Starting phenix.real_space_refine on Wed Mar 4 06:02:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dtv_30855/03_2026/7dtv_30855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtv_30855/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7dtv_30855/03_2026/7dtv_30855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtv_30855/03_2026/7dtv_30855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dtv_30855/03_2026/7dtv_30855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtv_30855/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: E, F Time building chain proxies: 2.74, per 1000 atoms: 0.24 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: 0.92 Conformation dependent library (CDL) restraints added in 561.3 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: 0.37 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: 1.84 Time building geometry restraints manager: 1.27 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: 6219 17.46 - 34.92: 643 34.92 - 52.38: 130 52.38 - 69.84: 32 69.84 - 87.30: 8 Dihedral angle restraints: 7032 sinusoidal: 2508 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 7029 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: 2.420 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: 11.630 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 14.961 87.299 4046 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 covalent geometry : bond 0.00818 (11504) covalent geometry : angle 0.93718 (15704) SS BOND : bond 0.06664 ( 18) SS BOND : angle 5.38466 ( 36) hydrogen bonds : bond 0.12702 ( 390) hydrogen bonds : angle 5.92824 ( 1134) link_BETA1-4 : bond 0.00632 ( 6) link_BETA1-4 : angle 3.24464 ( 18) link_NAG-ASN : bond 0.00870 ( 12) link_NAG-ASN : angle 6.95978 ( 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 : 0.470 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: 0.1007 time to fit residues: 16.6456 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 : 0.414 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.170769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139579 restraints weight = 15251.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137979 restraints weight = 23318.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139012 restraints weight = 22052.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139517 restraints weight = 16010.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139808 restraints weight = 15769.356| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11540 Z= 0.168 Angle : 0.724 18.106 15794 Z= 0.350 Chirality : 0.055 0.766 1846 Planarity : 0.004 0.045 2046 Dihedral : 10.228 111.924 2020 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.69 % Allowed : 20.66 % Favored : 77.65 % 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: -3.43 (0.19), residues: 1542 helix: -1.59 (0.19), residues: 608 sheet: -2.92 (0.36), residues: 158 loop : -2.73 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 54 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 A 359 Details of bonding type rmsd covalent geometry : bond 0.00388 (11504) covalent geometry : angle 0.63499 (15704) SS BOND : bond 0.00323 ( 18) SS BOND : angle 1.88521 ( 36) hydrogen bonds : bond 0.04007 ( 390) hydrogen bonds : angle 4.73611 ( 1134) link_BETA1-4 : bond 0.00299 ( 6) link_BETA1-4 : angle 2.00429 ( 18) link_NAG-ASN : bond 0.00487 ( 12) link_NAG-ASN : angle 6.94363 ( 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 : 0.428 Fit side-chains REVERT: A 74 MET cc_start: 0.8896 (ttt) cc_final: 0.8601 (ttt) REVERT: A 282 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 307 MET cc_start: 0.8253 (mtp) cc_final: 0.7960 (mtt) REVERT: B 74 MET cc_start: 0.8887 (ttt) cc_final: 0.8586 (ttt) REVERT: B 282 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 307 MET cc_start: 0.8252 (mtp) cc_final: 0.7964 (mtt) outliers start: 16 outliers final: 12 residues processed: 101 average time/residue: 0.0872 time to fit residues: 13.4302 Evaluate side-chains 94 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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: 0.5980 chunk 130 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 524 ASN B 90 ASN B 253 GLN B 524 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135319 restraints weight = 15007.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120474 restraints weight = 22362.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119539 restraints weight = 28060.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120092 restraints weight = 26695.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120663 restraints weight = 22887.152| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11540 Z= 0.231 Angle : 0.694 13.874 15794 Z= 0.344 Chirality : 0.048 0.270 1846 Planarity : 0.005 0.042 2046 Dihedral : 9.684 112.970 2020 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.66 % Allowed : 19.60 % Favored : 75.74 % 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: -2.82 (0.20), residues: 1542 helix: -0.94 (0.20), residues: 608 sheet: -2.62 (0.38), residues: 158 loop : -2.50 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 286 TYR 0.020 0.002 TYR A 510 PHE 0.009 0.001 PHE B 68 TRP 0.010 0.001 TRP A 675 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00555 (11504) covalent geometry : angle 0.62179 (15704) SS BOND : bond 0.00311 ( 18) SS BOND : angle 1.53695 ( 36) hydrogen bonds : bond 0.04181 ( 390) hydrogen bonds : angle 4.49934 ( 1134) link_BETA1-4 : bond 0.01127 ( 6) link_BETA1-4 : angle 2.81713 ( 18) link_NAG-ASN : bond 0.00472 ( 12) link_NAG-ASN : angle 6.01389 ( 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 123 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 79 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8222 (mtm110) outliers start: 44 outliers final: 35 residues processed: 113 average time/residue: 0.0756 time to fit residues: 13.5453 Evaluate side-chains 110 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 292 ILE Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 359 HIS 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 524 ASN Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 762 PHE 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 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 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 524 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 762 PHE 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: 1.9990 chunk 129 optimal weight: 0.0970 chunk 73 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS B 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134547 restraints weight = 14894.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133357 restraints weight = 28035.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134259 restraints weight = 27905.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.134166 restraints weight = 18505.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134669 restraints weight = 16951.692| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11540 Z= 0.129 Angle : 0.602 10.352 15794 Z= 0.302 Chirality : 0.045 0.240 1846 Planarity : 0.003 0.033 2046 Dihedral : 9.066 110.102 2020 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.50 % Allowed : 20.97 % Favored : 75.53 % 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: -2.36 (0.21), residues: 1542 helix: -0.48 (0.21), residues: 606 sheet: -2.18 (0.44), residues: 130 loop : -2.37 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 551 TYR 0.018 0.001 TYR A 510 PHE 0.006 0.001 PHE A 68 TRP 0.009 0.001 TRP A 352 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00290 (11504) covalent geometry : angle 0.54911 (15704) SS BOND : bond 0.00312 ( 18) SS BOND : angle 1.62294 ( 36) hydrogen bonds : bond 0.03457 ( 390) hydrogen bonds : angle 4.28413 ( 1134) link_BETA1-4 : bond 0.00717 ( 6) link_BETA1-4 : angle 1.81411 ( 18) link_NAG-ASN : bond 0.00501 ( 12) link_NAG-ASN : angle 4.80970 ( 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 129 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.331 Fit side-chains REVERT: A 307 MET cc_start: 0.8257 (mtp) cc_final: 0.7968 (mtt) REVERT: B 216 ASP cc_start: 0.8185 (p0) cc_final: 0.7908 (p0) REVERT: B 220 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8175 (mtm110) REVERT: B 307 MET cc_start: 0.8256 (mtp) cc_final: 0.7977 (mtt) REVERT: B 488 ASN cc_start: 0.6395 (p0) cc_final: 0.6191 (p0) outliers start: 33 outliers final: 26 residues processed: 122 average time/residue: 0.0860 time to fit residues: 16.0453 Evaluate side-chains 113 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 0.8980 chunk 134 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 131 optimal weight: 0.1980 chunk 96 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS B 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.162879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139695 restraints weight = 14750.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138126 restraints weight = 26277.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137845 restraints weight = 27788.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136309 restraints weight = 22432.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137008 restraints weight = 21183.592| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11540 Z= 0.128 Angle : 0.559 9.573 15794 Z= 0.283 Chirality : 0.044 0.241 1846 Planarity : 0.004 0.048 2046 Dihedral : 8.747 109.769 2020 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.60 % Allowed : 21.08 % 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: -1.88 (0.21), residues: 1542 helix: 0.09 (0.21), residues: 592 sheet: -2.03 (0.45), residues: 130 loop : -2.20 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 286 TYR 0.016 0.001 TYR A 510 PHE 0.012 0.001 PHE A 846 TRP 0.008 0.001 TRP A 352 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00298 (11504) covalent geometry : angle 0.52405 (15704) SS BOND : bond 0.00216 ( 18) SS BOND : angle 1.20933 ( 36) hydrogen bonds : bond 0.03295 ( 390) hydrogen bonds : angle 4.11155 ( 1134) link_BETA1-4 : bond 0.00510 ( 6) link_BETA1-4 : angle 1.71965 ( 18) link_NAG-ASN : bond 0.00545 ( 12) link_NAG-ASN : angle 3.78886 ( 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 126 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.407 Fit side-chains REVERT: A 307 MET cc_start: 0.8316 (mtp) cc_final: 0.7934 (mtt) REVERT: B 220 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8060 (mtm110) REVERT: B 307 MET cc_start: 0.8323 (mtp) cc_final: 0.7951 (mtt) outliers start: 34 outliers final: 29 residues processed: 116 average time/residue: 0.0797 time to fit residues: 14.6988 Evaluate side-chains 114 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 292 ILE 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 409 ILE 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 10 optimal weight: 0.0010 chunk 85 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 143 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 524 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.162065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136902 restraints weight = 14981.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135665 restraints weight = 29208.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136554 restraints weight = 25330.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136176 restraints weight = 17708.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136389 restraints weight = 18963.191| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1991 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= 0.141 Angle : 0.617 22.765 15794 Z= 0.298 Chirality : 0.047 0.622 1846 Planarity : 0.003 0.032 2046 Dihedral : 8.874 109.938 2020 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.77 % Allowed : 19.60 % Favored : 75.64 % 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: -1.65 (0.21), residues: 1542 helix: 0.33 (0.22), residues: 594 sheet: -1.95 (0.45), residues: 130 loop : -2.11 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.015 0.001 TYR A 435 PHE 0.007 0.001 PHE B 68 TRP 0.007 0.001 TRP A 352 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00333 (11504) covalent geometry : angle 0.54274 (15704) SS BOND : bond 0.00214 ( 18) SS BOND : angle 2.41560 ( 36) hydrogen bonds : bond 0.03261 ( 390) hydrogen bonds : angle 4.09692 ( 1134) link_BETA1-4 : bond 0.00486 ( 6) link_BETA1-4 : angle 2.34693 ( 18) link_NAG-ASN : bond 0.00582 ( 12) link_NAG-ASN : angle 5.48238 ( 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 137 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8200 (p0) cc_final: 0.7825 (p0) REVERT: A 220 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8041 (mtm110) REVERT: A 307 MET cc_start: 0.8331 (mtp) cc_final: 0.7947 (mtt) REVERT: B 216 ASP cc_start: 0.8089 (p0) cc_final: 0.7705 (p0) REVERT: B 220 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8006 (mtm110) REVERT: B 307 MET cc_start: 0.8332 (mtp) cc_final: 0.7947 (mtt) outliers start: 45 outliers final: 37 residues processed: 128 average time/residue: 0.0805 time to fit residues: 16.0492 Evaluate side-chains 127 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 404 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 471 ASN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 524 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.160088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 133)---------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124611 restraints weight = 14972.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 98)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115665 restraints weight = 21309.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.115673 restraints weight = 21390.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115816 restraints weight = 17289.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115869 restraints weight = 16199.019| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11540 Z= 0.228 Angle : 0.640 19.160 15794 Z= 0.313 Chirality : 0.050 0.711 1846 Planarity : 0.004 0.030 2046 Dihedral : 8.882 110.598 2020 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 4.77 % Allowed : 20.02 % 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: -1.69 (0.22), residues: 1542 helix: 0.19 (0.22), residues: 610 sheet: -1.95 (0.45), residues: 130 loop : -2.09 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.014 0.001 TYR B 435 PHE 0.011 0.001 PHE B 846 TRP 0.007 0.001 TRP B 208 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00555 (11504) covalent geometry : angle 0.58320 (15704) SS BOND : bond 0.00253 ( 18) SS BOND : angle 1.82607 ( 36) hydrogen bonds : bond 0.03638 ( 390) hydrogen bonds : angle 4.22698 ( 1134) link_BETA1-4 : bond 0.00320 ( 6) link_BETA1-4 : angle 1.75260 ( 18) link_NAG-ASN : bond 0.00517 ( 12) link_NAG-ASN : angle 5.14709 ( 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 133 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8155 (mtm110) REVERT: A 307 MET cc_start: 0.8428 (mtp) cc_final: 0.8032 (mtt) REVERT: B 220 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8056 (mtm110) REVERT: B 307 MET cc_start: 0.8425 (mtp) cc_final: 0.8026 (mtt) outliers start: 45 outliers final: 42 residues processed: 124 average time/residue: 0.0830 time to fit residues: 16.1448 Evaluate side-chains 130 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 292 ILE 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 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 524 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 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 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 524 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 85 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.0000 chunk 74 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 524 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137742 restraints weight = 14805.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136606 restraints weight = 27888.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137411 restraints weight = 25783.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137236 restraints weight = 17672.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137225 restraints weight = 19855.465| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2076 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= 0.124 Angle : 0.584 17.556 15794 Z= 0.286 Chirality : 0.047 0.682 1846 Planarity : 0.003 0.032 2046 Dihedral : 8.715 110.779 2020 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.24 % Allowed : 20.87 % Favored : 74.89 % 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: -1.40 (0.22), residues: 1542 helix: 0.61 (0.22), residues: 582 sheet: -1.87 (0.44), residues: 130 loop : -1.98 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 286 TYR 0.014 0.001 TYR A 510 PHE 0.011 0.001 PHE B 846 TRP 0.008 0.001 TRP A 208 HIS 0.002 0.000 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00293 (11504) covalent geometry : angle 0.53222 (15704) SS BOND : bond 0.00175 ( 18) SS BOND : angle 1.40320 ( 36) hydrogen bonds : bond 0.03262 ( 390) hydrogen bonds : angle 4.11227 ( 1134) link_BETA1-4 : bond 0.00434 ( 6) link_BETA1-4 : angle 1.73166 ( 18) link_NAG-ASN : bond 0.00593 ( 12) link_NAG-ASN : angle 4.74702 ( 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: 40 poor density : 94 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8103 (mtm110) REVERT: A 307 MET cc_start: 0.8343 (mtp) cc_final: 0.7964 (mtt) REVERT: B 216 ASP cc_start: 0.8059 (p0) cc_final: 0.7697 (p0) REVERT: B 220 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7991 (mtm110) REVERT: B 307 MET cc_start: 0.8340 (mtp) cc_final: 0.7968 (mtt) outliers start: 40 outliers final: 36 residues processed: 122 average time/residue: 0.0855 time to fit residues: 16.3140 Evaluate side-chains 133 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 524 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 220 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE 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 524 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: 0.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.0270 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 524 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.162988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138397 restraints weight = 14687.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137251 restraints weight = 27468.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138015 restraints weight = 25697.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137800 restraints weight = 17776.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137654 restraints weight = 20023.185| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11540 Z= 0.118 Angle : 0.574 16.829 15794 Z= 0.281 Chirality : 0.047 0.651 1846 Planarity : 0.003 0.031 2046 Dihedral : 8.586 110.530 2020 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.13 % Allowed : 20.87 % Favored : 75.00 % 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: 0.83 (0.22), residues: 574 sheet: -1.83 (0.44), residues: 140 loop : -1.93 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.014 0.001 TYR A 510 PHE 0.009 0.001 PHE B 846 TRP 0.007 0.001 TRP B 208 HIS 0.002 0.000 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00277 (11504) covalent geometry : angle 0.52547 (15704) SS BOND : bond 0.00170 ( 18) SS BOND : angle 1.25925 ( 36) hydrogen bonds : bond 0.03156 ( 390) hydrogen bonds : angle 4.04999 ( 1134) link_BETA1-4 : bond 0.00432 ( 6) link_BETA1-4 : angle 1.73136 ( 18) link_NAG-ASN : bond 0.00590 ( 12) link_NAG-ASN : angle 4.56214 ( 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 135 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8079 (mtm110) REVERT: A 307 MET cc_start: 0.8358 (mtp) cc_final: 0.7955 (mtt) REVERT: B 216 ASP cc_start: 0.8049 (p0) cc_final: 0.7689 (p0) REVERT: B 220 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7984 (mtm110) REVERT: B 307 MET cc_start: 0.8360 (mtp) cc_final: 0.7960 (mtt) outliers start: 39 outliers final: 37 residues processed: 123 average time/residue: 0.0831 time to fit residues: 16.0153 Evaluate side-chains 135 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 404 VAL 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 524 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 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 524 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 101 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 61 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 85 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 524 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137878 restraints weight = 14836.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136737 restraints weight = 26962.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137317 restraints weight = 25313.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136347 restraints weight = 19336.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137010 restraints weight = 17869.671| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2207 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= 0.128 Angle : 0.574 16.562 15794 Z= 0.282 Chirality : 0.047 0.634 1846 Planarity : 0.003 0.031 2046 Dihedral : 8.495 110.298 2020 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.45 % Allowed : 20.66 % Favored : 74.89 % 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: -1.20 (0.22), residues: 1542 helix: 0.85 (0.22), residues: 576 sheet: -1.81 (0.44), residues: 140 loop : -1.90 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.013 0.001 TYR A 510 PHE 0.009 0.001 PHE B 846 TRP 0.007 0.001 TRP B 208 HIS 0.002 0.000 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00304 (11504) covalent geometry : angle 0.52739 (15704) SS BOND : bond 0.00173 ( 18) SS BOND : angle 1.21113 ( 36) hydrogen bonds : bond 0.03159 ( 390) hydrogen bonds : angle 3.99712 ( 1134) link_BETA1-4 : bond 0.00370 ( 6) link_BETA1-4 : angle 1.72684 ( 18) link_NAG-ASN : bond 0.00570 ( 12) link_NAG-ASN : angle 4.47677 ( 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 140 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8090 (mtm110) REVERT: A 307 MET cc_start: 0.8365 (mtp) cc_final: 0.7958 (mtt) REVERT: B 216 ASP cc_start: 0.8025 (p0) cc_final: 0.7703 (p0) REVERT: B 220 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8037 (mtm110) REVERT: B 307 MET cc_start: 0.8361 (mtp) cc_final: 0.7959 (mtt) outliers start: 42 outliers final: 39 residues processed: 128 average time/residue: 0.0825 time to fit residues: 16.5659 Evaluate side-chains 139 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 524 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 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 524 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: 0.0170 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 524 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.163307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138159 restraints weight = 14766.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136986 restraints weight = 28868.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137767 restraints weight = 25896.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136624 restraints weight = 19921.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137316 restraints weight = 17024.974| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2262 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= 0.118 Angle : 0.568 16.230 15794 Z= 0.279 Chirality : 0.047 0.619 1846 Planarity : 0.003 0.031 2046 Dihedral : 8.405 110.062 2020 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.56 % Allowed : 20.66 % Favored : 74.79 % 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: -1.13 (0.22), residues: 1542 helix: 0.94 (0.22), residues: 576 sheet: -1.77 (0.44), residues: 140 loop : -1.87 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.014 0.001 TYR A 510 PHE 0.008 0.001 PHE B 846 TRP 0.007 0.001 TRP B 208 HIS 0.002 0.000 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00279 (11504) covalent geometry : angle 0.52365 (15704) SS BOND : bond 0.00167 ( 18) SS BOND : angle 1.15133 ( 36) hydrogen bonds : bond 0.03097 ( 390) hydrogen bonds : angle 3.95417 ( 1134) link_BETA1-4 : bond 0.00406 ( 6) link_BETA1-4 : angle 1.72399 ( 18) link_NAG-ASN : bond 0.00578 ( 12) link_NAG-ASN : angle 4.37456 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.05 seconds wall clock time: 28 minutes 19.36 seconds (1699.36 seconds total)