Starting phenix.real_space_refine (version: dev) on Mon Feb 20 00:18:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3j_23655/02_2023/7m3j_23655_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3j_23655/02_2023/7m3j_23655.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3j_23655/02_2023/7m3j_23655_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3j_23655/02_2023/7m3j_23655_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3j_23655/02_2023/7m3j_23655_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3j_23655/02_2023/7m3j_23655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3j_23655/02_2023/7m3j_23655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3j_23655/02_2023/7m3j_23655_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3j_23655/02_2023/7m3j_23655_updated.pdb" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.071 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 Process input model Symmetric amino acids flipped Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11001 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5438 Classifications: {'peptide': 777} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PTRANS': 29, 'TRANS': 747} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 771 Unresolved non-hydrogen angles: 989 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 5, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 10, 'GLU:plan': 36, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 407 Chain: "B" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5397 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 265} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain breaks: 3 Unresolved non-hydrogen bonds: 873 Unresolved non-hydrogen angles: 1107 Unresolved non-hydrogen dihedrals: 686 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 19, 'PHE:plan': 11, 'GLU:plan': 43, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 490 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 76 Unusual residues: {'NAG': 3, 'PO4': 1, 'YP1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {'NAG': 2, 'PO4': 1, 'YP1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.47, per 1000 atoms: 0.59 Number of scatterers: 11001 At special positions: 0 Unit cell: (88.8, 98.79, 192.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 51 16.00 P 2 15.00 O 1931 8.00 N 1888 7.00 C 7127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, 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=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=1.89 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.02 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 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=2.02 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 - 3.50 Amino acid : False - 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-ASN " NAG A 902 " - " ASN A 261 " " NAG A 903 " - " ASN A 468 " " NAG A 904 " - " ASN A 488 " " NAG B 902 " - " ASN B 541 " " NAG B 903 " - " ASN B 488 " " NAG C 1 " - " ASN A 541 " Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 1.9 seconds 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 10 sheets defined 41.2% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.748A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ASN A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 4.043A pdb=" N ASN A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 4.354A pdb=" N ALA A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE A 200 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.503A pdb=" N PHE A 311 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 417 through 436 Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.921A pdb=" N LEU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 462 " --> pdb=" O TRP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.750A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 644 No H-bonds generated for 'chain 'A' and resid 641 through 644' Processing helix chain 'A' and resid 650 through 668 removed outlier: 3.875A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N PHE A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 696 removed outlier: 5.740A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix removed outlier: 3.633A pdb=" N ILE A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 745 removed outlier: 3.838A pdb=" N CYS A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE A 738 " --> pdb=" O MET A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 793 removed outlier: 5.028A pdb=" N PHE A 775 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 786 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 827 removed outlier: 3.995A 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 833 through 851 removed outlier: 3.669A pdb=" N VAL A 838 " --> pdb=" O SER A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 861 Processing helix chain 'A' and resid 863 through 868 removed outlier: 4.375A pdb=" N ARG A 866 " --> pdb=" O LYS A 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.930A pdb=" N GLU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 123 removed outlier: 6.261A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 157 removed outlier: 3.557A pdb=" N ASN B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.751A pdb=" N ALA B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 232 removed outlier: 3.636A pdb=" N GLU B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 261 Processing helix chain 'B' and resid 274 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 330 through 333 No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 346 through 355 removed outlier: 3.644A pdb=" N LYS B 349 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B 350 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP B 352 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 354 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 355 " --> pdb=" O TRP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 435 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 611 through 636 removed outlier: 3.658A pdb=" N GLY B 623 " --> pdb=" O PHE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 668 removed outlier: 3.983A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 666 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N PHE B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 680 through 698 removed outlier: 3.655A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 745 removed outlier: 3.757A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 794 removed outlier: 3.643A pdb=" N LEU B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 827 removed outlier: 4.013A 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 833 through 861 removed outlier: 3.791A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.628A pdb=" N ALA A 26 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLY A 35 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 141 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY A 143 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL A 165 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.666A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.586A pdb=" N TYR A 489 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 602 through 604 removed outlier: 4.054A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 551 through 554 removed outlier: 3.858A pdb=" N ARG A 551 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 553 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU A 564 " --> pdb=" O GLY A 553 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 32 through 39 Processing sheet with id= G, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.921A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.074A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 510 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 522 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= J, first strand: chain 'B' and resid 602 through 604 removed outlier: 4.075A pdb=" N ILE B 763 " --> pdb=" O GLU B 604 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1176 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: 3.23 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1746 1.27 - 1.41: 3105 1.41 - 1.55: 6359 1.55 - 1.69: 5 1.69 - 1.83: 60 Bond restraints: 11275 Sorted by residual: bond pdb=" N LEU B 88 " pdb=" CA LEU B 88 " ideal model delta sigma weight residual 1.458 1.491 -0.034 7.40e-03 1.83e+04 2.06e+01 bond pdb=" C ILE B 822 " pdb=" N PRO B 823 " ideal model delta sigma weight residual 1.335 1.389 -0.053 1.36e-02 5.41e+03 1.54e+01 bond pdb=" N ILE B 288 " pdb=" CA ILE B 288 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.19e+01 bond pdb=" N CYS A 449 " pdb=" CA CYS A 449 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.35e+00 bond pdb=" N CYS A 437 " pdb=" CA CYS A 437 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.27e-02 6.20e+03 8.11e+00 ... (remaining 11270 not shown) Histogram of bond angle deviations from ideal: 96.74 - 113.30: 6181 113.30 - 129.87: 9157 129.87 - 146.43: 86 146.43 - 162.99: 0 162.99 - 179.55: 2 Bond angle restraints: 15426 Sorted by residual: angle pdb=" N THR A 436 " pdb=" CA THR A 436 " pdb=" C THR A 436 " ideal model delta sigma weight residual 110.44 118.67 -8.23 1.20e+00 6.94e-01 4.70e+01 angle pdb=" N LEU A 438 " pdb=" CA LEU A 438 " pdb=" CB LEU A 438 " ideal model delta sigma weight residual 110.05 102.82 7.23 1.44e+00 4.82e-01 2.52e+01 angle pdb=" CA GLU B 354 " pdb=" CB GLU B 354 " pdb=" CG GLU B 354 " ideal model delta sigma weight residual 114.10 123.33 -9.23 2.00e+00 2.50e-01 2.13e+01 angle pdb=" C THR A 436 " pdb=" CA THR A 436 " pdb=" CB THR A 436 " ideal model delta sigma weight residual 111.77 101.53 10.24 2.28e+00 1.92e-01 2.02e+01 angle pdb=" CA GLY A 830 " pdb=" C GLY A 830 " pdb=" O GLY A 830 " ideal model delta sigma weight residual 121.90 117.34 4.56 1.08e+00 8.57e-01 1.78e+01 ... (remaining 15421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 6283 24.55 - 49.09: 177 49.09 - 73.64: 9 73.64 - 98.18: 8 98.18 - 122.73: 4 Dihedral angle restraints: 6481 sinusoidal: 1940 harmonic: 4541 Sorted by residual: dihedral pdb=" CB CYS B 568 " pdb=" SG CYS B 568 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual -86.00 -176.01 90.01 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS B 437 " pdb=" SG CYS B 437 " pdb=" SG CYS B 449 " pdb=" CB CYS B 449 " ideal model delta sinusoidal sigma weight residual 93.00 178.89 -85.89 1 1.00e+01 1.00e-02 8.91e+01 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 -170.29 84.29 1 1.00e+01 1.00e-02 8.65e+01 ... (remaining 6478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1596 0.109 - 0.218: 170 0.218 - 0.326: 14 0.326 - 0.435: 4 0.435 - 0.544: 2 Chirality restraints: 1786 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 541 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" CA THR A 445 " pdb=" N THR A 445 " pdb=" C THR A 445 " pdb=" CB THR A 445 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA LEU A 438 " pdb=" N LEU A 438 " pdb=" C LEU A 438 " pdb=" CB LEU A 438 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.99e+00 ... (remaining 1783 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 425 " 0.035 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR B 425 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR B 425 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 425 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 425 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 425 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 425 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 425 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 640 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.46e+00 pdb=" N PRO A 641 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 84 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO B 85 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " 0.039 5.00e-02 4.00e+02 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3143 2.80 - 3.32: 9957 3.32 - 3.85: 16842 3.85 - 4.37: 17946 4.37 - 4.90: 30934 Nonbonded interactions: 78822 Sorted by model distance: nonbonded pdb=" O LEU A 842 " pdb=" OG SER A 845 " model vdw 2.274 2.440 nonbonded pdb=" OG SER A 150 " pdb=" OG SER A 169 " model vdw 2.313 2.440 nonbonded pdb=" O GLY A 43 " pdb=" N ILE A 61 " model vdw 2.341 2.520 nonbonded pdb=" OE1 GLN A 253 " pdb=" NH2 ARG A 286 " model vdw 2.351 2.520 nonbonded pdb=" OE1 GLU B 456 " pdb=" NE1 TRP B 458 " model vdw 2.359 2.520 ... (remaining 78817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 55 or (resid 56 and (name N or nam \ e CA or name C or name O or name CB )) or resid 57 through 116 or (resid 117 thr \ ough 120 and (name N or name CA or name C or name O or name CB )) or resid 136 t \ hrough 171 or (resid 172 and (name N or name CA or name C or name O or name CB ) \ ) or resid 173 through 178 or (resid 179 and (name N or name CA or name C or nam \ e O or name CB )) or resid 180 or (resid 181 and (name N or name CA or name C or \ name O or name CB )) or resid 182 through 190 or (resid 191 and (name N or name \ CA or name C or name O or name CB )) or resid 192 through 210 or (resid 211 and \ (name N or name CA or name C or name O or name CB )) or resid 212 through 231 o \ r (resid 232 through 234 and (name N or name CA or name C or name O or name CB ) \ ) or resid 235 through 242 or (resid 243 through 244 and (name N or name CA or n \ ame C or name O or name CB )) or resid 245 or (resid 246 through 259 and (name N \ or name CA or name C or name O or name CB )) or resid 260 or (resid 261 through \ 264 and (name N or name CA or name C or name O or name CB )) or resid 265 throu \ gh 270 or (resid 271 through 272 and (name N or name CA or name C or name O or n \ ame CB )) or resid 273 through 274 or (resid 275 and (name N or name CA or name \ C or name O or name CB )) or resid 276 or (resid 277 and (name N or name CA or n \ ame C or name O or name CB )) or resid 278 through 280 or (resid 281 and (name N \ or name CA or name C or name O or name CB )) or resid 282 through 284 or (resid \ 285 through 286 and (name N or name CA or name C or name O or name CB )) or res \ id 287 through 288 or (resid 289 and (name N or name CA or name C or name O or n \ ame CB )) or resid 290 through 291 or (resid 292 and (name N or name CA or name \ C or name O or name CB )) or resid 293 through 296 or (resid 297 through 298 and \ (name N or name CA or name C or name O or name CB )) or resid 299 through 300 o \ r (resid 301 through 302 and (name N or name CA or name C or name O or name CB ) \ ) or resid 303 or (resid 304 through 306 and (name N or name CA or name C or nam \ e O or name CB )) or resid 307 through 349 or (resid 350 and (name N or name CA \ or name C or name O or name CB )) or resid 351 through 354 or (resid 355 and (na \ me N or name CA or name C or name O or name CB )) or resid 356 through 357 or (r \ esid 403 through 406 and (name N or name CA or name C or name O or name CB )) or \ resid 407 through 409 or (resid 410 and (name N or name CA or name C or name O \ or name CB )) or resid 411 through 437 or (resid 438 and (name N or name CA or n \ ame C or name O or name CB )) or resid 439 through 458 or (resid 459 and (name N \ or name CA or name C or name O or name CB )) or resid 460 through 472 or (resid \ 473 and (name N or name CA or name C or name O or name CB )) or resid 474 throu \ gh 496 or (resid 497 and (name N or name CA or name C or name O or name CB )) or \ resid 498 through 501 or (resid 502 through 503 and (name N or name CA or name \ C or name O or name CB )) or resid 504 through 506 or (resid 507 and (name N or \ name CA or name C or name O or name CB )) or resid 508 through 518 or (resid 519 \ and (name N or name CA or name C or name O or name CB )) or resid 520 through 5 \ 24 or (resid 525 through 527 and (name N or name CA or name C or name O or name \ CB )) or resid 528 through 532 or (resid 533 through 534 and (name N or name CA \ or name C or name O or name CB )) or resid 535 through 542 or (resid 543 and (na \ me N or name CA or name C or name O or name CB )) or resid 544 through 546 or (r \ esid 547 through 548 and (name N or name CA or name C or name O or name CB )) or \ resid 549 or (resid 550 and (name N or name CA or name C or name O or name CB ) \ ) or resid 551 through 559 or (resid 560 and (name N or name CA or name C or nam \ e O or name CB )) or resid 561 through 582 or (resid 583 through 584 and (name N \ or name CA or name C or name O or name CB )) or resid 585 through 594 or (resid \ 595 through 597 and (name N or name CA or name C or name O or name CB )) or res \ id 598 through 604 or (resid 605 through 610 and (name N or name CA or name C or \ name O or name CB )) or resid 611 through 635 or (resid 636 through 640 and (na \ me N or name CA or name C or name O or name CB )) or resid 641 through 660 or (r \ esid 661 and (name N or name CA or name C or name O or name CB )) or resid 662 t \ hrough 685 or (resid 686 through 687 and (name N or name CA or name C or name O \ or name CB )) or resid 688 through 691 or (resid 692 through 693 and (name N or \ name CA or name C or name O or name CB )) or resid 694 through 695 or (resid 696 \ through 699 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 00 through 728 or (resid 729 through 737 and (name N or name CA or name C or nam \ e O or name CB )) or resid 738 through 741 or (resid 742 through 746 and (name N \ or name CA or name C or name O or name CB )) or resid 747 through 750 or (resid \ 751 and (name N or name CA or name C or name O or name CB )) or resid 752 throu \ gh 761 or (resid 762 through 764 and (name N or name CA or name C or name O or n \ ame CB )) or resid 765 or (resid 766 through 767 and (name N or name CA or name \ C or name O or name CB )) or (resid 768 through 773 and (name N or name CA or na \ me C or name O or name CB )) or resid 774 through 780 or (resid 781 through 786 \ and (name N or name CA or name C or name O or name CB )) or resid 787 through 78 \ 8 or (resid 789 and (name N or name CA or name C or name O or name CB )) or resi \ d 790 through 792 or (resid 793 through 797 and (name N or name CA or name C or \ name O or name CB )) or resid 798 through 844 or (resid 845 and (name N or name \ CA or name C or name O or name CB )) or resid 846 through 862 or (resid 863 thro \ ugh 874 and (name N or name CA or name C or name O or name CB )) or resid 903 th \ rough 905)) selection = (chain 'B' and (resid 26 through 46 or (resid 47 through 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 51 or (resid 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 53 through 60 or (res \ id 61 and (name N or name CA or name C or name O or name CB )) or resid 62 throu \ gh 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or r \ esid 89 through 99 or (resid 100 and (name N or name CA or name C or name O or n \ ame CB )) or resid 101 through 119 or (resid 120 and (name N or name CA or name \ C or name O or name CB )) or resid 136 through 144 or (resid 145 and (name N or \ name CA or name C or name O or name CB )) or resid 146 through 192 or (resid 193 \ through 194 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 95 through 237 or (resid 238 and (name N or name CA or name C or name O or name \ CB )) or resid 239 or (resid 240 through 241 and (name N or name CA or name C or \ name O or name CB )) or resid 242 through 357 or (resid 403 through 406 and (na \ me N or name CA or name C or name O or name CB )) or resid 407 through 411 or (r \ esid 412 and (name N or name CA or name C or name O or name CB )) or resid 413 t \ hrough 435 or (resid 436 and (name N or name CA or name C or name O or name CB ) \ ) or resid 437 through 479 or (resid 480 through 482 and (name N or name CA or n \ ame C or name O or name CB )) or resid 483 through 516 or (resid 517 and (name N \ or name CA or name C or name O or name CB )) or resid 518 through 525 or (resid \ 526 through 527 and (name N or name CA or name C or name O or name CB )) or res \ id 528 through 554 or (resid 555 through 556 and (name N or name CA or name C or \ name O or name CB )) or resid 557 through 565 or (resid 566 through 567 and (na \ me N or name CA or name C or name O or name CB )) or resid 568 through 576 or (r \ esid 577 through 581 and (name N or name CA or name C or name O or name CB )) or \ resid 582 through 593 or (resid 594 through 597 and (name N or name CA or name \ C or name O or name CB )) or resid 598 through 606 or (resid 607 through 610 and \ (name N or name CA or name C or name O or name CB )) or resid 611 through 613 o \ r (resid 614 through 618 and (name N or name CA or name C or name O or name CB ) \ ) or resid 619 through 621 or (resid 622 and (name N or name CA or name C or nam \ e O or name CB )) or resid 623 through 629 or (resid 630 through 631 and (name N \ or name CA or name C or name O or name CB )) or resid 632 or (resid 633 through \ 640 and (name N or name CA or name C or name O or name CB )) or resid 641 or (r \ esid 642 through 647 and (name N or name CA or name C or name O or name CB )) or \ resid 648 through 649 or (resid 650 through 661 and (name N or name CA or name \ C or name O or name CB )) or resid 662 through 668 or (resid 669 and (name N or \ name CA or name C or name O or name CB )) or resid 670 through 678 or (resid 679 \ through 680 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 81 through 700 or (resid 701 through 737 and (name N or name CA or name C or nam \ e O or name CB )) or resid 738 through 743 or (resid 744 through 746 and (name N \ or name CA or name C or name O or name CB )) or resid 747 or (resid 748 through \ 751 and (name N or name CA or name C or name O or name CB )) or resid 752 throu \ gh 760 or (resid 761 through 764 and (name N or name CA or name C or name O or n \ ame CB )) or resid 765 through 791 or (resid 792 through 797 and (name N or name \ CA or name C or name O or name CB )) or resid 798 through 812 or (resid 813 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 819 o \ r (resid 820 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 21 through 828 or (resid 829 and (name N or name CA or name C or name O or name \ CB )) or resid 830 through 837 or (resid 838 through 840 and (name N or name CA \ or name C or name O or name CB )) or resid 841 through 847 or (resid 848 and (na \ me N or name CA or name C or name O or name CB )) or resid 849 through 852 or (r \ esid 853 through 874 and (name N or name CA or name C or name O or name CB )) or \ resid 902 through 904)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 51 5.16 5 Cl 2 4.86 5 C 7127 2.51 5 N 1888 2.21 5 O 1931 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.930 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: 10.360 Check model and map are aligned: 0.150 Process input model: 30.680 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.010 0.122 11275 Z= 0.640 Angle : 1.092 12.621 15426 Z= 0.627 Chirality : 0.070 0.544 1786 Planarity : 0.008 0.077 1983 Dihedral : 12.018 122.729 3489 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.20 % 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: -2.70 (0.18), residues: 1546 helix: -1.45 (0.17), residues: 667 sheet: -1.51 (0.37), residues: 166 loop : -2.14 (0.20), residues: 713 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.174 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1693 time to fit residues: 27.0698 Evaluate side-chains 74 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 766 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11275 Z= 0.207 Angle : 0.563 9.289 15426 Z= 0.305 Chirality : 0.045 0.344 1786 Planarity : 0.005 0.051 1983 Dihedral : 8.052 120.666 1690 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.58 (0.20), residues: 1546 helix: -0.04 (0.20), residues: 669 sheet: -1.54 (0.36), residues: 169 loop : -1.90 (0.21), residues: 708 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.284 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1696 time to fit residues: 24.7676 Evaluate side-chains 75 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 139 optimal weight: 0.0470 chunk 48 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 11275 Z= 0.215 Angle : 0.532 8.604 15426 Z= 0.286 Chirality : 0.045 0.325 1786 Planarity : 0.004 0.049 1983 Dihedral : 7.725 122.769 1690 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.18 (0.21), residues: 1546 helix: 0.47 (0.20), residues: 662 sheet: -1.63 (0.36), residues: 177 loop : -1.78 (0.22), residues: 707 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.222 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1717 time to fit residues: 26.7429 Evaluate side-chains 74 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.449 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.7980 chunk 106 optimal weight: 0.0970 chunk 73 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 0.0050 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** B 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 11275 Z= 0.138 Angle : 0.497 11.121 15426 Z= 0.260 Chirality : 0.043 0.289 1786 Planarity : 0.004 0.047 1983 Dihedral : 7.477 121.411 1690 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.88 (0.21), residues: 1546 helix: 0.78 (0.21), residues: 665 sheet: -1.29 (0.38), residues: 165 loop : -1.76 (0.21), residues: 716 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.283 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1678 time to fit residues: 28.2149 Evaluate side-chains 75 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 103 optimal weight: 0.0270 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 HIS B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 11275 Z= 0.227 Angle : 0.523 9.630 15426 Z= 0.277 Chirality : 0.044 0.297 1786 Planarity : 0.004 0.045 1983 Dihedral : 7.440 121.948 1690 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.21), residues: 1546 helix: 0.90 (0.21), residues: 665 sheet: -1.65 (0.36), residues: 179 loop : -1.70 (0.22), residues: 702 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.331 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1666 time to fit residues: 26.6180 Evaluate side-chains 77 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 HIS A 476 GLN A 766 HIS ** B 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11275 Z= 0.199 Angle : 0.522 10.659 15426 Z= 0.271 Chirality : 0.044 0.286 1786 Planarity : 0.004 0.043 1983 Dihedral : 7.383 112.610 1690 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.73 (0.21), residues: 1546 helix: 0.99 (0.21), residues: 666 sheet: -1.58 (0.38), residues: 172 loop : -1.66 (0.22), residues: 708 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.338 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1691 time to fit residues: 26.3946 Evaluate side-chains 80 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.6980 chunk 85 optimal weight: 0.0770 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** B 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 11275 Z= 0.159 Angle : 0.493 8.061 15426 Z= 0.258 Chirality : 0.043 0.271 1786 Planarity : 0.004 0.042 1983 Dihedral : 7.392 128.215 1690 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.21), residues: 1546 helix: 1.05 (0.21), residues: 667 sheet: -1.53 (0.37), residues: 174 loop : -1.63 (0.22), residues: 705 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.303 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1852 time to fit residues: 31.5558 Evaluate side-chains 76 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 chunk 29 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** B 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11275 Z= 0.208 Angle : 0.521 10.790 15426 Z= 0.271 Chirality : 0.044 0.276 1786 Planarity : 0.004 0.043 1983 Dihedral : 7.440 127.176 1690 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.21), residues: 1546 helix: 1.10 (0.21), residues: 664 sheet: -1.57 (0.37), residues: 174 loop : -1.61 (0.22), residues: 708 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1633 time to fit residues: 25.9632 Evaluate side-chains 76 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 83 optimal weight: 0.0270 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 0.0970 chunk 131 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 11275 Z= 0.149 Angle : 0.504 12.100 15426 Z= 0.261 Chirality : 0.043 0.262 1786 Planarity : 0.004 0.042 1983 Dihedral : 7.358 126.039 1690 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.21), residues: 1546 helix: 1.14 (0.21), residues: 664 sheet: -1.51 (0.37), residues: 174 loop : -1.58 (0.22), residues: 708 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1708 time to fit residues: 28.0858 Evaluate side-chains 74 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 142 optimal weight: 0.0070 chunk 122 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 75 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** B 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11275 Z= 0.168 Angle : 0.506 10.671 15426 Z= 0.263 Chirality : 0.043 0.267 1786 Planarity : 0.004 0.040 1983 Dihedral : 7.338 126.156 1690 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.21), residues: 1546 helix: 1.13 (0.21), residues: 665 sheet: -1.52 (0.37), residues: 175 loop : -1.56 (0.22), residues: 706 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.269 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1713 time to fit residues: 27.1411 Evaluate side-chains 73 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 113 optimal weight: 0.0770 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 0.0870 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** B 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.093171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075137 restraints weight = 34254.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.075000 restraints weight = 23036.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075066 restraints weight = 17112.097| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 11275 Z= 0.142 Angle : 0.493 10.993 15426 Z= 0.255 Chirality : 0.043 0.259 1786 Planarity : 0.003 0.038 1983 Dihedral : 7.216 124.504 1690 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.52 (0.21), residues: 1546 helix: 1.11 (0.21), residues: 672 sheet: -1.44 (0.37), residues: 176 loop : -1.51 (0.22), residues: 698 =============================================================================== Job complete usr+sys time: 1860.38 seconds wall clock time: 34 minutes 53.23 seconds (2093.23 seconds total)