Starting phenix.real_space_refine on Wed Sep 25 21:35:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtt_30853/09_2024/7dtt_30853.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtt_30853/09_2024/7dtt_30853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtt_30853/09_2024/7dtt_30853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtt_30853/09_2024/7dtt_30853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtt_30853/09_2024/7dtt_30853.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtt_30853/09_2024/7dtt_30853.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 7072 2.51 5 N 1936 2.21 5 O 2146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11204 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5474 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 213} Link IDs: {'PTRANS': 29, 'TRANS': 749} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 775 Unresolved non-hydrogen angles: 997 Unresolved non-hydrogen dihedrals: 656 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 31, 'GLU:plan': 18, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 427 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: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CA': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, B Time building chain proxies: 11.70, per 1000 atoms: 1.04 Number of scatterers: 11204 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 2146 8.00 N 1936 7.00 C 7072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.07 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 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=2.25 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 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 A1103 " - " ASN A 261 " " NAG A1104 " - " ASN A 287 " " NAG A1105 " - " ASN A 446 " " NAG A1106 " - " 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: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 2928 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 43.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.583A pdb=" N ALA A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.526A pdb=" N ALA A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 removed outlier: 3.954A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.600A pdb=" N GLU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.692A pdb=" N LEU A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 329 through 336 removed outlier: 3.634A 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: 3.523A pdb=" N ASN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.536A pdb=" N VAL A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.573A pdb=" N PHE A 533 " --> pdb=" O TRP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 637 removed outlier: 4.055A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 removed outlier: 4.381A pdb=" N LEU A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.895A pdb=" N PHE A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 681 through 691 removed outlier: 4.599A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (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: 4.027A pdb=" N TYR A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 792 removed outlier: 4.512A pdb=" N CYS A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 785 " --> pdb=" O CYS A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 827 removed outlier: 3.823A 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 859 removed outlier: 4.029A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL A 836 " --> pdb=" O PHE A 832 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.583A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.526A pdb=" N ALA B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 205 removed outlier: 3.954A pdb=" N ILE B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 removed outlier: 3.601A pdb=" N GLU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.692A pdb=" N LEU B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.634A 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: 3.523A pdb=" N ASN B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.535A pdb=" N VAL B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.572A pdb=" N PHE B 533 " --> pdb=" O TRP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 637 removed outlier: 4.055A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 664 removed outlier: 4.380A pdb=" N LEU B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 removed outlier: 3.896A pdb=" N PHE B 668 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE B 669 " --> pdb=" O LEU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 669' Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 681 through 691 removed outlier: 4.600A pdb=" N SER B 687 " --> pdb=" O ALA B 683 " (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: 4.026A pdb=" N TYR B 744 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 792 removed outlier: 4.513A pdb=" N CYS B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU B 782 " --> pdb=" O GLY B 778 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 785 " --> pdb=" O CYS B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 827 removed outlier: 3.823A 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 859 removed outlier: 4.029A pdb=" N SER B 834 " --> pdb=" O GLY B 830 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL B 836 " --> pdb=" O PHE B 832 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU B 837 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 849 " --> pdb=" O SER B 845 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 854 " --> pdb=" O ALA B 850 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.303A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.932A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.759A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 267 " --> pdb=" O LEU A 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 495 Processing sheet with id=AA6, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.841A pdb=" N PHE A 522 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 589 through 590 removed outlier: 3.977A pdb=" N ALA A 600 " --> pdb=" O TRP A 590 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.302A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.932A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.759A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TRP B 208 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N VAL B 268 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE B 267 " --> pdb=" O LEU B 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AB3, first strand: chain 'B' and resid 492 through 495 Processing sheet with id=AB4, first strand: chain 'B' and resid 509 through 511 removed outlier: 3.841A pdb=" N PHE B 522 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 589 through 590 removed outlier: 3.977A pdb=" N ALA B 600 " --> pdb=" O TRP B 590 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 3.38 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: 3687 1.34 - 1.46: 2750 1.46 - 1.58: 4931 1.58 - 1.71: 0 1.71 - 1.83: 54 Bond restraints: 11422 Sorted by residual: bond pdb=" CA PHE B 270 " pdb=" CB PHE B 270 " ideal model delta sigma weight residual 1.528 1.445 0.084 2.61e-02 1.47e+03 1.03e+01 bond pdb=" CA PHE A 270 " pdb=" CB PHE A 270 " ideal model delta sigma weight residual 1.528 1.445 0.083 2.61e-02 1.47e+03 1.02e+01 bond pdb=" CA ASP B 217 " pdb=" C ASP B 217 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.80e-02 3.09e+03 7.11e+00 bond pdb=" CA ASP A 217 " pdb=" C ASP A 217 " ideal model delta sigma weight residual 1.523 1.476 0.048 1.80e-02 3.09e+03 7.04e+00 bond pdb=" C1 NAG A1105 " pdb=" O5 NAG A1105 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.03e+00 ... (remaining 11417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 14459 1.79 - 3.58: 964 3.58 - 5.37: 120 5.37 - 7.17: 35 7.17 - 8.96: 12 Bond angle restraints: 15590 Sorted by residual: angle pdb=" N THR A 145 " pdb=" CA THR A 145 " pdb=" C THR A 145 " ideal model delta sigma weight residual 111.33 116.10 -4.77 1.21e+00 6.83e-01 1.56e+01 angle pdb=" N THR B 145 " pdb=" CA THR B 145 " pdb=" C THR B 145 " ideal model delta sigma weight residual 111.33 116.10 -4.77 1.21e+00 6.83e-01 1.55e+01 angle pdb=" N CYS A 60 " pdb=" CA CYS A 60 " pdb=" C CYS A 60 " ideal model delta sigma weight residual 110.53 105.54 4.99 1.29e+00 6.01e-01 1.50e+01 angle pdb=" N CYS B 60 " pdb=" CA CYS B 60 " pdb=" C CYS B 60 " ideal model delta sigma weight residual 110.53 105.54 4.99 1.29e+00 6.01e-01 1.49e+01 angle pdb=" N GLY A 830 " pdb=" CA GLY A 830 " pdb=" C GLY A 830 " ideal model delta sigma weight residual 110.77 118.06 -7.29 1.93e+00 2.68e-01 1.43e+01 ... (remaining 15585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 6291 18.10 - 36.20: 540 36.20 - 54.30: 85 54.30 - 72.40: 34 72.40 - 90.50: 9 Dihedral angle restraints: 6959 sinusoidal: 2439 harmonic: 4520 Sorted by residual: dihedral pdb=" CB CYS A 236 " pdb=" SG CYS A 236 " pdb=" SG CYS A 561 " pdb=" CB CYS A 561 " ideal model delta sinusoidal sigma weight residual -86.00 -176.50 90.50 1 1.00e+01 1.00e-02 9.68e+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 -169.73 83.73 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS A 546 " pdb=" SG CYS A 546 " pdb=" SG CYS A 565 " pdb=" CB CYS A 565 " ideal model delta sinusoidal sigma weight residual -86.00 -164.31 78.31 1 1.00e+01 1.00e-02 7.65e+01 ... (remaining 6956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.232: 1834 0.232 - 0.464: 8 0.464 - 0.696: 0 0.696 - 0.928: 0 0.928 - 1.159: 2 Chirality restraints: 1844 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 -1.24 -1.16 2.00e-01 2.50e+01 3.36e+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 -1.24 -1.16 2.00e-01 2.50e+01 3.35e+01 chirality pdb=" C1 NAG B1105 " pdb=" ND2 ASN B 446 " pdb=" C2 NAG B1105 " pdb=" O5 NAG B1105 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1841 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 187 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 188 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 187 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 188 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 135 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ILE B 135 " -0.037 2.00e-02 2.50e+03 pdb=" O ILE B 135 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 136 " 0.013 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 131 2.60 - 3.17: 9275 3.17 - 3.75: 17252 3.75 - 4.32: 22564 4.32 - 4.90: 37410 Nonbonded interactions: 86632 Sorted by model distance: nonbonded pdb=" SG CYS B 236 " pdb=" SG CYS B 561 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS B 546 " pdb=" SG CYS B 565 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 568 " pdb=" SG CYS B 582 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B 358 " pdb=" SG CYS B 395 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " model vdw 2.031 3.760 ... (remaining 86627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain '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: 2.070 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.980 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.094 11422 Z= 0.707 Angle : 1.001 8.958 15590 Z= 0.570 Chirality : 0.072 1.159 1844 Planarity : 0.006 0.055 2030 Dihedral : 14.406 86.830 4004 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.73 % Favored : 90.14 % Rotamer: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.17), residues: 1542 helix: -2.71 (0.14), residues: 612 sheet: -2.59 (0.46), residues: 108 loop : -3.05 (0.18), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 208 HIS 0.005 0.002 HIS B 595 PHE 0.018 0.002 PHE B 539 TYR 0.028 0.003 TYR B 421 ARG 0.005 0.001 ARG B 172 *********************** 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 30 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 1.271 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2487 time to fit residues: 12.1872 Evaluate side-chains 18 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 193 GLN A 253 GLN A 338 HIS A 344 HIS A 466 HIS A 476 GLN A 524 ASN A 595 HIS B 117 GLN B 193 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS B 466 HIS B 476 GLN B 524 ASN B 595 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11422 Z= 0.218 Angle : 0.583 7.192 15590 Z= 0.313 Chirality : 0.050 0.732 1844 Planarity : 0.004 0.050 2030 Dihedral : 7.875 58.089 2018 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.16 % Favored : 93.71 % Rotamer: Outliers : 1.29 % Allowed : 11.96 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.19), residues: 1542 helix: -1.16 (0.18), residues: 616 sheet: -2.44 (0.46), residues: 118 loop : -2.65 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 675 HIS 0.004 0.001 HIS A 254 PHE 0.010 0.001 PHE B 333 TYR 0.020 0.001 TYR B 421 ARG 0.003 0.000 ARG A 286 *********************** 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 38 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 26 time to evaluate : 1.224 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 38 average time/residue: 0.1452 time to fit residues: 10.5508 Evaluate side-chains 25 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 140 optimal weight: 30.0000 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 47 optimal weight: 0.0050 chunk 112 optimal weight: 9.9990 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 27 GLN B 253 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11422 Z= 0.370 Angle : 0.605 6.635 15590 Z= 0.323 Chirality : 0.050 0.696 1844 Planarity : 0.004 0.047 2030 Dihedral : 7.440 59.866 2018 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.16 % Allowed : 14.66 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.20), residues: 1542 helix: -0.33 (0.20), residues: 612 sheet: -2.70 (0.37), residues: 166 loop : -2.31 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 494 HIS 0.004 0.001 HIS B 463 PHE 0.014 0.001 PHE B 563 TYR 0.011 0.001 TYR A 425 ARG 0.004 0.000 ARG B 551 *********************** 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 39 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 19 time to evaluate : 1.263 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 39 average time/residue: 0.1501 time to fit residues: 11.2397 Evaluate side-chains 32 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 19 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 0.0570 chunk 94 optimal weight: 0.9980 chunk 140 optimal weight: 40.0000 chunk 148 optimal weight: 40.0000 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 40 optimal weight: 0.0170 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11422 Z= 0.132 Angle : 0.494 6.125 15590 Z= 0.262 Chirality : 0.047 0.637 1844 Planarity : 0.003 0.045 2030 Dihedral : 6.366 55.138 2018 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.94 % Allowed : 15.84 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1542 helix: 0.28 (0.21), residues: 614 sheet: -1.79 (0.49), residues: 118 loop : -2.20 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 352 HIS 0.002 0.000 HIS B 41 PHE 0.011 0.001 PHE A 160 TYR 0.026 0.001 TYR B 435 ARG 0.002 0.000 ARG B 185 *********************** 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 38 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 20 time to evaluate : 1.428 Fit side-chains REVERT: B 818 TRP cc_start: 0.7109 (OUTLIER) cc_final: 0.6135 (m-90) outliers start: 18 outliers final: 11 residues processed: 37 average time/residue: 0.1458 time to fit residues: 10.3638 Evaluate side-chains 31 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 19 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 818 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.0030 chunk 127 optimal weight: 0.0670 chunk 102 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.9530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11422 Z= 0.169 Angle : 0.485 6.251 15590 Z= 0.257 Chirality : 0.047 0.630 1844 Planarity : 0.003 0.040 2030 Dihedral : 5.943 56.185 2018 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.80 % Allowed : 16.16 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1542 helix: 0.57 (0.21), residues: 618 sheet: -1.67 (0.50), residues: 118 loop : -2.01 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 675 HIS 0.003 0.000 HIS B 429 PHE 0.010 0.001 PHE B 469 TYR 0.019 0.001 TYR B 435 ARG 0.001 0.000 ARG B 551 *********************** 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 46 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 20 time to evaluate : 1.234 Fit side-chains REVERT: B 818 TRP cc_start: 0.7091 (OUTLIER) cc_final: 0.6117 (m-90) outliers start: 26 outliers final: 17 residues processed: 45 average time/residue: 0.1534 time to fit residues: 12.7324 Evaluate side-chains 38 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 20 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 818 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 10.0000 chunk 134 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11422 Z= 0.407 Angle : 0.591 6.427 15590 Z= 0.312 Chirality : 0.050 0.671 1844 Planarity : 0.003 0.037 2030 Dihedral : 6.038 59.969 2018 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.02 % Allowed : 17.13 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1542 helix: 0.73 (0.22), residues: 612 sheet: -2.13 (0.43), residues: 138 loop : -1.94 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 675 HIS 0.005 0.001 HIS B 41 PHE 0.012 0.001 PHE B 563 TYR 0.031 0.002 TYR A 435 ARG 0.004 0.000 ARG B 551 *********************** 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 48 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 20 time to evaluate : 1.404 Fit side-chains outliers start: 28 outliers final: 17 residues processed: 48 average time/residue: 0.2177 time to fit residues: 16.9840 Evaluate side-chains 36 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 19 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 125 optimal weight: 0.0070 chunk 83 optimal weight: 0.9980 chunk 148 optimal weight: 40.0000 chunk 92 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 68 optimal weight: 30.0000 chunk 91 optimal weight: 0.0770 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11422 Z= 0.130 Angle : 0.482 6.009 15590 Z= 0.255 Chirality : 0.047 0.622 1844 Planarity : 0.003 0.043 2030 Dihedral : 5.553 55.467 2018 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.16 % Allowed : 18.53 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1542 helix: 0.96 (0.21), residues: 618 sheet: -1.70 (0.50), residues: 116 loop : -1.87 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 208 HIS 0.002 0.000 HIS B 595 PHE 0.012 0.001 PHE B 469 TYR 0.029 0.002 TYR A 435 ARG 0.021 0.001 ARG B 285 *********************** 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 43 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 23 time to evaluate : 1.169 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 42 average time/residue: 0.1743 time to fit residues: 12.9777 Evaluate side-chains 33 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 19 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 550 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 50.0000 chunk 88 optimal weight: 0.0980 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 116 optimal weight: 0.3980 chunk 135 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11422 Z= 0.138 Angle : 0.470 5.864 15590 Z= 0.249 Chirality : 0.047 0.606 1844 Planarity : 0.003 0.040 2030 Dihedral : 5.332 55.467 2018 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.83 % Allowed : 18.32 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1542 helix: 1.14 (0.22), residues: 618 sheet: -1.49 (0.51), residues: 118 loop : -1.75 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 208 HIS 0.002 0.000 HIS B 41 PHE 0.011 0.001 PHE B 469 TYR 0.025 0.001 TYR A 435 ARG 0.012 0.000 ARG B 285 *********************** 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 37 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 20 time to evaluate : 1.287 Fit side-chains outliers start: 17 outliers final: 16 residues processed: 37 average time/residue: 0.1538 time to fit residues: 11.0692 Evaluate side-chains 34 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 18 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 550 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11422 Z= 0.346 Angle : 0.553 6.191 15590 Z= 0.293 Chirality : 0.049 0.652 1844 Planarity : 0.003 0.036 2030 Dihedral : 5.611 59.615 2018 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.94 % Allowed : 18.21 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1542 helix: 1.19 (0.22), residues: 614 sheet: -1.96 (0.43), residues: 138 loop : -1.74 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.005 0.001 HIS B 41 PHE 0.010 0.001 PHE B 563 TYR 0.025 0.001 TYR A 435 ARG 0.006 0.000 ARG B 285 *********************** 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 36 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 18 time to evaluate : 1.174 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 36 average time/residue: 0.1489 time to fit residues: 10.6363 Evaluate side-chains 33 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 18 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 550 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 40.0000 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 40.0000 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 141 optimal weight: 0.1980 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11422 Z= 0.186 Angle : 0.489 6.140 15590 Z= 0.258 Chirality : 0.047 0.628 1844 Planarity : 0.003 0.039 2030 Dihedral : 5.437 56.691 2018 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.83 % Allowed : 18.43 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1542 helix: 1.32 (0.22), residues: 612 sheet: -1.69 (0.49), residues: 116 loop : -1.71 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 208 HIS 0.002 0.001 HIS B 41 PHE 0.011 0.001 PHE B 469 TYR 0.023 0.001 TYR A 435 ARG 0.007 0.000 ARG B 285 ********************** 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 36 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 19 time to evaluate : 1.294 Fit side-chains outliers start: 17 outliers final: 16 residues processed: 36 average time/residue: 0.1494 time to fit residues: 10.5857 Evaluate side-chains 34 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 18 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 550 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 125 optimal weight: 0.0470 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.0370 chunk 107 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.080577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.056124 restraints weight = 39653.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057608 restraints weight = 24144.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058545 restraints weight = 18138.606| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11422 Z= 0.128 Angle : 0.477 15.292 15590 Z= 0.246 Chirality : 0.046 0.593 1844 Planarity : 0.003 0.039 2030 Dihedral : 5.223 54.874 2018 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.72 % Allowed : 18.64 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1542 helix: 1.37 (0.22), residues: 614 sheet: -1.39 (0.51), residues: 118 loop : -1.67 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 208 HIS 0.002 0.000 HIS B 338 PHE 0.012 0.001 PHE B 469 TYR 0.025 0.001 TYR A 435 ARG 0.007 0.000 ARG B 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1680.54 seconds wall clock time: 31 minutes 7.45 seconds (1867.45 seconds total)