Starting phenix.real_space_refine on Fri Feb 14 11:31:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y69_33638/02_2025/7y69_33638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y69_33638/02_2025/7y69_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_33638/02_2025/7y69_33638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y69_33638/02_2025/7y69_33638.map" model { file = "/net/cci-nas-00/data/ceres_data/7y69_33638/02_2025/7y69_33638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y69_33638/02_2025/7y69_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 9.38, per 1000 atoms: 0.93 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: 3.01 Conformation dependent library (CDL) restraints added in 1.2 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: 1.25 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: 3.06 Time building geometry restraints manager: 3.41 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.880 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.070 ------------------------------------------------------------------------------- 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 : 1.143 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: 0.2017 time to fit residues: 34.7452 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 : 1.084 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.126530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.086657 restraints weight = 18331.536| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.89 r_work: 0.3142 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 1.096 Fit side-chains REVERT: A 583 MET cc_start: 0.8676 (mmm) cc_final: 0.8407 (mmm) REVERT: A 733 TYR cc_start: 0.7648 (t80) cc_final: 0.7421 (t80) REVERT: B 733 TYR cc_start: 0.7658 (t80) cc_final: 0.7436 (t80) outliers start: 10 outliers final: 4 residues processed: 107 average time/residue: 0.2110 time to fit residues: 32.8446 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 : 1.121 ------------------------------------------------------------------------------- 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 97 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.124536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.084642 restraints weight = 18661.902| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.87 r_work: 0.3098 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 10310 Z= 0.439 Angle : 0.818 12.398 14034 Z= 0.388 Chirality : 0.050 0.300 1678 Planarity : 0.006 0.098 1756 Dihedral : 13.282 88.880 1658 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.33 % Allowed : 13.43 % Favored : 85.24 % 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: -1.45 (0.23), residues: 1258 helix: 0.10 (0.21), residues: 564 sheet: -1.43 (0.28), residues: 300 loop : -1.93 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 773 HIS 0.010 0.002 HIS A 641 PHE 0.054 0.002 PHE A 633 TYR 0.023 0.002 TYR B 173 ARG 0.004 0.001 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 120 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.229 Fit side-chains REVERT: A 94 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7628 (pp30) REVERT: A 689 MET cc_start: 0.7936 (mpp) cc_final: 0.7673 (pmm) REVERT: A 726 LEU cc_start: 0.9154 (tp) cc_final: 0.8803 (mm) REVERT: B 94 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7662 (pp30) REVERT: B 689 MET cc_start: 0.7935 (mpp) cc_final: 0.7677 (pmm) REVERT: B 726 LEU cc_start: 0.9136 (tp) cc_final: 0.8776 (mm) outliers start: 14 outliers final: 10 residues processed: 112 average time/residue: 0.2049 time to fit residues: 33.8065 Evaluate side-chains 117 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 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 94 GLN 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 49 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.127109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086683 restraints weight = 18319.976| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.94 r_work: 0.3136 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10310 Z= 0.229 Angle : 0.679 11.432 14034 Z= 0.326 Chirality : 0.045 0.277 1678 Planarity : 0.005 0.083 1756 Dihedral : 10.425 83.260 1658 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.43 % Allowed : 15.05 % 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: -1.09 (0.23), residues: 1258 helix: 0.44 (0.21), residues: 564 sheet: -1.24 (0.29), residues: 296 loop : -1.83 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 773 HIS 0.012 0.001 HIS B 641 PHE 0.047 0.002 PHE B 633 TYR 0.017 0.002 TYR B 486 ARG 0.002 0.000 ARG B 785 *********************** 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 124 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 721 ILE cc_start: 0.8692 (mp) cc_final: 0.8262 (tp) REVERT: A 726 LEU cc_start: 0.9138 (tp) cc_final: 0.8807 (mm) REVERT: B 721 ILE cc_start: 0.8694 (mp) cc_final: 0.8264 (tp) REVERT: B 726 LEU cc_start: 0.9118 (tp) cc_final: 0.8777 (mm) outliers start: 15 outliers final: 11 residues processed: 113 average time/residue: 0.2066 time to fit residues: 34.3253 Evaluate side-chains 116 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.128395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087794 restraints weight = 18109.082| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.94 r_work: 0.3157 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2029 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= 0.195 Angle : 0.634 10.816 14034 Z= 0.301 Chirality : 0.044 0.309 1678 Planarity : 0.005 0.087 1756 Dihedral : 9.619 84.159 1658 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.29 % Allowed : 15.24 % Favored : 82.48 % 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: -0.64 (0.24), residues: 1258 helix: 0.87 (0.22), residues: 560 sheet: -0.96 (0.29), residues: 296 loop : -1.74 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 700 HIS 0.004 0.001 HIS B 568 PHE 0.027 0.001 PHE B 633 TYR 0.016 0.001 TYR B 486 ARG 0.001 0.000 ARG A 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 134 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7648 (pp30) REVERT: A 689 MET cc_start: 0.7850 (mpp) cc_final: 0.7269 (pmm) REVERT: A 721 ILE cc_start: 0.8691 (mp) cc_final: 0.8293 (tp) REVERT: A 726 LEU cc_start: 0.9112 (tp) cc_final: 0.8795 (mm) REVERT: B 94 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7678 (pp30) REVERT: B 689 MET cc_start: 0.7864 (mpp) cc_final: 0.7291 (pmm) REVERT: B 721 ILE cc_start: 0.8694 (mp) cc_final: 0.8290 (tp) REVERT: B 726 LEU cc_start: 0.9110 (tp) cc_final: 0.8794 (mm) outliers start: 24 outliers final: 14 residues processed: 122 average time/residue: 0.2049 time to fit residues: 36.6387 Evaluate side-chains 123 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 570 CYS Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 776 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 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 817 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** ** A 254 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** B 492 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.125885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085291 restraints weight = 18305.929| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.89 r_work: 0.3110 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10310 Z= 0.413 Angle : 0.721 13.899 14034 Z= 0.350 Chirality : 0.047 0.304 1678 Planarity : 0.005 0.090 1756 Dihedral : 9.656 84.188 1658 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.67 % Allowed : 16.00 % Favored : 81.33 % 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: -0.78 (0.24), residues: 1258 helix: 0.66 (0.22), residues: 570 sheet: -0.96 (0.29), residues: 300 loop : -1.78 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 759 HIS 0.005 0.002 HIS A 641 PHE 0.051 0.002 PHE A 633 TYR 0.023 0.002 TYR A 173 ARG 0.004 0.000 ARG B 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 134 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7730 (pp30) REVERT: A 466 GLN cc_start: 0.8717 (mm110) cc_final: 0.8324 (mm-40) REVERT: A 689 MET cc_start: 0.7693 (mpp) cc_final: 0.7101 (pmm) REVERT: A 721 ILE cc_start: 0.8718 (mp) cc_final: 0.8344 (tp) REVERT: A 726 LEU cc_start: 0.9101 (tp) cc_final: 0.8796 (mm) REVERT: B 94 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7730 (pp30) REVERT: B 689 MET cc_start: 0.7692 (mpp) cc_final: 0.7111 (pmm) REVERT: B 721 ILE cc_start: 0.8653 (mp) cc_final: 0.8264 (tp) REVERT: B 726 LEU cc_start: 0.9114 (tp) cc_final: 0.8807 (mm) outliers start: 28 outliers final: 16 residues processed: 121 average time/residue: 0.2060 time to fit residues: 36.8654 Evaluate side-chains 124 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 18 optimal weight: 0.0170 chunk 11 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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** ** A 254 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 = 0.3941 r_free = 0.3941 target = 0.129114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.088529 restraints weight = 18257.634| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.93 r_work: 0.3157 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10310 Z= 0.162 Angle : 0.621 13.931 14034 Z= 0.295 Chirality : 0.044 0.291 1678 Planarity : 0.004 0.081 1756 Dihedral : 9.073 82.438 1658 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.90 % Allowed : 17.71 % Favored : 80.38 % 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: -0.45 (0.24), residues: 1258 helix: 0.96 (0.22), residues: 574 sheet: -0.81 (0.29), residues: 296 loop : -1.67 (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 0.047 0.002 PHE A 633 TYR 0.016 0.001 TYR B 486 ARG 0.001 0.000 ARG A 59 *********************** 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 141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7702 (pp30) REVERT: A 128 GLN cc_start: 0.8114 (mt0) cc_final: 0.7838 (mt0) REVERT: A 466 GLN cc_start: 0.8680 (mm110) cc_final: 0.8068 (mm-40) REVERT: A 721 ILE cc_start: 0.8668 (mp) cc_final: 0.8312 (tp) REVERT: A 726 LEU cc_start: 0.9100 (tp) cc_final: 0.8786 (mm) REVERT: B 94 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7692 (pp30) REVERT: B 128 GLN cc_start: 0.8109 (mt0) cc_final: 0.7835 (mt0) REVERT: B 466 GLN cc_start: 0.8734 (mm110) cc_final: 0.8135 (mm-40) REVERT: B 721 ILE cc_start: 0.8671 (mp) cc_final: 0.8314 (tp) REVERT: B 726 LEU cc_start: 0.9095 (tp) cc_final: 0.8780 (mm) outliers start: 20 outliers final: 15 residues processed: 130 average time/residue: 0.2193 time to fit residues: 42.0480 Evaluate side-chains 131 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 817 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 104 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** ** A 254 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 = 0.3902 r_free = 0.3902 target = 0.126297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085658 restraints weight = 18420.081| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.92 r_work: 0.3117 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2176 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= 0.373 Angle : 0.706 13.269 14034 Z= 0.339 Chirality : 0.047 0.299 1678 Planarity : 0.005 0.094 1756 Dihedral : 9.240 82.771 1658 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.38 % Allowed : 18.10 % Favored : 79.52 % 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: -0.56 (0.24), residues: 1258 helix: 0.82 (0.22), residues: 572 sheet: -0.81 (0.30), residues: 296 loop : -1.69 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 759 HIS 0.005 0.001 HIS B 568 PHE 0.052 0.002 PHE A 633 TYR 0.024 0.002 TYR A 173 ARG 0.004 0.000 ARG B 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 139 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7719 (pp30) REVERT: A 466 GLN cc_start: 0.8674 (mm110) cc_final: 0.8047 (mm-40) REVERT: A 726 LEU cc_start: 0.9093 (tp) cc_final: 0.8772 (mm) REVERT: B 94 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7715 (pp30) REVERT: B 466 GLN cc_start: 0.8738 (mm110) cc_final: 0.8148 (mm-40) REVERT: B 726 LEU cc_start: 0.9093 (tp) cc_final: 0.8766 (mm) outliers start: 25 outliers final: 19 residues processed: 125 average time/residue: 0.2065 time to fit residues: 38.0633 Evaluate side-chains 130 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 195 PHE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 309 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 817 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 86 optimal weight: 0.0470 chunk 47 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.8680 ------------------------------------------------------------------------------- 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** ** A 254 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 = 0.3937 r_free = 0.3937 target = 0.129085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088481 restraints weight = 18198.751| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.93 r_work: 0.3172 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10310 Z= 0.176 Angle : 0.645 13.347 14034 Z= 0.310 Chirality : 0.045 0.289 1678 Planarity : 0.004 0.078 1756 Dihedral : 8.817 80.614 1658 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.19 % Allowed : 18.48 % Favored : 79.33 % 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: -0.42 (0.24), residues: 1258 helix: 0.93 (0.21), residues: 574 sheet: -0.70 (0.30), residues: 296 loop : -1.65 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 700 HIS 0.005 0.001 HIS A 641 PHE 0.049 0.002 PHE B 633 TYR 0.022 0.001 TYR B 733 ARG 0.001 0.000 ARG A 105 *********************** 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: 23 poor density : 120 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7702 (pp30) REVERT: A 466 GLN cc_start: 0.8615 (mm110) cc_final: 0.8030 (mm-40) REVERT: A 721 ILE cc_start: 0.8423 (mp) cc_final: 0.8178 (tp) REVERT: A 726 LEU cc_start: 0.9102 (tp) cc_final: 0.8773 (mm) REVERT: B 94 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7684 (pp30) REVERT: B 466 GLN cc_start: 0.8717 (mm110) cc_final: 0.8106 (mm-40) REVERT: B 721 ILE cc_start: 0.8424 (mp) cc_final: 0.8178 (tp) REVERT: B 726 LEU cc_start: 0.9097 (tp) cc_final: 0.8760 (mm) outliers start: 23 outliers final: 14 residues processed: 130 average time/residue: 0.2032 time to fit residues: 38.7042 Evaluate side-chains 133 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 297 MET Chi-restraints excluded: chain A residue 309 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 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 817 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 88 optimal weight: 0.0770 chunk 107 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.130296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089616 restraints weight = 18221.690| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.97 r_work: 0.3193 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10310 Z= 0.164 Angle : 0.623 13.145 14034 Z= 0.299 Chirality : 0.044 0.281 1678 Planarity : 0.005 0.088 1756 Dihedral : 8.394 79.081 1658 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.62 % Allowed : 19.43 % Favored : 78.95 % 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: -0.14 (0.24), residues: 1258 helix: 1.20 (0.22), residues: 562 sheet: -0.52 (0.30), residues: 296 loop : -1.55 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 634 HIS 0.004 0.001 HIS A 641 PHE 0.049 0.002 PHE B 633 TYR 0.025 0.001 TYR A 733 ARG 0.002 0.000 ARG A 598 ********************** 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 137 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7716 (pp30) REVERT: A 466 GLN cc_start: 0.8572 (mm110) cc_final: 0.8069 (mm-40) REVERT: A 595 TYR cc_start: 0.7622 (t80) cc_final: 0.7366 (t80) REVERT: A 726 LEU cc_start: 0.9073 (tp) cc_final: 0.8743 (mm) REVERT: B 94 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7698 (pp30) REVERT: B 466 GLN cc_start: 0.8657 (mm110) cc_final: 0.8076 (mm-40) REVERT: B 595 TYR cc_start: 0.7655 (t80) cc_final: 0.7402 (t80) REVERT: B 726 LEU cc_start: 0.9081 (tp) cc_final: 0.8748 (mm) REVERT: B 795 ASP cc_start: 0.8048 (m-30) cc_final: 0.7841 (m-30) outliers start: 17 outliers final: 12 residues processed: 129 average time/residue: 0.1996 time to fit residues: 38.7412 Evaluate side-chains 126 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 297 MET 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 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 817 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 50.0000 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- 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 800 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 = 0.3893 r_free = 0.3893 target = 0.125613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085122 restraints weight = 18254.034| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.79 r_work: 0.3110 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 10310 Z= 0.507 Angle : 0.775 12.439 14034 Z= 0.384 Chirality : 0.049 0.296 1678 Planarity : 0.006 0.092 1756 Dihedral : 9.044 79.740 1658 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.52 % Allowed : 20.19 % 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: -0.71 (0.24), residues: 1258 helix: 0.61 (0.21), residues: 572 sheet: -0.81 (0.30), residues: 304 loop : -1.68 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 799 HIS 0.006 0.002 HIS B 641 PHE 0.050 0.003 PHE B 633 TYR 0.029 0.002 TYR A 173 ARG 0.005 0.001 ARG B 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.17 seconds wall clock time: 78 minutes 30.73 seconds (4710.73 seconds total)