Starting phenix.real_space_refine (version: dev) on Thu Feb 23 01:11:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvt_23542/02_2023/7lvt_23542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvt_23542/02_2023/7lvt_23542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvt_23542/02_2023/7lvt_23542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvt_23542/02_2023/7lvt_23542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvt_23542/02_2023/7lvt_23542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvt_23542/02_2023/7lvt_23542.pdb" } resolution = 4.6 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= 0.002 sd= 0.063 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 GLU 46": "OE1" <-> "OE2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 400": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18944 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 690} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 16, 'ASN:plan1': 10, 'TRP:plan': 7, 'ASP:plan': 17, 'PHE:plan': 16, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 540 Chain: "B" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 691} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 16, 'ASN:plan1': 10, 'TRP:plan': 7, 'ASP:plan': 17, 'PHE:plan': 16, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 540 Chain: "C" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 689} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 16, 'ASN:plan1': 10, 'TRP:plan': 7, 'ASP:plan': 17, 'PHE:plan': 16, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 540 Chain: "D" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 691} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 16, 'ASN:plan1': 10, 'TRP:plan': 7, 'ASP:plan': 17, 'PHE:plan': 16, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 540 Time building chain proxies: 11.42, per 1000 atoms: 0.60 Number of scatterers: 18944 At special positions: 0 Unit cell: (124.944, 162.208, 187.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 3612 8.00 N 3448 7.00 C 11816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " 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 Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 3.4 seconds 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5416 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 37 sheets defined 50.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.946A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.544A pdb=" N LEU A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 195 Proline residue: A 192 - end of helix Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.319A pdb=" N GLU A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 317 through 337 Processing helix chain 'A' and resid 355 through 365 removed outlier: 4.145A pdb=" N ASN A 361 " --> pdb=" O PRO A 357 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 457 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.593A pdb=" N LYS A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 556 removed outlier: 3.638A pdb=" N ASN A 556 " --> pdb=" O PHE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 575 removed outlier: 3.649A pdb=" N LEU A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 581 removed outlier: 3.625A pdb=" N VAL A 579 " --> pdb=" O CYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 661 removed outlier: 3.995A pdb=" N VAL A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 675 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'A' and resid 719 through 730 Processing helix chain 'A' and resid 738 through 746 Processing helix chain 'A' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS A 776 " --> pdb=" O PRO A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 removed outlier: 3.858A pdb=" N PHE A 823 " --> pdb=" O ILE A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 833 removed outlier: 3.804A pdb=" N LEU A 830 " --> pdb=" O LEU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.547A pdb=" N ALA A 837 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 838 " --> pdb=" O PHE A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 838' Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.515A pdb=" N TYR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 303 removed outlier: 4.336A pdb=" N ALA B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 337 Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 454 through 457 Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 498 through 506 Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.593A pdb=" N LYS B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 554 Processing helix chain 'B' and resid 559 through 581 removed outlier: 4.128A pdb=" N LEU B 567 " --> pdb=" O TRP B 563 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 568 " --> pdb=" O MET B 564 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 574 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 579 " --> pdb=" O CYS B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 664 removed outlier: 3.966A pdb=" N ILE B 638 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE B 642 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU B 664 " --> pdb=" O VAL B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 698 through 711 Processing helix chain 'B' and resid 711 through 716 Processing helix chain 'B' and resid 719 through 730 Processing helix chain 'B' and resid 738 through 746 Processing helix chain 'B' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS B 776 " --> pdb=" O PRO B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET B 792 " --> pdb=" O GLY B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 Processing helix chain 'B' and resid 822 through 835 removed outlier: 3.682A pdb=" N LEU B 830 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 831 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 834 " --> pdb=" O LEU B 830 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 835 " --> pdb=" O VAL B 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.702A pdb=" N LEU C 55 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.752A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 178 through 191 removed outlier: 5.471A pdb=" N GLU C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.718A pdb=" N ALA C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.021A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 317 through 337 removed outlier: 3.568A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 519 through 524 removed outlier: 3.593A pdb=" N LYS C 524 " --> pdb=" O TYR C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 556 removed outlier: 3.638A pdb=" N ASN C 556 " --> pdb=" O PHE C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 575 removed outlier: 3.648A pdb=" N LEU C 567 " --> pdb=" O TRP C 563 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.590A pdb=" N VAL C 579 " --> pdb=" O CYS C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 661 removed outlier: 3.944A pdb=" N VAL C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 698 through 711 Processing helix chain 'C' and resid 711 through 716 Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 738 through 746 Processing helix chain 'C' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS C 776 " --> pdb=" O PRO C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET C 792 " --> pdb=" O GLY C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 826 removed outlier: 3.859A pdb=" N PHE C 823 " --> pdb=" O ILE C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 833 removed outlier: 3.805A pdb=" N LEU C 830 " --> pdb=" O LEU C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 838 removed outlier: 3.504A pdb=" N ALA C 837 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE C 838 " --> pdb=" O PHE C 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 834 through 838' Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 152 through 168 Processing helix chain 'D' and resid 178 through 185 Processing helix chain 'D' and resid 185 through 191 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 246 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 266 through 271 Processing helix chain 'D' and resid 286 through 303 removed outlier: 3.877A pdb=" N ALA D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 337 Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 498 through 506 Processing helix chain 'D' and resid 519 through 524 removed outlier: 3.594A pdb=" N LYS D 524 " --> pdb=" O TYR D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 554 Processing helix chain 'D' and resid 559 through 581 removed outlier: 4.128A pdb=" N LEU D 567 " --> pdb=" O TRP D 563 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 568 " --> pdb=" O MET D 564 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 574 " --> pdb=" O CYS D 570 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 579 " --> pdb=" O CYS D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 664 removed outlier: 4.079A pdb=" N ILE D 638 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE D 642 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU D 664 " --> pdb=" O VAL D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 698 through 711 Processing helix chain 'D' and resid 711 through 716 Processing helix chain 'D' and resid 719 through 730 Processing helix chain 'D' and resid 738 through 746 Processing helix chain 'D' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS D 776 " --> pdb=" O PRO D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET D 792 " --> pdb=" O GLY D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 821 Processing helix chain 'D' and resid 822 through 835 removed outlier: 3.674A pdb=" N LEU D 830 " --> pdb=" O LEU D 826 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL D 831 " --> pdb=" O ALA D 827 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 834 " --> pdb=" O LEU D 830 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 835 " --> pdb=" O VAL D 831 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 80 removed outlier: 3.562A pdb=" N ILE A 38 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N ALA A 105 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ARG A 37 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE A 107 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY A 39 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS A 129 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 149 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN A 131 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A 384 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR A 150 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 201 removed outlier: 4.350A pdb=" N TYR A 225 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA4, first strand: chain 'A' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU A 433 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 435 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 528 Processing sheet with id=AA7, first strand: chain 'A' and resid 533 through 535 removed outlier: 3.928A pdb=" N MET A 533 " --> pdb=" O TYR A 763 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 682 removed outlier: 6.572A pdb=" N GLU A 680 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU A 735 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 682 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLU A 737 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 539 " --> pdb=" O ILE A 754 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 75 through 83 removed outlier: 6.036A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLN B 81 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 131 removed outlier: 8.056A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ASN B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.277A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 225 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.277A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 225 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=AB5, first strand: chain 'B' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU B 433 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS B 481 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 435 " --> pdb=" O LYS B 481 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB7, first strand: chain 'B' and resid 526 through 528 Processing sheet with id=AB8, first strand: chain 'B' and resid 533 through 535 removed outlier: 3.927A pdb=" N MET B 533 " --> pdb=" O TYR B 763 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 680 through 682 removed outlier: 6.572A pdb=" N GLU B 680 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU B 735 " --> pdb=" O GLU B 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY B 682 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLU B 737 " --> pdb=" O GLY B 682 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 539 " --> pdb=" O ILE B 754 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 76 through 83 removed outlier: 6.235A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN C 81 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 201 through 203 removed outlier: 7.821A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 256 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 279 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 389 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 404 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AC5, first strand: chain 'C' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU C 433 " --> pdb=" O ASP C 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL C 435 " --> pdb=" O LYS C 481 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC7, first strand: chain 'C' and resid 526 through 528 Processing sheet with id=AC8, first strand: chain 'C' and resid 533 through 535 removed outlier: 3.927A pdb=" N MET C 533 " --> pdb=" O TYR C 763 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 680 through 682 removed outlier: 6.573A pdb=" N GLU C 680 " --> pdb=" O ALA C 733 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU C 735 " --> pdb=" O GLU C 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY C 682 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU C 737 " --> pdb=" O GLY C 682 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 539 " --> pdb=" O ILE C 754 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 75 through 83 Processing sheet with id=AD2, first strand: chain 'D' and resid 129 through 131 removed outlier: 7.992A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ASN D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 198 through 203 removed outlier: 6.436A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR D 225 " --> pdb=" O THR D 171 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=AD5, first strand: chain 'D' and resid 388 through 395 removed outlier: 3.690A pdb=" N GLY D 403 " --> pdb=" O ILE D 391 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER D 393 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS D 401 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS D 395 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 404 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU D 433 " --> pdb=" O ASP D 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS D 481 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL D 435 " --> pdb=" O LYS D 481 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 528 Processing sheet with id=AD9, first strand: chain 'D' and resid 533 through 535 removed outlier: 3.927A pdb=" N MET D 533 " --> pdb=" O TYR D 763 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 680 through 682 removed outlier: 6.574A pdb=" N GLU D 680 " --> pdb=" O ALA D 733 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 735 " --> pdb=" O GLU D 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY D 682 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU D 737 " --> pdb=" O GLY D 682 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 539 " --> pdb=" O ILE D 754 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3141 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: 7.45 Time building geometry restraints manager: 8.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3343 1.31 - 1.44: 4746 1.44 - 1.56: 10956 1.56 - 1.68: 39 1.68 - 1.81: 120 Bond restraints: 19204 Sorted by residual: bond pdb=" C TRP C 296 " pdb=" O TRP C 296 " ideal model delta sigma weight residual 1.237 1.318 -0.081 1.17e-02 7.31e+03 4.84e+01 bond pdb=" C PRO B 304 " pdb=" O PRO B 304 " ideal model delta sigma weight residual 1.240 1.187 0.053 1.12e-02 7.97e+03 2.26e+01 bond pdb=" N ARG C 300 " pdb=" CA ARG C 300 " ideal model delta sigma weight residual 1.457 1.514 -0.056 1.29e-02 6.01e+03 1.91e+01 bond pdb=" C GLU D 267 " pdb=" O GLU D 267 " ideal model delta sigma weight residual 1.237 1.288 -0.052 1.19e-02 7.06e+03 1.89e+01 bond pdb=" C LEU B 301 " pdb=" O LEU B 301 " ideal model delta sigma weight residual 1.233 1.287 -0.054 1.46e-02 4.69e+03 1.37e+01 ... (remaining 19199 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.69: 396 105.69 - 112.85: 9870 112.85 - 120.01: 6887 120.01 - 127.17: 8928 127.17 - 134.33: 155 Bond angle restraints: 26236 Sorted by residual: angle pdb=" N PRO B 304 " pdb=" CA PRO B 304 " pdb=" C PRO B 304 " ideal model delta sigma weight residual 110.70 100.22 10.48 1.22e+00 6.72e-01 7.38e+01 angle pdb=" N SER D 738 " pdb=" CA SER D 738 " pdb=" C SER D 738 " ideal model delta sigma weight residual 111.75 121.99 -10.24 1.28e+00 6.10e-01 6.40e+01 angle pdb=" N SER C 738 " pdb=" CA SER C 738 " pdb=" C SER C 738 " ideal model delta sigma weight residual 111.75 121.98 -10.23 1.28e+00 6.10e-01 6.39e+01 angle pdb=" N SER B 738 " pdb=" CA SER B 738 " pdb=" C SER B 738 " ideal model delta sigma weight residual 111.75 121.98 -10.23 1.28e+00 6.10e-01 6.38e+01 angle pdb=" N SER A 738 " pdb=" CA SER A 738 " pdb=" C SER A 738 " ideal model delta sigma weight residual 111.75 121.93 -10.18 1.28e+00 6.10e-01 6.32e+01 ... (remaining 26231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 10453 16.98 - 33.95: 783 33.95 - 50.93: 155 50.93 - 67.91: 23 67.91 - 84.88: 6 Dihedral angle restraints: 11420 sinusoidal: 3088 harmonic: 8332 Sorted by residual: dihedral pdb=" CA GLU C 48 " pdb=" C GLU C 48 " pdb=" N PRO C 49 " pdb=" CA PRO C 49 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" C GLU D 48 " pdb=" N GLU D 48 " pdb=" CA GLU D 48 " pdb=" CB GLU D 48 " ideal model delta harmonic sigma weight residual -122.60 -136.79 14.19 0 2.50e+00 1.60e-01 3.22e+01 dihedral pdb=" CA ILE D 638 " pdb=" C ILE D 638 " pdb=" N TRP D 639 " pdb=" CA TRP D 639 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 11417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2363 0.092 - 0.185: 590 0.185 - 0.277: 174 0.277 - 0.369: 34 0.369 - 0.461: 3 Chirality restraints: 3164 Sorted by residual: chirality pdb=" CA PHE C 583 " pdb=" N PHE C 583 " pdb=" C PHE C 583 " pdb=" CB PHE C 583 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CA GLU D 48 " pdb=" N GLU D 48 " pdb=" C GLU D 48 " pdb=" CB GLU D 48 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 3161 not shown) Planarity restraints: 3496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 178 " 0.027 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C ASP A 178 " -0.098 2.00e-02 2.50e+03 pdb=" O ASP A 178 " 0.037 2.00e-02 2.50e+03 pdb=" N SER A 179 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 297 " -0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C SER B 297 " 0.088 2.00e-02 2.50e+03 pdb=" O SER B 297 " -0.033 2.00e-02 2.50e+03 pdb=" N MET B 298 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 298 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" C MET B 298 " -0.067 2.00e-02 2.50e+03 pdb=" O MET B 298 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU B 299 " 0.023 2.00e-02 2.50e+03 ... (remaining 3493 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 236 2.63 - 3.19: 16783 3.19 - 3.76: 29198 3.76 - 4.33: 36625 4.33 - 4.90: 60629 Nonbonded interactions: 143471 Sorted by model distance: nonbonded pdb=" CB ALA B 706 " pdb=" O LYS C 697 " model vdw 2.057 3.460 nonbonded pdb=" O MET A 247 " pdb=" OH TYR A 254 " model vdw 2.275 2.440 nonbonded pdb=" OD1 ASP B 260 " pdb=" OG1 THR B 318 " model vdw 2.306 2.440 nonbonded pdb=" O LYS A 385 " pdb=" OG SER A 407 " model vdw 2.309 2.440 nonbonded pdb=" O ALA D 100 " pdb=" OG SER D 344 " model vdw 2.319 2.440 ... (remaining 143466 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 11816 2.51 5 N 3448 2.21 5 O 3612 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.670 Check model and map are aligned: 0.310 Process input model: 50.670 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 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 : 0.008 0.081 19204 Z= 0.530 Angle : 1.359 10.481 26236 Z= 0.950 Chirality : 0.092 0.461 3164 Planarity : 0.007 0.074 3496 Dihedral : 13.036 84.885 5992 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.40 % Favored : 93.32 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.11 % 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: -2.96 (0.14), residues: 2828 helix: -1.41 (0.12), residues: 1321 sheet: -2.48 (0.21), residues: 468 loop : -2.19 (0.17), residues: 1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.1606 time to fit residues: 19.4268 Evaluate side-chains 57 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0386 time to fit residues: 0.7467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 145 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 222 optimal weight: 0.0060 chunk 86 optimal weight: 0.7980 chunk 135 optimal weight: 50.0000 chunk 165 optimal weight: 1.9990 chunk 257 optimal weight: 30.0000 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3819 moved from start: 7.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.132 19204 Z= 0.393 Angle : 1.040 18.183 26236 Z= 0.670 Chirality : 0.056 0.497 3164 Planarity : 0.007 0.073 3496 Dihedral : 8.591 154.723 3008 Min Nonbonded Distance : 1.252 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 2.12 % Allowed : 6.22 % Favored : 91.65 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.87 % 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: -1.86 (0.15), residues: 2828 helix: 0.04 (0.14), residues: 1292 sheet: -2.29 (0.20), residues: 492 loop : -2.22 (0.17), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.1462 time to fit residues: 14.3301 Evaluate side-chains 45 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0484 time to fit residues: 0.8401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 214 optimal weight: 0.2980 chunk 175 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 chunk 230 optimal weight: 0.0050 chunk 256 optimal weight: 10.0000 chunk 88 optimal weight: 0.2980 chunk 207 optimal weight: 30.0000 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3810 moved from start: 7.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 19204 Z= 0.239 Angle : 0.775 13.462 26236 Z= 0.479 Chirality : 0.043 0.250 3164 Planarity : 0.006 0.065 3496 Dihedral : 7.042 136.095 3008 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.38 % Favored : 95.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -0.86 (0.16), residues: 2828 helix: 0.69 (0.14), residues: 1332 sheet: -1.86 (0.22), residues: 484 loop : -1.50 (0.19), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1477 time to fit residues: 12.3067 Evaluate side-chains 47 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 0.2980 chunk 194 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 173 optimal weight: 0.0870 chunk 259 optimal weight: 0.0070 chunk 274 optimal weight: 20.0000 chunk 135 optimal weight: 30.0000 chunk 245 optimal weight: 0.0770 chunk 73 optimal weight: 0.8980 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3799 moved from start: 7.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 19204 Z= 0.197 Angle : 0.661 6.731 26236 Z= 0.402 Chirality : 0.041 0.136 3164 Planarity : 0.004 0.034 3496 Dihedral : 6.775 136.259 3008 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.81 % Favored : 94.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: -0.41 (0.16), residues: 2828 helix: 1.01 (0.14), residues: 1340 sheet: -1.40 (0.23), residues: 484 loop : -1.35 (0.20), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1443 time to fit residues: 11.7313 Evaluate side-chains 41 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.597 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 0.7980 chunk 155 optimal weight: 0.1980 chunk 3 optimal weight: 0.0030 chunk 204 optimal weight: 0.0980 chunk 113 optimal weight: 0.6980 chunk 234 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 140 optimal weight: 50.0000 chunk 246 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3795 moved from start: 7.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19204 Z= 0.180 Angle : 0.646 7.461 26236 Z= 0.392 Chirality : 0.041 0.142 3164 Planarity : 0.004 0.031 3496 Dihedral : 6.653 135.685 3008 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.53 % Favored : 95.19 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: -0.22 (0.16), residues: 2828 helix: 1.21 (0.14), residues: 1360 sheet: -1.13 (0.25), residues: 468 loop : -1.50 (0.20), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.562 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.1347 time to fit residues: 10.3822 Evaluate side-chains 46 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 274 optimal weight: 30.0000 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 144 optimal weight: 0.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3902 moved from start: 7.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19204 Z= 0.216 Angle : 0.679 7.239 26236 Z= 0.406 Chirality : 0.041 0.158 3164 Planarity : 0.004 0.033 3496 Dihedral : 6.735 137.238 3008 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.95 % Favored : 94.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: 0.10 (0.17), residues: 2828 helix: 1.43 (0.15), residues: 1368 sheet: -1.12 (0.25), residues: 464 loop : -1.23 (0.20), residues: 996 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.532 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1290 time to fit residues: 9.7357 Evaluate side-chains 40 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 273 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3913 moved from start: 7.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19204 Z= 0.198 Angle : 0.666 7.312 26236 Z= 0.397 Chirality : 0.041 0.160 3164 Planarity : 0.004 0.031 3496 Dihedral : 6.795 137.279 3008 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.73 % 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: 0.13 (0.17), residues: 2828 helix: 1.45 (0.15), residues: 1364 sheet: -0.96 (0.26), residues: 456 loop : -1.26 (0.20), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.564 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1211 time to fit residues: 10.2485 Evaluate side-chains 38 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 174 optimal weight: 0.9980 chunk 186 optimal weight: 40.0000 chunk 135 optimal weight: 50.0000 chunk 25 optimal weight: 0.3980 chunk 215 optimal weight: 0.0980 chunk 249 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3945 moved from start: 7.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 19204 Z= 0.209 Angle : 0.675 7.260 26236 Z= 0.398 Chirality : 0.041 0.161 3164 Planarity : 0.004 0.030 3496 Dihedral : 6.786 137.496 3008 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.37 % Favored : 94.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.87 % 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: 0.18 (0.17), residues: 2828 helix: 1.48 (0.15), residues: 1372 sheet: -1.03 (0.25), residues: 456 loop : -1.19 (0.20), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.538 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1136 time to fit residues: 9.1574 Evaluate side-chains 38 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 10.0000 chunk 239 optimal weight: 0.6980 chunk 255 optimal weight: 40.0000 chunk 153 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 167 optimal weight: 0.2980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3932 moved from start: 7.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 19204 Z= 0.189 Angle : 0.675 7.315 26236 Z= 0.395 Chirality : 0.041 0.163 3164 Planarity : 0.004 0.033 3496 Dihedral : 6.750 137.204 3008 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.23 % Favored : 94.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.87 % 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: 0.18 (0.17), residues: 2828 helix: 1.46 (0.15), residues: 1372 sheet: -1.30 (0.25), residues: 440 loop : -1.02 (0.20), residues: 1016 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.531 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1166 time to fit residues: 9.4024 Evaluate side-chains 39 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 282 optimal weight: 50.0000 chunk 260 optimal weight: 30.0000 chunk 225 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 174 optimal weight: 0.0970 chunk 138 optimal weight: 20.0000 chunk 178 optimal weight: 0.0870 overall best weight: 1.4360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3945 moved from start: 7.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 19204 Z= 0.192 Angle : 0.666 7.988 26236 Z= 0.390 Chirality : 0.041 0.161 3164 Planarity : 0.004 0.030 3496 Dihedral : 6.723 136.839 3008 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.23 % Favored : 94.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.87 % 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: 0.19 (0.17), residues: 2828 helix: 1.49 (0.15), residues: 1372 sheet: -1.33 (0.24), residues: 488 loop : -0.99 (0.21), residues: 968 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1177 time to fit residues: 10.3084 Evaluate side-chains 43 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 207 optimal weight: 0.0060 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 225 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.076079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058279 restraints weight = 22997.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.059990 restraints weight = 13459.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.061143 restraints weight = 9060.680| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4509 moved from start: 7.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19204 Z= 0.182 Angle : 0.668 7.730 26236 Z= 0.389 Chirality : 0.041 0.163 3164 Planarity : 0.004 0.029 3496 Dihedral : 6.655 136.805 3008 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.52 % Favored : 94.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.87 % 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: 0.32 (0.17), residues: 2828 helix: 1.60 (0.15), residues: 1376 sheet: -1.17 (0.24), residues: 476 loop : -1.02 (0.21), residues: 976 =============================================================================== Job complete usr+sys time: 2062.66 seconds wall clock time: 38 minutes 55.00 seconds (2335.00 seconds total)