Starting phenix.real_space_refine on Thu Jul 2 20:29:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y69_33638/07_2026/7y69_33638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y69_33638/07_2026/7y69_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7y69_33638/07_2026/7y69_33638.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y69_33638/07_2026/7y69_33638.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y69_33638/07_2026/7y69_33638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y69_33638/07_2026/7y69_33638.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y69_33638/07_2026/7y69_33638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y69_33638/07_2026/7y69_33638.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.070 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'PHE:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 4, 'ARG:plan': 3, 'GLU:plan': 1} 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 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 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 chiralities: 3 Restraints were copied for chains: B, E, F Time building chain proxies: 4.04, per 1000 atoms: 0.40 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=8, 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 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 570 " distance=2.04 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 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: 0.89 Conformation dependent library (CDL) restraints added in 256.3 milliseconds 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: 0.28 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: 1.86 Time building geometry restraints manager: 1.16 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 - 17.58: 5360 17.58 - 35.16: 496 35.16 - 52.73: 86 52.73 - 70.31: 18 70.31 - 87.89: 8 Dihedral angle restraints: 5968 sinusoidal: 2224 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 5965 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: 2.20 - 2.74: 1140 2.74 - 3.28: 10315 3.28 - 3.82: 16485 3.82 - 4.36: 19442 4.36 - 4.90: 33598 Nonbonded interactions: 80980 Sorted by model distance: nonbonded pdb=" OH TYR A 51 " pdb=" OH TYR A 144 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR B 51 " pdb=" OH TYR B 144 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR A 121 " pdb=" OE2 GLU A 126 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR B 121 " pdb=" OE2 GLU B 126 " model vdw 2.213 3.040 nonbonded pdb=" NZ LYS A 188 " pdb=" OG SER A 285 " model vdw 2.213 3.120 ... (remaining 80975 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: 0.02 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: 1.570 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.270 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.011 0.684 10337 Z= 0.439 Angle : 0.880 16.844 14092 Z= 0.453 Chirality : 0.058 0.479 1678 Planarity : 0.006 0.101 1756 Dihedral : 14.188 87.889 3520 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.003 0.000 ARG A 114 TYR 0.025 0.002 TYR A 173 PHE 0.037 0.003 PHE A 637 TRP 0.012 0.002 TRP A 773 HIS 0.006 0.002 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.37 (10310) covalent geometry : angle 0.83027 / 0.44 (14034) SS BOND : bond 0.00317 / 0.24 ( 8) SS BOND : angle 1.65013 / 0.94 ( 16) hydrogen bonds : bond 0.15619 / 10.63 ( 508) hydrogen bonds : angle 6.89491 / 4.90 ( 1458) metal coordination : bond 0.32520 / 17.18 ( 5) link_BETA1-4 : bond 0.02299 / 1.38 ( 4) link_BETA1-4 : angle 7.51236 / 4.77 ( 12) link_NAG-ASN : bond 0.00725 / 0.55 ( 10) link_NAG-ASN : angle 4.18165 / 2.69 ( 30) *********************** 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 : 0.393 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: 0.0839 time to fit residues: 14.8332 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 : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 50.0000 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3932 r_free = 0.3932 target = 0.127660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087884 restraints weight = 18429.953| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.90 r_work: 0.3163 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10337 Z= 0.144 Angle : 0.715 13.573 14092 Z= 0.345 Chirality : 0.052 0.371 1678 Planarity : 0.005 0.082 1756 Dihedral : 5.563 46.675 1364 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.86 % Allowed : 8.00 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.24), residues: 1258 helix: 0.18 (0.22), residues: 552 sheet: -1.46 (0.28), residues: 292 loop : -1.75 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 688 TYR 0.022 0.002 TYR A 595 PHE 0.050 0.002 PHE A 633 TRP 0.009 0.001 TRP A 773 HIS 0.009 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (10310) covalent geometry : angle 0.68032 / 0.34 (14034) SS BOND : bond 0.00202 / 0.15 ( 8) SS BOND : angle 1.18583 / 0.65 ( 16) hydrogen bonds : bond 0.05061 / 3.49 ( 508) hydrogen bonds : angle 4.97938 / 3.51 ( 1458) metal coordination : bond 0.00686 / 0.37 ( 5) link_BETA1-4 : bond 0.01604 / 0.92 ( 4) link_BETA1-4 : angle 6.25317 / 3.89 ( 12) link_NAG-ASN : bond 0.00931 / 0.70 ( 10) link_NAG-ASN : angle 2.73086 / 1.88 ( 30) *********************** 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 121 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 733 TYR cc_start: 0.7593 (t80) cc_final: 0.7373 (t80) REVERT: A 751 CYS cc_start: 0.7599 (m) cc_final: 0.7298 (m) REVERT: B 583 MET cc_start: 0.8635 (mmm) cc_final: 0.8377 (mmm) REVERT: B 733 TYR cc_start: 0.7645 (t80) cc_final: 0.7416 (t80) REVERT: B 751 CYS cc_start: 0.7640 (m) cc_final: 0.7342 (m) outliers start: 9 outliers final: 4 residues processed: 114 average time/residue: 0.0909 time to fit residues: 15.4866 Evaluate side-chains 104 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 50.0000 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 699 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.127821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087580 restraints weight = 18533.210| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.94 r_work: 0.3156 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10337 Z= 0.154 Angle : 0.678 12.672 14092 Z= 0.326 Chirality : 0.050 0.390 1678 Planarity : 0.005 0.089 1756 Dihedral : 5.249 45.353 1364 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.05 % Allowed : 11.05 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1258 helix: 0.39 (0.21), residues: 556 sheet: -1.16 (0.29), residues: 296 loop : -1.77 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 100 TYR 0.017 0.001 TYR A 173 PHE 0.052 0.002 PHE A 633 TRP 0.006 0.001 TRP B 773 HIS 0.005 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (10310) covalent geometry : angle 0.64569 / 0.32 (14034) SS BOND : bond 0.00170 / 0.12 ( 8) SS BOND : angle 1.07874 / 0.61 ( 16) hydrogen bonds : bond 0.04596 / 3.16 ( 508) hydrogen bonds : angle 4.67365 / 3.28 ( 1458) metal coordination : bond 0.00307 / 0.24 ( 5) link_BETA1-4 : bond 0.01461 / 0.85 ( 4) link_BETA1-4 : angle 5.78994 / 3.59 ( 12) link_NAG-ASN : bond 0.00808 / 0.60 ( 10) link_NAG-ASN : angle 2.66887 / 1.84 ( 30) *********************** 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 119 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.376 Fit side-chains REVERT: A 726 LEU cc_start: 0.9106 (tp) cc_final: 0.8761 (mm) REVERT: A 733 TYR cc_start: 0.7503 (t80) cc_final: 0.7239 (t80) REVERT: B 583 MET cc_start: 0.8597 (mmm) cc_final: 0.8316 (mmm) REVERT: B 689 MET cc_start: 0.7957 (mpp) cc_final: 0.7717 (pmm) REVERT: B 726 LEU cc_start: 0.9110 (tp) cc_final: 0.8752 (mm) REVERT: B 733 TYR cc_start: 0.7504 (t80) cc_final: 0.7230 (t80) outliers start: 11 outliers final: 9 residues processed: 112 average time/residue: 0.0900 time to fit residues: 15.0019 Evaluate side-chains 111 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 B residue 166 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3915 r_free = 0.3915 target = 0.126872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.086923 restraints weight = 18465.111| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.88 r_work: 0.3143 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10337 Z= 0.193 Angle : 0.699 11.863 14092 Z= 0.335 Chirality : 0.051 0.408 1678 Planarity : 0.005 0.085 1756 Dihedral : 5.191 45.805 1364 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.90 % Allowed : 13.33 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.23), residues: 1258 helix: 0.57 (0.21), residues: 554 sheet: -1.02 (0.29), residues: 300 loop : -1.76 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.019 0.002 TYR A 173 PHE 0.047 0.002 PHE A 633 TRP 0.006 0.001 TRP A 773 HIS 0.011 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (10310) covalent geometry : angle 0.67007 / 0.33 (14034) SS BOND : bond 0.00176 / 0.13 ( 8) SS BOND : angle 1.13623 / 0.65 ( 16) hydrogen bonds : bond 0.04494 / 3.08 ( 508) hydrogen bonds : angle 4.62623 / 3.25 ( 1458) metal coordination : bond 0.00442 / 0.32 ( 5) link_BETA1-4 : bond 0.01400 / 0.82 ( 4) link_BETA1-4 : angle 5.42405 / 3.36 ( 12) link_NAG-ASN : bond 0.00710 / 0.52 ( 10) link_NAG-ASN : angle 2.64915 / 1.81 ( 30) *********************** 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 130 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.478 Fit side-chains REVERT: A 94 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7694 (pp30) REVERT: A 721 ILE cc_start: 0.8634 (mp) cc_final: 0.8193 (tp) REVERT: A 726 LEU cc_start: 0.9119 (tp) cc_final: 0.8774 (mm) REVERT: B 94 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7726 (pp30) REVERT: B 689 MET cc_start: 0.7988 (mpp) cc_final: 0.7714 (pmm) REVERT: B 721 ILE cc_start: 0.8650 (mp) cc_final: 0.8215 (tp) REVERT: B 726 LEU cc_start: 0.9116 (tp) cc_final: 0.8772 (mm) REVERT: B 733 TYR cc_start: 0.7553 (t80) cc_final: 0.7295 (t80) REVERT: B 775 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7525 (mmtt) outliers start: 20 outliers final: 12 residues processed: 116 average time/residue: 0.0906 time to fit residues: 15.8121 Evaluate side-chains 119 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 271 VAL 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 271 VAL 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 115 optimal weight: 0.6980 chunk 38 optimal weight: 0.0030 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3952 r_free = 0.3952 target = 0.129628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089347 restraints weight = 18356.277| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.94 r_work: 0.3173 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10337 Z= 0.116 Angle : 0.654 15.274 14092 Z= 0.308 Chirality : 0.049 0.358 1678 Planarity : 0.004 0.082 1756 Dihedral : 4.858 44.275 1364 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.81 % Allowed : 13.90 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1258 helix: 0.85 (0.22), residues: 564 sheet: -0.77 (0.29), residues: 296 loop : -1.65 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 100 TYR 0.014 0.001 TYR A 308 PHE 0.049 0.002 PHE A 633 TRP 0.004 0.001 TRP B 700 HIS 0.004 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (10310) covalent geometry : angle 0.62564 / 0.30 (14034) SS BOND : bond 0.00148 / 0.11 ( 8) SS BOND : angle 0.97080 / 0.54 ( 16) hydrogen bonds : bond 0.04050 / 2.77 ( 508) hydrogen bonds : angle 4.36000 / 3.05 ( 1458) metal coordination : bond 0.00134 / 0.10 ( 5) link_BETA1-4 : bond 0.01286 / 0.76 ( 4) link_BETA1-4 : angle 5.32154 / 3.30 ( 12) link_NAG-ASN : bond 0.00843 / 0.63 ( 10) link_NAG-ASN : angle 2.47787 / 1.72 ( 30) *********************** 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 139 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7624 (pp30) REVERT: A 215 ASN cc_start: 0.8025 (m110) cc_final: 0.7743 (m110) REVERT: A 595 TYR cc_start: 0.7567 (t80) cc_final: 0.7289 (t80) REVERT: A 721 ILE cc_start: 0.8668 (mp) cc_final: 0.8279 (tp) REVERT: A 726 LEU cc_start: 0.9114 (tp) cc_final: 0.8799 (mm) REVERT: A 751 CYS cc_start: 0.7376 (m) cc_final: 0.7063 (m) REVERT: B 94 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7681 (pp30) REVERT: B 466 GLN cc_start: 0.8710 (mm110) cc_final: 0.8080 (mm-40) REVERT: B 689 MET cc_start: 0.7974 (mpp) cc_final: 0.7716 (pmm) REVERT: B 721 ILE cc_start: 0.8662 (mp) cc_final: 0.8260 (tp) REVERT: B 726 LEU cc_start: 0.9106 (tp) cc_final: 0.8804 (mm) outliers start: 19 outliers final: 11 residues processed: 130 average time/residue: 0.0922 time to fit residues: 17.8823 Evaluate side-chains 125 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 776 THR 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 309 LEU Chi-restraints excluded: chain B residue 549 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 45 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 49 optimal weight: 0.0470 chunk 28 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.8094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3929 r_free = 0.3929 target = 0.128126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087545 restraints weight = 18381.556| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.92 r_work: 0.3153 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10337 Z= 0.171 Angle : 0.674 13.362 14092 Z= 0.317 Chirality : 0.050 0.392 1678 Planarity : 0.005 0.085 1756 Dihedral : 4.874 44.319 1364 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.10 % Allowed : 15.62 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1258 helix: 0.99 (0.22), residues: 562 sheet: -0.68 (0.30), residues: 300 loop : -1.60 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 114 TYR 0.019 0.001 TYR A 173 PHE 0.031 0.002 PHE B 633 TRP 0.004 0.001 TRP B 759 HIS 0.004 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (10310) covalent geometry : angle 0.64884 / 0.31 (14034) SS BOND : bond 0.00169 / 0.12 ( 8) SS BOND : angle 1.06968 / 0.62 ( 16) hydrogen bonds : bond 0.04080 / 2.76 ( 508) hydrogen bonds : angle 4.36765 / 3.05 ( 1458) metal coordination : bond 0.00388 / 0.30 ( 5) link_BETA1-4 : bond 0.01242 / 0.73 ( 4) link_BETA1-4 : angle 4.92509 / 3.05 ( 12) link_NAG-ASN : bond 0.00673 / 0.50 ( 10) link_NAG-ASN : angle 2.51531 / 1.71 ( 30) *********************** 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: 22 poor density : 112 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7753 (pp30) REVERT: A 128 GLN cc_start: 0.8072 (mt0) cc_final: 0.7663 (mt0) REVERT: A 466 GLN cc_start: 0.8649 (mm-40) cc_final: 0.7991 (mm-40) REVERT: A 721 ILE cc_start: 0.8739 (mp) cc_final: 0.8370 (tp) REVERT: A 726 LEU cc_start: 0.9102 (tp) cc_final: 0.8799 (mm) REVERT: B 94 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7756 (pp30) REVERT: B 128 GLN cc_start: 0.8053 (mt0) cc_final: 0.7622 (mt0) REVERT: B 466 GLN cc_start: 0.8741 (mm110) cc_final: 0.8126 (mm-40) REVERT: B 689 MET cc_start: 0.8021 (mpp) cc_final: 0.7737 (pmm) REVERT: B 721 ILE cc_start: 0.8670 (mp) cc_final: 0.8291 (tp) REVERT: B 726 LEU cc_start: 0.9100 (tp) cc_final: 0.8791 (mm) outliers start: 22 outliers final: 15 residues processed: 122 average time/residue: 0.0936 time to fit residues: 16.9244 Evaluate side-chains 124 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 271 VAL 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 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 549 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 723 ILE 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 92 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.126108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.085772 restraints weight = 18455.366| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.90 r_work: 0.3103 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.006 0.041 10337 Z= 0.267 Angle : 0.735 12.090 14092 Z= 0.352 Chirality : 0.052 0.434 1678 Planarity : 0.005 0.089 1756 Dihedral : 5.185 46.554 1364 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.00 % Allowed : 15.62 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.24), residues: 1258 helix: 0.82 (0.22), residues: 572 sheet: -0.77 (0.30), residues: 304 loop : -1.70 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 114 TYR 0.023 0.002 TYR B 173 PHE 0.049 0.002 PHE A 633 TRP 0.007 0.001 TRP A 759 HIS 0.006 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.27 (10310) covalent geometry : angle 0.71255 / 0.35 (14034) SS BOND : bond 0.00200 / 0.14 ( 8) SS BOND : angle 1.30425 / 0.76 ( 16) hydrogen bonds : bond 0.04506 / 3.07 ( 508) hydrogen bonds : angle 4.58621 / 3.20 ( 1458) metal coordination : bond 0.00711 / 0.54 ( 5) link_BETA1-4 : bond 0.01204 / 0.71 ( 4) link_BETA1-4 : angle 4.69290 / 2.90 ( 12) link_NAG-ASN : bond 0.00554 / 0.41 ( 10) link_NAG-ASN : angle 2.55129 / 1.70 ( 30) *********************** 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 129 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7726 (pp30) REVERT: A 466 GLN cc_start: 0.8616 (mm-40) cc_final: 0.7928 (mm-40) REVERT: A 726 LEU cc_start: 0.9099 (tp) cc_final: 0.8781 (mm) REVERT: B 94 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7727 (pp30) REVERT: B 466 GLN cc_start: 0.8702 (mm110) cc_final: 0.8104 (mm-40) REVERT: B 689 MET cc_start: 0.8100 (mpp) cc_final: 0.7698 (pmm) REVERT: B 726 LEU cc_start: 0.9094 (tp) cc_final: 0.8771 (mm) outliers start: 21 outliers final: 16 residues processed: 118 average time/residue: 0.0952 time to fit residues: 16.7671 Evaluate side-chains 119 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 309 LEU Chi-restraints excluded: chain B residue 570 CYS 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 53 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 50.0000 chunk 114 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3930 r_free = 0.3930 target = 0.128435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088120 restraints weight = 18310.878| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.91 r_work: 0.3163 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10337 Z= 0.136 Angle : 0.654 11.996 14092 Z= 0.310 Chirality : 0.049 0.380 1678 Planarity : 0.004 0.080 1756 Dihedral : 4.923 45.462 1364 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.10 % Allowed : 16.29 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1258 helix: 1.02 (0.22), residues: 574 sheet: -0.59 (0.30), residues: 296 loop : -1.66 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.015 0.001 TYR B 173 PHE 0.027 0.002 PHE B 732 TRP 0.004 0.001 TRP A 634 HIS 0.012 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (10310) covalent geometry : angle 0.63016 / 0.30 (14034) SS BOND : bond 0.00141 / 0.10 ( 8) SS BOND : angle 0.99956 / 0.56 ( 16) hydrogen bonds : bond 0.04072 / 2.77 ( 508) hydrogen bonds : angle 4.33584 / 3.03 ( 1458) metal coordination : bond 0.00221 / 0.16 ( 5) link_BETA1-4 : bond 0.01200 / 0.71 ( 4) link_BETA1-4 : angle 4.78888 / 2.98 ( 12) link_NAG-ASN : bond 0.00700 / 0.52 ( 10) link_NAG-ASN : angle 2.31058 / 1.58 ( 30) *********************** 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 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7650 (pp30) REVERT: A 466 GLN cc_start: 0.8608 (mm-40) cc_final: 0.7915 (mm-40) REVERT: A 721 ILE cc_start: 0.8450 (mp) cc_final: 0.8202 (tp) REVERT: A 726 LEU cc_start: 0.9112 (tp) cc_final: 0.8783 (mm) REVERT: B 94 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7657 (pp30) REVERT: B 466 GLN cc_start: 0.8683 (mm110) cc_final: 0.8063 (mm-40) REVERT: B 582 PHE cc_start: 0.8819 (t80) cc_final: 0.8581 (t80) REVERT: B 689 MET cc_start: 0.7969 (mpp) cc_final: 0.7615 (pmm) REVERT: B 721 ILE cc_start: 0.8460 (mp) cc_final: 0.8212 (tp) REVERT: B 726 LEU cc_start: 0.9102 (tp) cc_final: 0.8774 (mm) outliers start: 22 outliers final: 14 residues processed: 122 average time/residue: 0.0954 time to fit residues: 17.2668 Evaluate side-chains 127 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 271 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 570 CYS 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 104 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.129497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088979 restraints weight = 18352.748| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.93 r_work: 0.3180 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10337 Z= 0.128 Angle : 0.641 11.952 14092 Z= 0.303 Chirality : 0.049 0.362 1678 Planarity : 0.004 0.084 1756 Dihedral : 4.730 43.760 1364 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.52 % Allowed : 16.86 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1258 helix: 1.25 (0.22), residues: 562 sheet: -0.44 (0.30), residues: 296 loop : -1.60 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.015 0.001 TYR A 173 PHE 0.026 0.002 PHE B 732 TRP 0.004 0.001 TRP B 700 HIS 0.008 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10310) covalent geometry : angle 0.61822 / 0.30 (14034) SS BOND : bond 0.00156 / 0.11 ( 8) SS BOND : angle 0.97347 / 0.56 ( 16) hydrogen bonds : bond 0.03864 / 2.62 ( 508) hydrogen bonds : angle 4.24160 / 2.97 ( 1458) metal coordination : bond 0.00199 / 0.14 ( 5) link_BETA1-4 : bond 0.01140 / 0.68 ( 4) link_BETA1-4 : angle 4.55469 / 2.83 ( 12) link_NAG-ASN : bond 0.00705 / 0.52 ( 10) link_NAG-ASN : angle 2.27083 / 1.55 ( 30) *********************** 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 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7716 (pp30) REVERT: A 466 GLN cc_start: 0.8624 (mm-40) cc_final: 0.7943 (mm-40) REVERT: A 595 TYR cc_start: 0.7568 (t80) cc_final: 0.7306 (t80) REVERT: A 721 ILE cc_start: 0.8452 (mp) cc_final: 0.8239 (tp) REVERT: A 726 LEU cc_start: 0.9104 (tp) cc_final: 0.8779 (mm) REVERT: A 750 LEU cc_start: 0.7549 (mt) cc_final: 0.7321 (mt) REVERT: B 94 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7711 (pp30) REVERT: B 466 GLN cc_start: 0.8618 (mm110) cc_final: 0.8026 (mm-40) REVERT: B 559 MET cc_start: 0.7905 (mmt) cc_final: 0.7630 (tpt) REVERT: B 582 PHE cc_start: 0.8804 (t80) cc_final: 0.8588 (t80) REVERT: B 595 TYR cc_start: 0.7608 (t80) cc_final: 0.7356 (t80) REVERT: B 689 MET cc_start: 0.7896 (mpp) cc_final: 0.7656 (pmm) REVERT: B 721 ILE cc_start: 0.8451 (mp) cc_final: 0.8235 (tp) REVERT: B 726 LEU cc_start: 0.9097 (tp) cc_final: 0.8772 (mm) REVERT: B 775 LYS cc_start: 0.7524 (mmtt) cc_final: 0.7147 (mtpp) outliers start: 16 outliers final: 10 residues processed: 120 average time/residue: 0.0878 time to fit residues: 15.8594 Evaluate side-chains 122 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 570 CYS Chi-restraints excluded: chain A residue 776 THR 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 549 LEU Chi-restraints excluded: chain B residue 570 CYS 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 93 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 86 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.128140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087678 restraints weight = 18100.726| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.89 r_work: 0.3156 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10337 Z= 0.178 Angle : 0.667 11.548 14092 Z= 0.317 Chirality : 0.050 0.387 1678 Planarity : 0.005 0.083 1756 Dihedral : 4.818 44.613 1364 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.24 % Allowed : 17.24 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1258 helix: 1.21 (0.22), residues: 562 sheet: -0.54 (0.30), residues: 300 loop : -1.57 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 114 TYR 0.019 0.002 TYR B 173 PHE 0.025 0.002 PHE A 633 TRP 0.005 0.001 TRP B 759 HIS 0.004 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (10310) covalent geometry : angle 0.64650 / 0.31 (14034) SS BOND : bond 0.00157 / 0.11 ( 8) SS BOND : angle 1.04280 / 0.60 ( 16) hydrogen bonds : bond 0.04017 / 2.72 ( 508) hydrogen bonds : angle 4.31540 / 3.02 ( 1458) metal coordination : bond 0.00400 / 0.30 ( 5) link_BETA1-4 : bond 0.01071 / 0.64 ( 4) link_BETA1-4 : angle 4.35755 / 2.70 ( 12) link_NAG-ASN : bond 0.00631 / 0.47 ( 10) link_NAG-ASN : angle 2.31548 / 1.56 ( 30) ********************** 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 128 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7705 (pp30) REVERT: A 128 GLN cc_start: 0.8088 (mt0) cc_final: 0.7664 (mt0) REVERT: A 466 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8045 (mm-40) REVERT: A 721 ILE cc_start: 0.8450 (mp) cc_final: 0.8238 (tp) REVERT: A 726 LEU cc_start: 0.9101 (tp) cc_final: 0.8775 (mm) REVERT: A 750 LEU cc_start: 0.7590 (mt) cc_final: 0.7344 (mt) REVERT: B 94 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7741 (pp30) REVERT: B 466 GLN cc_start: 0.8609 (mm110) cc_final: 0.8023 (mm-40) REVERT: B 582 PHE cc_start: 0.8800 (t80) cc_final: 0.8565 (t80) REVERT: B 595 TYR cc_start: 0.7668 (t80) cc_final: 0.7435 (t80) REVERT: B 689 MET cc_start: 0.7997 (mpp) cc_final: 0.7715 (pmm) REVERT: B 721 ILE cc_start: 0.8445 (mp) cc_final: 0.8232 (tp) REVERT: B 726 LEU cc_start: 0.9093 (tp) cc_final: 0.8768 (mm) REVERT: B 775 LYS cc_start: 0.7480 (mmtt) cc_final: 0.7130 (mtpp) outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.0879 time to fit residues: 15.8777 Evaluate side-chains 126 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 570 CYS 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 271 VAL Chi-restraints excluded: chain B residue 570 CYS 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 106 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 108 optimal weight: 40.0000 chunk 96 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.128965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088306 restraints weight = 18174.808| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.94 r_work: 0.3167 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10337 Z= 0.150 Angle : 0.660 11.434 14092 Z= 0.312 Chirality : 0.049 0.370 1678 Planarity : 0.004 0.082 1756 Dihedral : 4.772 44.330 1364 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.24 % Allowed : 17.33 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1258 helix: 1.24 (0.22), residues: 562 sheet: -0.42 (0.30), residues: 296 loop : -1.56 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.017 0.001 TYR B 173 PHE 0.024 0.002 PHE A 633 TRP 0.004 0.001 TRP A 700 HIS 0.003 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10310) covalent geometry : angle 0.63966 / 0.31 (14034) SS BOND : bond 0.00144 / 0.11 ( 8) SS BOND : angle 0.99316 / 0.57 ( 16) hydrogen bonds : bond 0.03946 / 2.68 ( 508) hydrogen bonds : angle 4.27664 / 2.99 ( 1458) metal coordination : bond 0.00296 / 0.21 ( 5) link_BETA1-4 : bond 0.01083 / 0.65 ( 4) link_BETA1-4 : angle 4.32598 / 2.69 ( 12) link_NAG-ASN : bond 0.00653 / 0.49 ( 10) link_NAG-ASN : angle 2.23991 / 1.51 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.51 seconds wall clock time: 40 minutes 52.20 seconds (2452.20 seconds total)