Starting phenix.real_space_refine on Fri Jul 3 01:22:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dtv_30855/07_2026/7dtv_30855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtv_30855/07_2026/7dtv_30855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dtv_30855/07_2026/7dtv_30855.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dtv_30855/07_2026/7dtv_30855.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dtv_30855/07_2026/7dtv_30855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtv_30855/07_2026/7dtv_30855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dtv_30855/07_2026/7dtv_30855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtv_30855/07_2026/7dtv_30855.map" } resolution = 3.5 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= 0.003 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 Ca 4 9.91 5 S 46 5.16 5 C 7126 2.51 5 N 1940 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11276 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5495 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PTRANS': 29, 'TRANS': 749} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 750 Unresolved non-hydrogen angles: 965 Unresolved non-hydrogen dihedrals: 633 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 8, 'GLU:plan': 16, 'PHE:plan': 30, 'HIS:plan': 2, 'ARG:plan': 5, 'TYR:plan': 6, 'TRP:plan': 2, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 413 Chain: "B" Number of atoms: 5495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5495 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PTRANS': 29, 'TRANS': 749} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 750 Unresolved non-hydrogen angles: 965 Unresolved non-hydrogen dihedrals: 633 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 8, 'GLU:plan': 16, 'PHE:plan': 30, 'HIS:plan': 2, 'ARG:plan': 5, 'TYR:plan': 6, 'TRP:plan': 2, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 413 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: E, F Time building chain proxies: 2.92, per 1000 atoms: 0.26 Number of scatterers: 11276 At special positions: 0 Unit cell: (90.246, 94.302, 179.478, 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) Ca 4 19.99 S 46 16.00 O 2160 8.00 N 1940 7.00 C 7126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.14 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.20 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.02 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.02 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.14 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.20 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.02 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.02 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " 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 D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " NAG-ASN " NAG A1104 " - " ASN A 261 " " NAG A1105 " - " ASN A 287 " " NAG A1106 " - " ASN A 446 " " NAG A1107 " - " ASN A 468 " " NAG B1103 " - " ASN B 261 " " NAG B1104 " - " ASN B 287 " " NAG B1105 " - " ASN B 446 " " NAG B1106 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 613.6 milliseconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2932 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 18 sheets defined 41.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.524A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.648A pdb=" N ALA A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.526A pdb=" N SER A 175 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.728A pdb=" N ALA A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.728A pdb=" N GLU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.516A pdb=" N GLU A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.721A pdb=" N LYS A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.672A pdb=" N ASN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 433 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.597A pdb=" N VAL A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.617A pdb=" N PHE A 533 " --> pdb=" O TRP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 637 removed outlier: 3.537A pdb=" N VAL A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 removed outlier: 4.534A pdb=" N LEU A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 681 through 691 removed outlier: 4.320A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 731 through 746 removed outlier: 4.839A pdb=" N TYR A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 802 through 827 removed outlier: 4.252A pdb=" N ILE A 822 " --> pdb=" O TRP A 818 " (cutoff:3.500A) Proline residue: A 823 - end of helix Processing helix chain 'A' and resid 830 through 835 removed outlier: 3.849A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 835' Processing helix chain 'A' and resid 836 through 851 removed outlier: 3.543A pdb=" N GLY A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 858 Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.524A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.648A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.526A pdb=" N SER B 175 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.727A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 230 removed outlier: 3.728A pdb=" N GLU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.517A pdb=" N GLU B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.722A pdb=" N LYS B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.672A pdb=" N ASN B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 433 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.598A pdb=" N VAL B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.617A pdb=" N PHE B 533 " --> pdb=" O TRP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 637 removed outlier: 3.537A pdb=" N VAL B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 664 removed outlier: 4.534A pdb=" N LEU B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 681 through 691 removed outlier: 4.321A pdb=" N SER B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 727 through 730 Processing helix chain 'B' and resid 731 through 746 removed outlier: 4.839A pdb=" N TYR B 744 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 780 Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 802 through 827 removed outlier: 4.252A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 830 through 835 removed outlier: 3.849A pdb=" N SER B 834 " --> pdb=" O GLY B 830 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 830 through 835' Processing helix chain 'B' and resid 836 through 851 removed outlier: 3.543A pdb=" N GLY B 847 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 849 " --> pdb=" O SER B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 858 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.256A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.331A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.727A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 243 removed outlier: 7.822A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.541A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 495 Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.664A pdb=" N PHE A 522 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AA9, first strand: chain 'A' and resid 589 through 590 removed outlier: 3.815A pdb=" N ALA A 600 " --> pdb=" O TRP A 590 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.256A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.331A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.727A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 237 through 243 removed outlier: 7.822A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.541A pdb=" N PHE B 469 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 492 through 495 Processing sheet with id=AB7, first strand: chain 'B' and resid 509 through 511 removed outlier: 3.664A pdb=" N PHE B 522 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AB9, first strand: chain 'B' and resid 589 through 590 removed outlier: 3.815A pdb=" N ALA B 600 " --> pdb=" O TRP B 590 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1134 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: 1.77 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3683 1.34 - 1.46: 2278 1.46 - 1.58: 5489 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 11504 Sorted by residual: bond pdb=" C1 NAG B1105 " pdb=" O5 NAG B1105 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C1 NAG A1106 " pdb=" O5 NAG A1106 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C1 NAG A1104 " pdb=" O5 NAG A1104 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" C1 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" C1 NAG D 3 " pdb=" O5 NAG D 3 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.04e+00 ... (remaining 11499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 15000 2.02 - 4.05: 596 4.05 - 6.07: 74 6.07 - 8.10: 22 8.10 - 10.12: 12 Bond angle restraints: 15704 Sorted by residual: angle pdb=" N ASP B 570 " pdb=" CA ASP B 570 " pdb=" C ASP B 570 " ideal model delta sigma weight residual 111.02 120.03 -9.01 1.25e+00 6.40e-01 5.19e+01 angle pdb=" N ASP A 570 " pdb=" CA ASP A 570 " pdb=" C ASP A 570 " ideal model delta sigma weight residual 111.02 120.01 -8.99 1.25e+00 6.40e-01 5.18e+01 angle pdb=" N PHE B 128 " pdb=" CA PHE B 128 " pdb=" C PHE B 128 " ideal model delta sigma weight residual 111.37 120.19 -8.82 1.64e+00 3.72e-01 2.89e+01 angle pdb=" N PHE A 128 " pdb=" CA PHE A 128 " pdb=" C PHE A 128 " ideal model delta sigma weight residual 111.37 120.17 -8.80 1.64e+00 3.72e-01 2.88e+01 angle pdb=" N GLU B 127 " pdb=" CA GLU B 127 " pdb=" C GLU B 127 " ideal model delta sigma weight residual 110.80 100.68 10.12 2.13e+00 2.20e-01 2.26e+01 ... (remaining 15699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5909 17.46 - 34.92: 597 34.92 - 52.38: 114 52.38 - 69.84: 26 69.84 - 87.30: 8 Dihedral angle restraints: 6654 sinusoidal: 2130 harmonic: 4524 Sorted by residual: dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -162.61 76.61 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual -86.00 -162.61 76.61 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 568 " pdb=" SG CYS A 568 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 157.37 -64.37 1 1.00e+01 1.00e-02 5.45e+01 ... (remaining 6651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 1838 0.256 - 0.511: 6 0.511 - 0.767: 0 0.767 - 1.023: 0 1.023 - 1.278: 2 Chirality restraints: 1846 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 488 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-01 2.50e+01 4.09e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 488 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-01 2.50e+01 4.08e+01 chirality pdb=" CA CYS A 765 " pdb=" N CYS A 765 " pdb=" C CYS A 765 " pdb=" CB CYS A 765 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1843 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 797 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.89e+00 pdb=" N PRO B 798 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 798 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 798 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 797 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 798 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 798 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 798 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 610 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.63e+00 pdb=" N PRO A 611 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.035 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 879 2.73 - 3.27: 10480 3.27 - 3.82: 17494 3.82 - 4.36: 20337 4.36 - 4.90: 35982 Nonbonded interactions: 85172 Sorted by model distance: nonbonded pdb=" OE2 GLU B 282 " pdb=" CD ARG B 286 " model vdw 2.189 3.440 nonbonded pdb=" OE2 GLU A 282 " pdb=" CD ARG A 286 " model vdw 2.189 3.440 nonbonded pdb=" O ALA A 144 " pdb=" OG SER A 150 " model vdw 2.207 3.040 nonbonded pdb=" O ALA B 144 " pdb=" OG SER B 150 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 218 " pdb=" OG SER B 296 " model vdw 2.215 3.040 ... (remaining 85167 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' and (resid 20 through 1102 or resid 1104 through 1106)) selection = (chain 'B' and (resid 20 through 1102 or resid 1104 through 1106)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.070 Find NCS groups from input model: 0.260 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.009 0.170 11540 Z= 0.380 Angle : 1.030 20.819 15794 Z= 0.553 Chirality : 0.074 1.278 1846 Planarity : 0.007 0.079 2046 Dihedral : 14.927 87.299 3668 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.79 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 17.58 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.17), residues: 1542 helix: -2.99 (0.15), residues: 604 sheet: -3.32 (0.35), residues: 158 loop : -3.15 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.013 0.002 TYR A 63 PHE 0.014 0.002 PHE A 539 TRP 0.015 0.002 TRP B 299 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.36 (11504) covalent geometry : angle 0.93718 / 0.53 (15704) SS BOND : bond 0.06664 / 3.05 ( 18) SS BOND : angle 5.38466 / 3.62 ( 36) hydrogen bonds : bond 0.12702 / 7.71 ( 390) hydrogen bonds : angle 5.92824 / 4.10 ( 1134) link_BETA1-4 : bond 0.00632 / 0.32 ( 6) link_BETA1-4 : angle 3.24464 / 1.77 ( 18) link_NAG-ASN : bond 0.00870 / 0.38 ( 12) link_NAG-ASN : angle 6.95978 / 4.65 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8954 (ttt) cc_final: 0.8717 (ttt) REVERT: B 74 MET cc_start: 0.8960 (ttt) cc_final: 0.8719 (ttt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1037 time to fit residues: 17.2045 Evaluate side-chains 80 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 30.0000 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 193 GLN A 466 HIS A 476 GLN B 72 GLN B 193 GLN B 466 HIS B 476 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.170800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139400 restraints weight = 15256.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137039 restraints weight = 22724.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.138006 restraints weight = 24142.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138758 restraints weight = 16279.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138955 restraints weight = 15495.614| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11540 Z= 0.169 Angle : 0.712 17.889 15794 Z= 0.347 Chirality : 0.054 0.698 1846 Planarity : 0.004 0.045 2046 Dihedral : 5.336 24.516 1642 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.69 % Allowed : 20.13 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.19), residues: 1542 helix: -1.58 (0.19), residues: 608 sheet: -2.90 (0.36), residues: 158 loop : -2.72 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.014 0.001 TYR A 510 PHE 0.011 0.001 PHE A 589 TRP 0.010 0.001 TRP B 352 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (11504) covalent geometry : angle 0.63213 / 0.33 (15704) SS BOND : bond 0.00374 / 0.20 ( 18) SS BOND : angle 1.95880 / 1.31 ( 36) hydrogen bonds : bond 0.03988 / 2.63 ( 390) hydrogen bonds : angle 4.73978 / 3.33 ( 1134) link_BETA1-4 : bond 0.00379 / 0.19 ( 6) link_BETA1-4 : angle 1.49858 / 0.82 ( 18) link_NAG-ASN : bond 0.01063 / 0.49 ( 12) link_NAG-ASN : angle 6.58599 / 4.47 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.308 Fit side-chains REVERT: A 282 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 307 MET cc_start: 0.8266 (mtp) cc_final: 0.7972 (mtt) REVERT: B 74 MET cc_start: 0.8891 (ttt) cc_final: 0.8589 (ttt) REVERT: B 282 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 307 MET cc_start: 0.8264 (mtp) cc_final: 0.7969 (mtt) outliers start: 16 outliers final: 12 residues processed: 101 average time/residue: 0.0858 time to fit residues: 13.3712 Evaluate side-chains 92 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 82 optimal weight: 0.2980 chunk 130 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 0.0570 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 GLN A 338 HIS A 524 ASN B 90 ASN B 253 GLN B 338 HIS B 524 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.172116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.144812 restraints weight = 15335.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.143531 restraints weight = 24501.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144517 restraints weight = 23140.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143320 restraints weight = 18554.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144031 restraints weight = 17025.355| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11540 Z= 0.145 Angle : 0.643 13.805 15794 Z= 0.315 Chirality : 0.047 0.297 1846 Planarity : 0.004 0.040 2046 Dihedral : 4.952 20.196 1642 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.39 % Allowed : 20.34 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.20), residues: 1542 helix: -0.84 (0.20), residues: 606 sheet: -2.56 (0.38), residues: 158 loop : -2.49 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 551 TYR 0.020 0.001 TYR B 510 PHE 0.009 0.001 PHE A 589 TRP 0.010 0.001 TRP A 352 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (11504) covalent geometry : angle 0.56477 / 0.30 (15704) SS BOND : bond 0.00247 / 0.14 ( 18) SS BOND : angle 1.32948 / 0.86 ( 36) hydrogen bonds : bond 0.03654 / 2.42 ( 390) hydrogen bonds : angle 4.35357 / 3.06 ( 1134) link_BETA1-4 : bond 0.01117 / 0.57 ( 6) link_BETA1-4 : angle 2.66006 / 1.42 ( 18) link_NAG-ASN : bond 0.00506 / 0.24 ( 12) link_NAG-ASN : angle 6.08502 / 4.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 22 residues processed: 112 average time/residue: 0.0880 time to fit residues: 15.4612 Evaluate side-chains 104 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 103 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.0060 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137376 restraints weight = 14805.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136348 restraints weight = 25165.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137428 restraints weight = 22852.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.136403 restraints weight = 17635.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137081 restraints weight = 16333.919| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11540 Z= 0.112 Angle : 0.561 10.002 15794 Z= 0.284 Chirality : 0.044 0.273 1846 Planarity : 0.003 0.039 2046 Dihedral : 4.497 17.855 1642 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.71 % Allowed : 19.70 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.21), residues: 1542 helix: -0.16 (0.21), residues: 594 sheet: -2.04 (0.44), residues: 130 loop : -2.29 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 286 TYR 0.018 0.001 TYR A 510 PHE 0.017 0.001 PHE A 846 TRP 0.009 0.001 TRP A 352 HIS 0.002 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11504) covalent geometry : angle 0.51896 / 0.27 (15704) SS BOND : bond 0.00259 / 0.14 ( 18) SS BOND : angle 1.14146 / 0.74 ( 36) hydrogen bonds : bond 0.03238 / 2.12 ( 390) hydrogen bonds : angle 4.15043 / 2.93 ( 1134) link_BETA1-4 : bond 0.00837 / 0.43 ( 6) link_BETA1-4 : angle 1.48105 / 0.80 ( 18) link_NAG-ASN : bond 0.00541 / 0.23 ( 12) link_NAG-ASN : angle 4.23682 / 3.03 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.482 Fit side-chains REVERT: A 307 MET cc_start: 0.8282 (mtp) cc_final: 0.7946 (mtt) REVERT: B 282 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 307 MET cc_start: 0.8286 (mtp) cc_final: 0.7945 (mtt) outliers start: 35 outliers final: 28 residues processed: 123 average time/residue: 0.0830 time to fit residues: 15.9756 Evaluate side-chains 111 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 HIS B 253 GLN B 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.157810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125150 restraints weight = 14989.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114210 restraints weight = 20110.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113254 restraints weight = 19914.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112705 restraints weight = 16889.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112978 restraints weight = 15889.236| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11540 Z= 0.302 Angle : 0.750 22.304 15794 Z= 0.363 Chirality : 0.053 0.603 1846 Planarity : 0.005 0.049 2046 Dihedral : 4.915 19.986 1642 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 4.77 % Allowed : 20.66 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.21), residues: 1542 helix: -0.27 (0.21), residues: 610 sheet: -2.44 (0.38), residues: 158 loop : -2.21 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 286 TYR 0.015 0.002 TYR A 63 PHE 0.011 0.002 PHE A 42 TRP 0.010 0.002 TRP A 675 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.30 (11504) covalent geometry : angle 0.66627 / 0.34 (15704) SS BOND : bond 0.00404 / 0.21 ( 18) SS BOND : angle 1.69005 / 1.12 ( 36) hydrogen bonds : bond 0.04247 / 2.77 ( 390) hydrogen bonds : angle 4.41703 / 3.12 ( 1134) link_BETA1-4 : bond 0.00589 / 0.30 ( 6) link_BETA1-4 : angle 1.99845 / 1.08 ( 18) link_NAG-ASN : bond 0.00552 / 0.27 ( 12) link_NAG-ASN : angle 6.93616 / 4.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 0.434 Fit side-chains REVERT: A 220 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8031 (ttm110) REVERT: A 307 MET cc_start: 0.8390 (mtp) cc_final: 0.7986 (mtt) REVERT: B 220 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7947 (ttm110) REVERT: B 307 MET cc_start: 0.8368 (mtp) cc_final: 0.7960 (mtt) outliers start: 45 outliers final: 38 residues processed: 115 average time/residue: 0.0858 time to fit residues: 15.5518 Evaluate side-chains 120 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 80 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 10 optimal weight: 0.0570 chunk 85 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 143 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134911 restraints weight = 14950.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133645 restraints weight = 27247.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134937 restraints weight = 23564.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134498 restraints weight = 16052.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134950 restraints weight = 16386.863| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11540 Z= 0.121 Angle : 0.632 18.129 15794 Z= 0.303 Chirality : 0.049 0.580 1846 Planarity : 0.003 0.031 2046 Dihedral : 4.434 20.284 1642 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.50 % Allowed : 21.19 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.70 (0.21), residues: 1542 helix: 0.30 (0.22), residues: 592 sheet: -2.02 (0.44), residues: 130 loop : -2.13 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 286 TYR 0.015 0.001 TYR A 510 PHE 0.008 0.001 PHE B 846 TRP 0.009 0.001 TRP B 352 HIS 0.002 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11504) covalent geometry : angle 0.55268 / 0.28 (15704) SS BOND : bond 0.00369 / 0.23 ( 18) SS BOND : angle 2.80632 / 1.76 ( 36) hydrogen bonds : bond 0.03249 / 2.13 ( 390) hydrogen bonds : angle 4.18627 / 2.96 ( 1134) link_BETA1-4 : bond 0.00422 / 0.21 ( 6) link_BETA1-4 : angle 1.35443 / 0.73 ( 18) link_NAG-ASN : bond 0.00818 / 0.42 ( 12) link_NAG-ASN : angle 5.77447 / 4.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8222 (mtm110) REVERT: A 307 MET cc_start: 0.8337 (mtp) cc_final: 0.7956 (mtt) REVERT: B 307 MET cc_start: 0.8296 (mtp) cc_final: 0.7908 (mtt) outliers start: 33 outliers final: 28 residues processed: 121 average time/residue: 0.0840 time to fit residues: 16.0877 Evaluate side-chains 122 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135931 restraints weight = 14921.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134743 restraints weight = 27628.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.135881 restraints weight = 23410.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135492 restraints weight = 15987.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136194 restraints weight = 16170.393| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11540 Z= 0.139 Angle : 0.605 17.804 15794 Z= 0.292 Chirality : 0.048 0.506 1846 Planarity : 0.003 0.030 2046 Dihedral : 4.285 19.997 1642 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.92 % Allowed : 20.76 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.50 (0.21), residues: 1542 helix: 0.51 (0.22), residues: 592 sheet: -1.97 (0.44), residues: 130 loop : -2.04 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.014 0.001 TYR A 435 PHE 0.008 0.001 PHE A 68 TRP 0.007 0.001 TRP A 352 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (11504) covalent geometry : angle 0.53792 / 0.28 (15704) SS BOND : bond 0.00278 / 0.15 ( 18) SS BOND : angle 1.84971 / 1.16 ( 36) hydrogen bonds : bond 0.03269 / 2.14 ( 390) hydrogen bonds : angle 4.10367 / 2.89 ( 1134) link_BETA1-4 : bond 0.00414 / 0.21 ( 6) link_BETA1-4 : angle 1.41919 / 0.77 ( 18) link_NAG-ASN : bond 0.00771 / 0.40 ( 12) link_NAG-ASN : angle 5.45795 / 3.75 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8143 (mtm110) REVERT: A 307 MET cc_start: 0.8370 (mtp) cc_final: 0.7973 (mtt) REVERT: B 220 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8105 (mtm110) REVERT: B 307 MET cc_start: 0.8346 (mtp) cc_final: 0.7942 (mtt) outliers start: 37 outliers final: 33 residues processed: 123 average time/residue: 0.0857 time to fit residues: 16.5556 Evaluate side-chains 128 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 85 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.162944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133717 restraints weight = 14810.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131543 restraints weight = 25128.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132344 restraints weight = 28427.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133447 restraints weight = 17757.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133567 restraints weight = 15502.541| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11540 Z= 0.129 Angle : 0.589 16.805 15794 Z= 0.285 Chirality : 0.048 0.481 1846 Planarity : 0.003 0.031 2046 Dihedral : 4.165 18.351 1642 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.03 % Allowed : 20.76 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.22), residues: 1542 helix: 0.81 (0.22), residues: 574 sheet: -1.92 (0.43), residues: 140 loop : -1.96 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.013 0.001 TYR A 510 PHE 0.010 0.001 PHE B 270 TRP 0.008 0.001 TRP A 208 HIS 0.002 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11504) covalent geometry : angle 0.53046 / 0.27 (15704) SS BOND : bond 0.00180 / 0.11 ( 18) SS BOND : angle 1.46398 / 0.93 ( 36) hydrogen bonds : bond 0.03172 / 2.08 ( 390) hydrogen bonds : angle 3.99714 / 2.82 ( 1134) link_BETA1-4 : bond 0.00460 / 0.24 ( 6) link_BETA1-4 : angle 1.32711 / 0.72 ( 18) link_NAG-ASN : bond 0.00773 / 0.39 ( 12) link_NAG-ASN : angle 5.14874 / 3.54 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8181 (mtm110) REVERT: A 307 MET cc_start: 0.8361 (mtp) cc_final: 0.7957 (mtt) REVERT: B 220 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8184 (mtm110) REVERT: B 307 MET cc_start: 0.8337 (mtp) cc_final: 0.7958 (mtt) outliers start: 38 outliers final: 34 residues processed: 124 average time/residue: 0.0724 time to fit residues: 14.4555 Evaluate side-chains 130 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 129 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.163601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140530 restraints weight = 14694.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139498 restraints weight = 25720.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132559 restraints weight = 27605.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128039 restraints weight = 26267.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128486 restraints weight = 27464.710| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11540 Z= 0.118 Angle : 0.568 16.341 15794 Z= 0.277 Chirality : 0.047 0.458 1846 Planarity : 0.003 0.030 2046 Dihedral : 4.039 19.046 1642 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.03 % Allowed : 20.66 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.12 (0.22), residues: 1542 helix: 0.98 (0.22), residues: 574 sheet: -1.71 (0.44), residues: 142 loop : -1.90 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.013 0.001 TYR B 510 PHE 0.006 0.001 PHE B 821 TRP 0.007 0.001 TRP A 208 HIS 0.003 0.000 HIS B 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (11504) covalent geometry : angle 0.51308 / 0.26 (15704) SS BOND : bond 0.00185 / 0.11 ( 18) SS BOND : angle 1.26280 / 0.80 ( 36) hydrogen bonds : bond 0.03068 / 2.01 ( 390) hydrogen bonds : angle 3.93232 / 2.78 ( 1134) link_BETA1-4 : bond 0.00444 / 0.22 ( 6) link_BETA1-4 : angle 1.33507 / 0.72 ( 18) link_NAG-ASN : bond 0.00792 / 0.41 ( 12) link_NAG-ASN : angle 4.94403 / 3.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8108 (mtm110) REVERT: A 307 MET cc_start: 0.8386 (mtp) cc_final: 0.7966 (mtt) REVERT: B 220 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8048 (mtm110) REVERT: B 307 MET cc_start: 0.8372 (mtp) cc_final: 0.7962 (mtt) outliers start: 38 outliers final: 34 residues processed: 125 average time/residue: 0.0812 time to fit residues: 16.0805 Evaluate side-chains 131 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 61 optimal weight: 0.0870 chunk 99 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 93 optimal weight: 0.4980 chunk 141 optimal weight: 20.0000 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134953 restraints weight = 14872.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133723 restraints weight = 28564.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134524 restraints weight = 27594.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134626 restraints weight = 18075.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135174 restraints weight = 16338.931| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11540 Z= 0.173 Angle : 0.600 16.963 15794 Z= 0.293 Chirality : 0.048 0.449 1846 Planarity : 0.003 0.029 2046 Dihedral : 4.152 17.281 1642 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.92 % Allowed : 20.66 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.22), residues: 1542 helix: 0.75 (0.22), residues: 592 sheet: -1.85 (0.43), residues: 140 loop : -1.92 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.012 0.001 TYR A 510 PHE 0.008 0.001 PHE A 68 TRP 0.008 0.001 TRP A 675 HIS 0.002 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (11504) covalent geometry : angle 0.54538 / 0.28 (15704) SS BOND : bond 0.00226 / 0.13 ( 18) SS BOND : angle 1.29199 / 0.83 ( 36) hydrogen bonds : bond 0.03374 / 2.21 ( 390) hydrogen bonds : angle 4.02294 / 2.85 ( 1134) link_BETA1-4 : bond 0.00468 / 0.24 ( 6) link_BETA1-4 : angle 1.37852 / 0.74 ( 18) link_NAG-ASN : bond 0.00716 / 0.36 ( 12) link_NAG-ASN : angle 5.03504 / 3.43 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8228 (mtm110) REVERT: A 307 MET cc_start: 0.8377 (mtp) cc_final: 0.7965 (mtt) REVERT: B 220 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8230 (mtm110) REVERT: B 307 MET cc_start: 0.8367 (mtp) cc_final: 0.7953 (mtt) outliers start: 37 outliers final: 35 residues processed: 121 average time/residue: 0.0802 time to fit residues: 15.0823 Evaluate side-chains 128 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.163176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135733 restraints weight = 14778.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134228 restraints weight = 27114.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135055 restraints weight = 28077.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134922 restraints weight = 17883.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135518 restraints weight = 16755.623| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11540 Z= 0.132 Angle : 0.574 16.282 15794 Z= 0.281 Chirality : 0.047 0.444 1846 Planarity : 0.003 0.030 2046 Dihedral : 4.063 18.819 1642 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.92 % Allowed : 20.76 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.16 (0.22), residues: 1542 helix: 0.84 (0.22), residues: 592 sheet: -1.82 (0.43), residues: 140 loop : -1.88 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 286 TYR 0.013 0.001 TYR A 510 PHE 0.011 0.001 PHE B 270 TRP 0.008 0.001 TRP A 208 HIS 0.002 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (11504) covalent geometry : angle 0.52148 / 0.27 (15704) SS BOND : bond 0.00196 / 0.12 ( 18) SS BOND : angle 1.19387 / 0.76 ( 36) hydrogen bonds : bond 0.03174 / 2.07 ( 390) hydrogen bonds : angle 3.97357 / 2.81 ( 1134) link_BETA1-4 : bond 0.00458 / 0.23 ( 6) link_BETA1-4 : angle 1.33877 / 0.72 ( 18) link_NAG-ASN : bond 0.00762 / 0.39 ( 12) link_NAG-ASN : angle 4.87505 / 3.33 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1571.15 seconds wall clock time: 27 minutes 57.81 seconds (1677.81 seconds total)