00 angle pdb=" N CYS A 570 " pdb=" CA CYS A 570 " pdb=" CB CYS A 570 " ideal model delta sigma weight residual 111.09 114.81 -3.72 1.24e+00 6.50e-01 9.02e+00 angle pdb=" N CYS B 570 " pdb=" CA CYS B 570 " pdb=" CB CYS B 570 " ideal model delta sigma weight residual 111.09 114.77 -3.68 1.24e+00 6.50e-01 8.80e+00 angle pdb=" C VAL B 95 " pdb=" N PRO B 96 " pdb=" CA PRO B 96 " ideal model delta sigma weight residual 127.00 134.10 -7.10 2.40e+00 1.74e-01 8.74e+00 ... (remaining 14029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 5731 23.47 - 46.94: 368 46.94 - 70.41: 67 70.41 - 93.88: 18 93.88 - 117.35: 66 Dihedral angle restraints: 6250 sinusoidal: 2506 harmonic: 3744 Sorted by residual: dihedral pdb=" CA PHE A 195 " pdb=" C PHE A 195 " pdb=" N PRO A 196 " pdb=" CA PRO A 196 " ideal model delta harmonic sigma weight residual 180.00 129.13 50.87 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA PHE B 195 " pdb=" C PHE B 195 " pdb=" N PRO B 196 " pdb=" CA PRO B 196 " ideal model delta harmonic sigma weight residual 180.00 129.20 50.80 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CB CYS A 197 " pdb=" SG CYS A 197 " pdb=" SG CYS A 256 " pdb=" CB CYS A 256 " ideal model delta sinusoidal sigma weight residual 93.00 157.03 -64.03 1 1.00e+01 1.00e-02 5.40e+01 ... (remaining 6247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1569 0.096 - 0.192: 95 0.192 - 0.288: 8 0.288 - 0.383: 0 0.383 - 0.479: 6 Chirality restraints: 1678 Sorted by residual: chirality pdb=" C1 NAG A 904 " pdb=" ND2 ASN A 123 " pdb=" C2 NAG A 904 " pdb=" O5 NAG A 904 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C1 NAG B 904 " pdb=" ND2 ASN B 123 " pdb=" C2 NAG B 904 " pdb=" O5 NAG B 904 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 27 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.45e+00 ... (remaining 1675 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 195 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO B 196 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 195 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A 196 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 747 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.52e+00 pdb=" N PRO B 748 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 748 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 748 " -0.036 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 134 2.60 - 3.18: 9179 3.18 - 3.75: 15293 3.75 - 4.33: 21142 4.33 - 4.90: 35244 Nonbonded interactions: 80992 Sorted by model distance: nonbonded pdb=" SG CYS B 490 " pdb=" SG CYS B 787 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 197 " pdb=" SG CYS B 256 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 117 " pdb=" SG CYS B 207 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS B 484 " pdb=" SG CYS B 570 " model vdw 2.036 3.760 nonbonded pdb=" OH TYR A 51 " pdb=" OH TYR A 144 " model vdw 2.196 3.040 ... (remaining 80987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.550 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 10310 Z= 0.533 Angle : 0.830 9.292 14034 Z= 0.443 Chirality : 0.058 0.479 1678 Planarity : 0.006 0.101 1756 Dihedral : 21.161 117.351 3814 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -2.24 (0.23), residues: 1258 helix: -0.64 (0.21), residues: 532 sheet: -1.86 (0.28), residues: 296 loop : -2.04 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 773 HIS 0.006 0.002 HIS A 275 PHE 0.037 0.003 PHE A 637 TYR 0.025 0.002 TYR A 173 ARG 0.003 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.208 Fit side-chains REVERT: A 721 ILE cc_start: 0.8995 (mp) cc_final: 0.8775 (mp) REVERT: B 297 MET cc_start: 0.7426 (mpp) cc_final: 0.7120 (mpp) REVERT: B 721 ILE cc_start: 0.8997 (mp) cc_final: 0.8773 (mp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2071 time to fit residues: 35.7322 Evaluate side-chains 93 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 145 GLN B 104 GLN B 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10310 Z= 0.274 Angle : 0.781 10.541 14034 Z= 0.369 Chirality : 0.051 0.348 1678 Planarity : 0.006 0.085 1756 Dihedral : 18.139 97.047 1658 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.95 % Allowed : 8.86 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.54 (0.23), residues: 1258 helix: 0.11 (0.22), residues: 550 sheet: -1.52 (0.28), residues: 300 loop : -1.99 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 773 HIS 0.011 0.002 HIS B 568 PHE 0.052 0.002 PHE A 633 TYR 0.023 0.002 TYR A 595 ARG 0.021 0.001 ARG B 688 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 1.313 Fit side-chains REVERT: A 583 MET cc_start: 0.8508 (mmm) cc_final: 0.8276 (mmm) REVERT: A 637 PHE cc_start: 0.8046 (m-80) cc_final: 0.7835 (m-10) REVERT: A 733 TYR cc_start: 0.7656 (t80) cc_final: 0.7443 (t80) REVERT: B 637 PHE cc_start: 0.8022 (m-80) cc_final: 0.7817 (m-10) REVERT: B 733 TYR cc_start: 0.7667 (t80) cc_final: 0.7460 (t80) outliers start: 10 outliers final: 4 residues processed: 107 average time/residue: 0.2190 time to fit residues: 34.2251 Evaluate side-chains 97 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10310 Z= 0.381 Angle : 0.785 12.346 14034 Z= 0.369 Chirality : 0.049 0.305 1678 Planarity : 0.005 0.095 1756 Dihedral : 13.339 88.603 1658 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.05 % Allowed : 13.14 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.35 (0.23), residues: 1258 helix: 0.21 (0.21), residues: 564 sheet: -1.37 (0.28), residues: 300 loop : -1.92 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 773 HIS 0.008 0.002 HIS B 641 PHE 0.047 0.002 PHE B 633 TYR 0.021 0.002 TYR A 173 ARG 0.003 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.395 Fit side-chains REVERT: A 726 LEU cc_start: 0.9204 (tp) cc_final: 0.8892 (mm) REVERT: A 733 TYR cc_start: 0.7590 (t80) cc_final: 0.7362 (t80) REVERT: B 726 LEU cc_start: 0.9188 (tp) cc_final: 0.8864 (mm) REVERT: B 733 TYR cc_start: 0.7586 (t80) cc_final: 0.7367 (t80) outliers start: 11 outliers final: 10 residues processed: 107 average time/residue: 0.2322 time to fit residues: 36.3353 Evaluate side-chains 113 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 9.9990 chunk 86 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10310 Z= 0.380 Angle : 0.744 12.063 14034 Z= 0.357 Chirality : 0.047 0.281 1678 Planarity : 0.005 0.090 1756 Dihedral : 10.712 84.015 1658 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.00 % Allowed : 14.48 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.22 (0.23), residues: 1258 helix: 0.32 (0.21), residues: 564 sheet: -1.31 (0.29), residues: 300 loop : -1.87 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 773 HIS 0.007 0.002 HIS B 641 PHE 0.046 0.002 PHE A 633 TYR 0.021 0.002 TYR A 173 ARG 0.003 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.200 Fit side-chains REVERT: A 94 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7582 (pp30) REVERT: A 297 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7311 (mpp) REVERT: A 689 MET cc_start: 0.7624 (mpp) cc_final: 0.7358 (pmm) REVERT: A 721 ILE cc_start: 0.8578 (mp) cc_final: 0.8089 (tp) REVERT: A 726 LEU cc_start: 0.9171 (tp) cc_final: 0.8859 (mm) REVERT: A 733 TYR cc_start: 0.7642 (t80) cc_final: 0.7423 (t80) REVERT: B 94 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7503 (pp30) REVERT: B 689 MET cc_start: 0.7646 (mpp) cc_final: 0.7168 (pmm) REVERT: B 721 ILE cc_start: 0.8648 (mp) cc_final: 0.8155 (tp) REVERT: B 726 LEU cc_start: 0.9183 (tp) cc_final: 0.8865 (mm) REVERT: B 733 TYR cc_start: 0.7638 (t80) cc_final: 0.7414 (t80) outliers start: 21 outliers final: 13 residues processed: 114 average time/residue: 0.2042 time to fit residues: 34.3473 Evaluate side-chains 118 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 109 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10310 Z= 0.219 Angle : 0.650 10.567 14034 Z= 0.311 Chirality : 0.045 0.303 1678 Planarity : 0.005 0.086 1756 Dihedral : 9.892 83.720 1658 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.00 % Allowed : 16.00 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.89 (0.24), residues: 1258 helix: 0.66 (0.21), residues: 564 sheet: -1.16 (0.29), residues: 296 loop : -1.82 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 773 HIS 0.004 0.001 HIS B 568 PHE 0.029 0.001 PHE B 633 TYR 0.017 0.001 TYR B 486 ARG 0.001 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7516 (pp30) REVERT: A 721 ILE cc_start: 0.8646 (mp) cc_final: 0.8175 (tp) REVERT: A 726 LEU cc_start: 0.9173 (tp) cc_final: 0.8867 (mm) REVERT: A 733 TYR cc_start: 0.7650 (t80) cc_final: 0.7404 (t80) REVERT: B 94 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7523 (pp30) REVERT: B 689 MET cc_start: 0.7544 (mpp) cc_final: 0.7074 (pmm) REVERT: B 721 ILE cc_start: 0.8652 (mp) cc_final: 0.8178 (tp) REVERT: B 726 LEU cc_start: 0.9169 (tp) cc_final: 0.8859 (mm) REVERT: B 733 TYR cc_start: 0.7619 (t80) cc_final: 0.7337 (t80) outliers start: 21 outliers final: 15 residues processed: 121 average time/residue: 0.2104 time to fit residues: 37.2333 Evaluate side-chains 123 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10310 Z= 0.268 Angle : 0.666 14.663 14034 Z= 0.318 Chirality : 0.045 0.306 1678 Planarity : 0.005 0.088 1756 Dihedral : 9.528 83.768 1658 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.76 % Allowed : 16.57 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.69 (0.24), residues: 1258 helix: 0.79 (0.21), residues: 570 sheet: -0.99 (0.29), residues: 296 loop : -1.75 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 773 HIS 0.005 0.001 HIS B 568 PHE 0.047 0.002 PHE A 633 TYR 0.018 0.001 TYR A 173 ARG 0.002 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7507 (pp30) REVERT: A 721 ILE cc_start: 0.8628 (mp) cc_final: 0.8169 (tp) REVERT: A 726 LEU cc_start: 0.9149 (tp) cc_final: 0.8872 (mm) REVERT: A 733 TYR cc_start: 0.7633 (t80) cc_final: 0.7362 (t80) REVERT: B 94 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7500 (pp30) REVERT: B 721 ILE cc_start: 0.8630 (mp) cc_final: 0.8182 (tp) REVERT: B 726 LEU cc_start: 0.9144 (tp) cc_final: 0.8861 (mm) REVERT: B 733 TYR cc_start: 0.7603 (t80) cc_final: 0.7312 (t80) outliers start: 29 outliers final: 19 residues processed: 126 average time/residue: 0.2186 time to fit residues: 40.5237 Evaluate side-chains 129 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10310 Z= 0.283 Angle : 0.665 13.965 14034 Z= 0.316 Chirality : 0.045 0.296 1678 Planarity : 0.005 0.086 1756 Dihedral : 9.318 82.972 1658 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.57 % Allowed : 17.62 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.58 (0.24), residues: 1258 helix: 0.86 (0.21), residues: 572 sheet: -0.90 (0.29), residues: 296 loop : -1.73 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 799 HIS 0.004 0.001 HIS B 568 PHE 0.042 0.002 PHE A 633 TYR 0.020 0.002 TYR A 308 ARG 0.003 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7508 (pp30) REVERT: A 466 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7758 (mm-40) REVERT: A 721 ILE cc_start: 0.8624 (mp) cc_final: 0.8211 (tp) REVERT: A 726 LEU cc_start: 0.9147 (tp) cc_final: 0.8856 (mm) REVERT: A 733 TYR cc_start: 0.7640 (t80) cc_final: 0.7365 (t80) REVERT: B 94 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7544 (pp30) REVERT: B 466 GLN cc_start: 0.8453 (mm110) cc_final: 0.7951 (mm-40) REVERT: B 721 ILE cc_start: 0.8628 (mp) cc_final: 0.8212 (tp) REVERT: B 726 LEU cc_start: 0.9145 (tp) cc_final: 0.8849 (mm) REVERT: B 733 TYR cc_start: 0.7573 (t80) cc_final: 0.7282 (t80) outliers start: 27 outliers final: 19 residues processed: 127 average time/residue: 0.2121 time to fit residues: 39.3547 Evaluate side-chains 134 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10310 Z= 0.189 Angle : 0.621 13.648 14034 Z= 0.294 Chirality : 0.044 0.290 1678 Planarity : 0.004 0.083 1756 Dihedral : 8.876 81.355 1658 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.10 % Allowed : 19.05 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.38 (0.24), residues: 1258 helix: 1.04 (0.22), residues: 574 sheet: -0.75 (0.30), residues: 296 loop : -1.71 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 700 HIS 0.003 0.001 HIS B 641 PHE 0.045 0.002 PHE B 633 TYR 0.016 0.001 TYR B 486 ARG 0.001 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7517 (pp30) REVERT: A 215 ASN cc_start: 0.7658 (m110) cc_final: 0.7438 (m-40) REVERT: A 466 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7636 (mm-40) REVERT: A 721 ILE cc_start: 0.8603 (mp) cc_final: 0.8208 (tp) REVERT: A 726 LEU cc_start: 0.9085 (tp) cc_final: 0.8779 (mm) REVERT: A 733 TYR cc_start: 0.7611 (t80) cc_final: 0.7390 (t80) REVERT: B 94 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7515 (pp30) REVERT: B 215 ASN cc_start: 0.7614 (m110) cc_final: 0.7413 (m-40) REVERT: B 466 GLN cc_start: 0.8398 (mm110) cc_final: 0.7933 (mm-40) REVERT: B 721 ILE cc_start: 0.8616 (mp) cc_final: 0.8211 (tp) REVERT: B 726 LEU cc_start: 0.9081 (tp) cc_final: 0.8770 (mm) REVERT: B 733 TYR cc_start: 0.7575 (t80) cc_final: 0.7346 (t80) outliers start: 22 outliers final: 17 residues processed: 134 average time/residue: 0.2034 time to fit residues: 40.0224 Evaluate side-chains 136 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10310 Z= 0.345 Angle : 0.677 13.371 14034 Z= 0.326 Chirality : 0.046 0.296 1678 Planarity : 0.005 0.090 1756 Dihedral : 9.000 81.308 1658 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.48 % Allowed : 19.14 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.46 (0.24), residues: 1258 helix: 0.92 (0.22), residues: 572 sheet: -0.76 (0.30), residues: 296 loop : -1.68 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 759 HIS 0.004 0.001 HIS A 275 PHE 0.049 0.002 PHE B 633 TYR 0.022 0.002 TYR A 173 ARG 0.003 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7555 (pp30) REVERT: A 466 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7664 (mm-40) REVERT: A 726 LEU cc_start: 0.9151 (tp) cc_final: 0.8843 (mm) REVERT: A 733 TYR cc_start: 0.7593 (t80) cc_final: 0.7213 (t80) REVERT: B 94 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7548 (pp30) REVERT: B 128 GLN cc_start: 0.7875 (mt0) cc_final: 0.7541 (mt0) REVERT: B 466 GLN cc_start: 0.8423 (mm110) cc_final: 0.7954 (mm-40) REVERT: B 726 LEU cc_start: 0.9150 (tp) cc_final: 0.8837 (mm) outliers start: 26 outliers final: 22 residues processed: 130 average time/residue: 0.2086 time to fit residues: 39.4179 Evaluate side-chains 139 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10310 Z= 0.197 Angle : 0.633 13.415 14034 Z= 0.301 Chirality : 0.044 0.286 1678 Planarity : 0.005 0.080 1756 Dihedral : 8.669 79.494 1658 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.71 % Allowed : 20.10 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.32 (0.24), residues: 1258 helix: 1.03 (0.22), residues: 574 sheet: -0.68 (0.30), residues: 296 loop : -1.63 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 700 HIS 0.003 0.001 HIS B 568 PHE 0.046 0.002 PHE B 633 TYR 0.023 0.001 TYR B 733 ARG 0.001 0.000 ARG B 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7519 (pp30) REVERT: A 215 ASN cc_start: 0.7635 (m110) cc_final: 0.7425 (m-40) REVERT: A 466 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7645 (mm-40) REVERT: A 721 ILE cc_start: 0.8291 (mp) cc_final: 0.8027 (tp) REVERT: A 726 LEU cc_start: 0.9126 (tp) cc_final: 0.8799 (mm) REVERT: B 94 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7519 (pp30) REVERT: B 215 ASN cc_start: 0.7616 (m110) cc_final: 0.7407 (m-40) REVERT: B 466 GLN cc_start: 0.8393 (mm110) cc_final: 0.7919 (mm-40) REVERT: B 721 ILE cc_start: 0.8298 (mp) cc_final: 0.8027 (tp) REVERT: B 726 LEU cc_start: 0.9121 (tp) cc_final: 0.8789 (mm) outliers start: 18 outliers final: 13 residues processed: 127 average time/residue: 0.2396 time to fit residues: 44.1585 Evaluate side-chains 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 776 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 14 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.0000 chunk 41 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.4286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** 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 = 0.3957 r_free = 0.3957 target = 0.130487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090138 restraints weight = 17994.517| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.94 r_work: 0.3205 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10310 Z= 0.156 Angle : 0.605 13.221 14034 Z= 0.289 Chirality : 0.044 0.278 1678 Planarity : 0.004 0.086 1756 Dihedral : 8.231 77.502 1658 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.43 % Allowed : 20.29 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.02 (0.24), residues: 1258 helix: 1.33 (0.22), residues: 562 sheet: -0.51 (0.30), residues: 296 loop : -1.50 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 634 HIS 0.002 0.001 HIS B 568 PHE 0.043 0.002 PHE B 633 TYR 0.017 0.001 TYR B 733 ARG 0.003 0.000 ARG A 598 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1953.71 seconds wall clock time: 36 minutes 59.17 seconds (2219.17 seconds total)