Starting phenix.real_space_refine on Sun May 18 03:15:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lld_63198/05_2025/9lld_63198.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lld_63198/05_2025/9lld_63198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lld_63198/05_2025/9lld_63198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lld_63198/05_2025/9lld_63198.map" model { file = "/net/cci-nas-00/data/ceres_data/9lld_63198/05_2025/9lld_63198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lld_63198/05_2025/9lld_63198.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10293 2.51 5 N 2815 2.21 5 O 3134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16287 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 3850 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 22, 'TRANS': 530} Chain breaks: 1 Unresolved non-hydrogen bonds: 584 Unresolved non-hydrogen angles: 741 Unresolved non-hydrogen dihedrals: 479 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 18, 'TYR:plan': 12, 'ASN:plan1': 9, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 376 Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 817 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 776 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 3834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 3834 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PTRANS': 22, 'TRANS': 530} Chain breaks: 1 Unresolved non-hydrogen bonds: 600 Unresolved non-hydrogen angles: 758 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 15, 'TYR:plan': 12, 'ASN:plan1': 10, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 380 Chain: "D" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 821 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 776 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 3864 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 22, 'TRANS': 530} Chain breaks: 1 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 724 Unresolved non-hydrogen dihedrals: 464 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 14, 'TYR:plan': 12, 'ASN:plan1': 8, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 343 Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 813 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "G" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 736 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 10.41, per 1000 atoms: 0.64 Number of scatterers: 16287 At special positions: 0 Unit cell: (127.395, 132.525, 198.36, 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 45 16.00 O 3134 8.00 N 2815 7.00 C 10293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 362 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 2.1 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 36 sheets defined 12.3% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 363 through 379 removed outlier: 3.729A pdb=" N ASN C 368 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 498 removed outlier: 3.737A pdb=" N GLN C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 510 removed outlier: 3.756A pdb=" N VAL C 505 " --> pdb=" O ASN C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 652 removed outlier: 3.502A pdb=" N LYS C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 652 " --> pdb=" O LYS C 648 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.216A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 362 through 379 removed outlier: 4.435A pdb=" N ASP A 366 " --> pdb=" O CYS A 362 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 498 removed outlier: 3.711A pdb=" N GLN A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.753A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 651 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 362 through 379 removed outlier: 4.490A pdb=" N ASP B 366 " --> pdb=" O CYS B 362 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B 368 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 498 removed outlier: 3.740A pdb=" N GLN B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.791A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 644 through 651 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 75 through 77 removed outlier: 3.907A pdb=" N SER C 515 " --> pdb=" O THR C 526 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 95 through 103 removed outlier: 6.631A pdb=" N GLY C 96 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG C 325 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS C 321 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS C 102 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU C 319 " --> pdb=" O LYS C 102 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 317 through 327 current: chain 'C' and resid 398 through 406 Processing sheet with id=AA3, first strand: chain 'C' and resid 108 through 123 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 134 through 135 current: chain 'C' and resid 197 through 198 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 245 through 246 current: chain 'C' and resid 293 through 297 Processing sheet with id=AA4, first strand: chain 'C' and resid 158 through 159 Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 163 removed outlier: 4.014A pdb=" N LYS C 162 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AA7, first strand: chain 'C' and resid 536 through 538 removed outlier: 6.458A pdb=" N VAL C 556 " --> pdb=" O PHE C 567 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE C 567 " --> pdb=" O VAL C 556 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE C 558 " --> pdb=" O ASN C 565 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN C 565 " --> pdb=" O PHE C 558 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 560 " --> pdb=" O SER C 563 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 596 through 597 removed outlier: 3.519A pdb=" N THR C 601 " --> pdb=" O ILE C 613 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 613 " --> pdb=" O THR C 601 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 611 " --> pdb=" O VAL C 603 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 619 through 620 removed outlier: 6.891A pdb=" N SER C 619 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 75 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 525 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 515 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.568A pdb=" N GLU H 10 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR H 115 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 8 through 9 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 8 through 9 current: chain 'L' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 49 current: chain 'L' and resid 97 through 100 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AB5, first strand: chain 'A' and resid 95 through 103 removed outlier: 6.684A pdb=" N GLY A 96 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 325 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A 321 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LYS A 102 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU A 319 " --> pdb=" O LYS A 102 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 317 through 327 current: chain 'A' and resid 398 through 406 Processing sheet with id=AB6, first strand: chain 'A' and resid 108 through 123 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 134 through 135 current: chain 'A' and resid 197 through 198 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 245 through 246 current: chain 'A' and resid 293 through 297 Processing sheet with id=AB7, first strand: chain 'A' and resid 157 through 159 Processing sheet with id=AB8, first strand: chain 'A' and resid 334 through 339 removed outlier: 3.895A pdb=" N ALA A 348 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 536 through 538 Processing sheet with id=AC1, first strand: chain 'A' and resid 593 through 597 Processing sheet with id=AC2, first strand: chain 'A' and resid 620 through 621 removed outlier: 3.733A pdb=" N LEU A 621 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER B 515 " --> pdb=" O THR B 526 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.567A pdb=" N GLU D 10 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR D 115 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 8 through 9 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 8 through 9 current: chain 'F' and resid 45 through 50 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 50 current: chain 'F' and resid 97 through 100 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AC7, first strand: chain 'B' and resid 317 through 327 removed outlier: 7.232A pdb=" N VAL B 100 " --> pdb=" O TRP B 320 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR B 322 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B 98 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLY B 96 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 108 through 123 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 134 through 135 current: chain 'B' and resid 197 through 199 removed outlier: 3.622A pdb=" N CYS B 222 " --> pdb=" O SER B 199 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 245 through 246 current: chain 'B' and resid 293 through 297 Processing sheet with id=AC9, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AD1, first strand: chain 'B' and resid 334 through 339 removed outlier: 3.925A pdb=" N ALA B 348 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 382 through 383 Processing sheet with id=AD3, first strand: chain 'B' and resid 536 through 538 Processing sheet with id=AD4, first strand: chain 'B' and resid 592 through 597 Processing sheet with id=AD5, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.615A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.557A pdb=" N GLU E 10 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR E 115 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 8 through 9 Processing sheet with id=AD8, first strand: chain 'G' and resid 17 through 22 Processing sheet with id=AD9, first strand: chain 'G' and resid 45 through 49 removed outlier: 6.983A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1266 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: 5.07 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5311 1.34 - 1.46: 3222 1.46 - 1.58: 8037 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 16624 Sorted by residual: bond pdb=" N GLU A 206 " pdb=" CA GLU A 206 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.62e+01 bond pdb=" N VAL A 202 " pdb=" CA VAL A 202 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" N VAL D 93 " pdb=" CA VAL D 93 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.21e-02 6.83e+03 9.08e+00 bond pdb=" N GLY H 109 " pdb=" CA GLY H 109 " ideal model delta sigma weight residual 1.450 1.478 -0.028 9.40e-03 1.13e+04 8.89e+00 bond pdb=" N SER D 84 " pdb=" CA SER D 84 " ideal model delta sigma weight residual 1.452 1.488 -0.035 1.22e-02 6.72e+03 8.27e+00 ... (remaining 16619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 22510 2.05 - 4.11: 313 4.11 - 6.16: 20 6.16 - 8.22: 2 8.22 - 10.27: 2 Bond angle restraints: 22847 Sorted by residual: angle pdb=" C GLN B 633 " pdb=" N ASN B 634 " pdb=" CA ASN B 634 " ideal model delta sigma weight residual 122.73 112.46 10.27 1.62e+00 3.81e-01 4.02e+01 angle pdb=" C SER B 652 " pdb=" CA SER B 652 " pdb=" CB SER B 652 " ideal model delta sigma weight residual 116.54 111.39 5.15 1.15e+00 7.56e-01 2.01e+01 angle pdb=" N LEU B 378 " pdb=" CA LEU B 378 " pdb=" C LEU B 378 " ideal model delta sigma weight residual 113.17 118.75 -5.58 1.26e+00 6.30e-01 1.96e+01 angle pdb=" N ILE B 632 " pdb=" CA ILE B 632 " pdb=" C ILE B 632 " ideal model delta sigma weight residual 109.30 104.16 5.14 1.31e+00 5.83e-01 1.54e+01 angle pdb=" C PHE B 631 " pdb=" N ILE B 632 " pdb=" CA ILE B 632 " ideal model delta sigma weight residual 120.69 114.98 5.71 1.46e+00 4.69e-01 1.53e+01 ... (remaining 22842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 8749 17.59 - 35.17: 801 35.17 - 52.76: 168 52.76 - 70.34: 40 70.34 - 87.93: 15 Dihedral angle restraints: 9773 sinusoidal: 2933 harmonic: 6840 Sorted by residual: dihedral pdb=" SG CYS B 68 " pdb=" CB CYS B 528 " pdb=" SG CYS B 528 " pdb=" CA CYS B 528 " ideal model delta sinusoidal sigma weight residual -73.00 0.36 -73.36 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" SG CYS C 68 " pdb=" CB CYS C 528 " pdb=" SG CYS C 528 " pdb=" CA CYS C 528 " ideal model delta sinusoidal sigma weight residual -73.00 -2.17 -70.83 1 2.00e+01 2.50e-03 1.61e+01 dihedral pdb=" SG CYS A 68 " pdb=" CB CYS A 528 " pdb=" SG CYS A 528 " pdb=" CA CYS A 528 " ideal model delta sinusoidal sigma weight residual -73.00 -3.05 -69.95 1 2.00e+01 2.50e-03 1.58e+01 ... (remaining 9770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2279 0.050 - 0.101: 379 0.101 - 0.151: 124 0.151 - 0.201: 8 0.201 - 0.252: 2 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CA ILE B 632 " pdb=" N ILE B 632 " pdb=" C ILE B 632 " pdb=" CB ILE B 632 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU B 378 " pdb=" N LEU B 378 " pdb=" C LEU B 378 " pdb=" CB LEU B 378 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE E 102 " pdb=" N ILE E 102 " pdb=" C ILE E 102 " pdb=" CB ILE E 102 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 2789 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 101 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C ALA H 101 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA H 101 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE H 102 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 82 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C GLN D 82 " 0.049 2.00e-02 2.50e+03 pdb=" O GLN D 82 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU D 83 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 402 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO C 403 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 403 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 403 " 0.018 5.00e-02 4.00e+02 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2297 2.76 - 3.29: 16027 3.29 - 3.83: 26772 3.83 - 4.36: 28297 4.36 - 4.90: 49730 Nonbonded interactions: 123123 Sorted by model distance: nonbonded pdb=" O VAL B 279 " pdb=" OG1 THR B 286 " model vdw 2.221 3.040 nonbonded pdb=" O THR C 120 " pdb=" OG1 THR C 218 " model vdw 2.229 3.040 nonbonded pdb=" NZ LYS B 377 " pdb=" CD2 LEU B 378 " model vdw 2.231 3.540 nonbonded pdb=" OD1 ASP H 100 " pdb=" N ALA H 101 " model vdw 2.233 3.120 nonbonded pdb=" OG1 THR B 601 " pdb=" O ILE B 613 " model vdw 2.261 3.040 ... (remaining 123118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 58 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 86 or (resid 87 through 94 and (na \ me N or name CA or name C or name O or name CB )) or resid 95 through 96 or (res \ id 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throu \ gh 163 or (resid 164 through 166 and (name N or name CA or name C or name O or n \ ame CB )) or resid 167 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 177 or (resid 178 and (name N or \ name CA or name C or name O or name CB )) or resid 179 through 189 or (resid 190 \ through 193 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 94 through 220 or (resid 221 and (name N or name CA or name C or name O or name \ CB )) or resid 222 through 229 or (resid 230 and (name N or name CA or name C or \ name O or name CB )) or resid 231 through 254 or (resid 255 and (name N or name \ CA or name C or name O or name CB )) or resid 256 through 268 or (resid 269 thr \ ough 275 and (name N or name CA or name C or name O or name CB )) or resid 276 t \ hrough 295 or (resid 296 through 297 and (name N or name CA or name C or name O \ or name CB )) or resid 298 through 332 or (resid 333 and (name N or name CA or n \ ame C or name O or name CB )) or resid 334 through 339 or (resid 340 through 341 \ and (name N or name CA or name C or name O or name CB )) or resid 342 through 4 \ 78 or (resid 479 and (name N or name CA or name C or name O or name CB )) or res \ id 480 through 495 or (resid 496 and (name N or name CA or name C or name O or n \ ame CB )) or resid 497 through 524 or (resid 525 and (name N or name CA or name \ C or name O or name CB )) or resid 526 through 543 or (resid 544 and (name N or \ name CA or name C or name O or name CB )) or resid 545 through 591 or (resid 592 \ and (name N or name CA or name C or name O or name CB )) or resid 593 through 5 \ 98 or (resid 599 through 600 and (name N or name CA or name C or name O or name \ CB )) or resid 601 through 622 or (resid 623 and (name N or name CA or name C or \ name O or name CB )) or resid 624 through 629 or (resid 630 and (name N or name \ CA or name C or name O or name CB )) or resid 631 or (resid 632 through 636 and \ (name N or name CA or name C or name O or name CB )) or resid 637 through 640 o \ r (resid 641 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 42 through 653)) selection = (chain 'B' and (resid 58 through 92 or (resid 93 through 94 and (name N or name \ CA or name C or name O or name CB )) or resid 95 through 96 or (resid 97 and (na \ me N or name CA or name C or name O or name CB )) or resid 98 through 140 or (re \ sid 141 and (name N or name CA or name C or name O or name CB )) or resid 142 th \ rough 169 or (resid 170 and (name N or name CA or name C or name O or name CB )) \ or resid 171 through 192 or (resid 193 and (name N or name CA or name C or name \ O or name CB )) or resid 194 through 202 or (resid 203 through 206 and (name N \ or name CA or name C or name O or name CB )) or resid 207 through 218 or (resid \ 219 and (name N or name CA or name C or name O or name CB )) or resid 220 or (re \ sid 221 and (name N or name CA or name C or name O or name CB )) or resid 222 th \ rough 229 or (resid 230 and (name N or name CA or name C or name O or name CB )) \ or resid 231 through 270 or (resid 271 through 275 and (name N or name CA or na \ me C or name O or name CB )) or resid 276 through 291 or (resid 292 and (name N \ or name CA or name C or name O or name CB )) or resid 293 through 307 or (resid \ 308 and (name N or name CA or name C or name O or name CB )) or resid 309 throug \ h 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) or \ resid 334 through 339 or (resid 340 through 341 and (name N or name CA or name C \ or name O or name CB )) or resid 342 through 454 or (resid 455 through 456 and \ (name N or name CA or name C or name O or name CB )) or resid 457 through 466 or \ (resid 467 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 8 or (resid 469 through 470 and (name N or name CA or name C or name O or name C \ B )) or resid 471 through 477 or (resid 478 through 479 and (name N or name CA o \ r name C or name O or name CB )) or resid 480 through 489 or (resid 490 and (nam \ e N or name CA or name C or name O or name CB )) or resid 491 through 500 or (re \ sid 501 and (name N or name CA or name C or name O or name CB )) or resid 502 th \ rough 518 or (resid 519 and (name N or name CA or name C or name O or name CB )) \ or resid 520 or (resid 521 through 522 and (name N or name CA or name C or name \ O or name CB )) or resid 523 through 524 or (resid 525 and (name N or name CA o \ r name C or name O or name CB )) or resid 526 through 591 or (resid 592 and (nam \ e N or name CA or name C or name O or name CB )) or resid 593 through 618 or (re \ sid 619 and (name N or name CA or name C or name O or name CB )) or resid 620 th \ rough 629 or (resid 630 and (name N or name CA or name C or name O or name CB )) \ or resid 631 through 634 or (resid 635 through 636 and (name N or name CA or na \ me C or name O or name CB )) or resid 637 through 640 or (resid 641 and (name N \ or name CA or name C or name O or name CB )) or resid 642 through 644 or (resid \ 645 through 647 and (name N or name CA or name C or name O or name CB )) or resi \ d 648 or (resid 649 and (name N or name CA or name C or name O or name CB )) or \ resid 650 through 653)) selection = (chain 'C' and (resid 58 through 80 or (resid 81 through 82 and (name N or name \ CA or name C or name O or name CB )) or resid 83 through 93 or (resid 94 and (na \ me N or name CA or name C or name O or name CB )) or resid 95 through 102 or (re \ sid 103 and (name N or name CA or name C or name O or name CB )) or resid 104 th \ rough 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) \ or resid 142 or (resid 143 and (name N or name CA or name C or name O or name C \ B )) or resid 144 through 163 or (resid 164 through 166 and (name N or name CA o \ r name C or name O or name CB )) or resid 167 through 177 or (resid 178 and (nam \ e N or name CA or name C or name O or name CB )) or resid 179 through 189 or (re \ sid 190 through 193 and (name N or name CA or name C or name O or name CB )) or \ resid 194 through 199 or (resid 200 and (name N or name CA or name C or name O o \ r name CB )) or resid 201 through 202 or (resid 203 through 206 and (name N or n \ ame CA or name C or name O or name CB )) or resid 207 through 218 or (resid 219 \ and (name N or name CA or name C or name O or name CB )) or resid 220 through 26 \ 7 or (resid 268 through 275 and (name N or name CA or name C or name O or name C \ B )) or resid 276 through 291 or (resid 292 and (name N or name CA or name C or \ name O or name CB )) or resid 293 through 295 or (resid 296 through 297 and (nam \ e N or name CA or name C or name O or name CB )) or resid 298 through 307 or (re \ sid 308 and (name N or name CA or name C or name O or name CB )) or resid 309 th \ rough 466 or (resid 467 and (name N or name CA or name C or name O or name CB )) \ or resid 468 or (resid 469 through 470 and (name N or name CA or name C or name \ O or name CB )) or resid 471 through 478 or (resid 479 and (name N or name CA o \ r name C or name O or name CB )) or resid 480 or (resid 481 through 482 and (nam \ e N or name CA or name C or name O or name CB )) or resid 483 through 500 or (re \ sid 501 and (name N or name CA or name C or name O or name CB )) or resid 502 th \ rough 518 or (resid 519 and (name N or name CA or name C or name O or name CB )) \ or resid 520 through 543 or (resid 544 and (name N or name CA or name C or name \ O or name CB )) or resid 545 through 598 or (resid 599 through 600 and (name N \ or name CA or name C or name O or name CB )) or resid 601 through 622 or (resid \ 623 and (name N or name CA or name C or name O or name CB )) or resid 624 throug \ h 644 or (resid 645 through 647 and (name N or name CA or name C or name O or na \ me CB )) or resid 648 through 653)) } ncs_group { reference = (chain 'D' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 70 or (resid 71 through 72 and (name \ N or name CA or name C or name O or name CB )) or resid 73 through 85 or (resid \ 86 through 92 and (name N or name CA or name C or name O or name CB )) or resid \ 93 through 98 or (resid 99 and (name N or name CA or name C or name O or name C \ B )) or resid 100 through 102 or (resid 103 and (name N or name CA or name C or \ name O or name CB )) or resid 104 or (resid 105 and (name N or name CA or name C \ or name O or name CB )) or resid 106 through 116)) selection = (chain 'E' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 84 or (resid 85 through 92 and (name N or name CA \ or name C or name O or name CB )) or resid 93 through 102 or (resid 103 and (na \ me N or name CA or name C or name O or name CB )) or resid 104 or (resid 105 and \ (name N or name CA or name C or name O or name CB )) or resid 106 through 116)) \ selection = (chain 'H' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 42 or (resid 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 70 or (resid 71 throug \ h 72 and (name N or name CA or name C or name O or name CB )) or resid 73 throug \ h 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or re \ sid 84 or (resid 85 through 92 and (name N or name CA or name C or name O or nam \ e CB )) or resid 93 through 116)) } ncs_group { reference = (chain 'F' and (resid 1 through 2 or (resid 3 through 4 and (name N or name CA o \ r name C or name O or name CB )) or resid 5 through 17 or (resid 18 and (name N \ or name CA or name C or name O or name CB )) or resid 19 through 24 or (resid 25 \ through 27 and (name N or name CA or name C or name O or name CB )) or resid 28 \ through 46 or (resid 47 and (name N or name CA or name C or name O or name CB ) \ ) or resid 48 through 52 or (resid 53 through 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 73 or (resid 74 and (name N or nam \ e CA or name C or name O or name CB )) or resid 75 through 79 or (resid 80 throu \ gh 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ gh 109)) selection = (chain 'G' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 56 or (resid 57 and (name N or name CA \ or name C or name O or name CB )) or resid 58 through 109)) selection = (chain 'L' and (resid 1 through 2 or (resid 3 through 4 and (name N or name CA o \ r name C or name O or name CB )) or resid 5 through 24 or (resid 25 through 27 a \ nd (name N or name CA or name C or name O or name CB )) or resid 28 through 46 o \ r (resid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 \ through 52 or (resid 53 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 or (resid 57 and (name N or name CA or name C or name O \ or name CB )) or resid 58 through 73 or (resid 74 and (name N or name CA or nam \ e C or name O or name CB )) or resid 75 through 79 or (resid 80 through 86 and ( \ name N or name CA or name C or name O or name CB )) or resid 87 through 104 or ( \ resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 \ through 109)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.450 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 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 : 0.003 0.038 16639 Z= 0.217 Angle : 0.555 10.273 22877 Z= 0.344 Chirality : 0.043 0.252 2792 Planarity : 0.003 0.034 2952 Dihedral : 14.894 87.928 5294 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.07 % Allowed : 31.35 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.19), residues: 2310 helix: 3.10 (0.33), residues: 228 sheet: 0.21 (0.20), residues: 807 loop : -1.54 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 483 HIS 0.003 0.000 HIS B 382 PHE 0.011 0.001 PHE A 624 TYR 0.011 0.001 TYR A 197 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.15929 ( 482) hydrogen bonds : angle 5.69052 ( 1266) SS BOND : bond 0.00287 ( 15) SS BOND : angle 0.99144 ( 30) covalent geometry : bond 0.00334 (16624) covalent geometry : angle 0.55442 (22847) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 19 ILE cc_start: -0.1452 (mp) cc_final: -0.1778 (pt) REVERT: F 76 ILE cc_start: 0.1018 (pt) cc_final: 0.0610 (pt) REVERT: F 106 LEU cc_start: -0.1949 (tt) cc_final: -0.2301 (tt) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.2381 time to fit residues: 48.6895 Evaluate side-chains 66 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.2980 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 0.0270 chunk 116 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 207 optimal weight: 20.0000 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 491 ASN A 491 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.035309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.026033 restraints weight = 181822.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.026652 restraints weight = 97387.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.027037 restraints weight = 64973.273| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16639 Z= 0.095 Angle : 0.491 7.171 22877 Z= 0.260 Chirality : 0.043 0.266 2792 Planarity : 0.003 0.049 2952 Dihedral : 3.495 18.349 2468 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 3.01 % Allowed : 29.75 % Favored : 67.25 % 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: -0.44 (0.18), residues: 2310 helix: 2.90 (0.32), residues: 252 sheet: 0.58 (0.20), residues: 768 loop : -1.59 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 55 HIS 0.007 0.001 HIS L 40 PHE 0.018 0.001 PHE C 77 TYR 0.010 0.001 TYR B 197 ARG 0.003 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 482) hydrogen bonds : angle 4.47762 ( 1266) SS BOND : bond 0.00402 ( 15) SS BOND : angle 1.04638 ( 30) covalent geometry : bond 0.00204 (16624) covalent geometry : angle 0.48974 (22847) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8397 (mmm-85) REVERT: H 83 LEU cc_start: 0.9124 (mp) cc_final: 0.8378 (tp) REVERT: L 19 ILE cc_start: 0.9241 (mp) cc_final: 0.9025 (pt) REVERT: A 325 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8456 (mmm-85) REVERT: F 83 ASP cc_start: 0.8711 (p0) cc_final: 0.8235 (p0) REVERT: F 106 LEU cc_start: 0.8774 (tt) cc_final: 0.8501 (tt) REVERT: E 38 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8449 (ttp80) outliers start: 45 outliers final: 15 residues processed: 119 average time/residue: 0.2414 time to fit residues: 46.0714 Evaluate side-chains 82 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 38 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 153 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 204 optimal weight: 0.0370 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN A 221 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.033551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.023900 restraints weight = 189150.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.024485 restraints weight = 99506.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.024846 restraints weight = 66537.191| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16639 Z= 0.169 Angle : 0.516 6.729 22877 Z= 0.277 Chirality : 0.041 0.208 2792 Planarity : 0.004 0.039 2952 Dihedral : 3.673 18.282 2468 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.51 % Rotamer: Outliers : 3.28 % Allowed : 29.14 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.43 (0.18), residues: 2310 helix: 3.21 (0.32), residues: 252 sheet: 0.42 (0.20), residues: 741 loop : -1.50 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.004 0.001 HIS L 40 PHE 0.013 0.001 PHE B 77 TYR 0.011 0.001 TYR B 101 ARG 0.003 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 482) hydrogen bonds : angle 4.53956 ( 1266) SS BOND : bond 0.00321 ( 15) SS BOND : angle 1.06059 ( 30) covalent geometry : bond 0.00362 (16624) covalent geometry : angle 0.51505 (22847) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 68 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8432 (mmm-85) REVERT: C 566 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9242 (mp) REVERT: H 83 LEU cc_start: 0.9251 (mp) cc_final: 0.8524 (tp) REVERT: A 325 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8541 (mmm-85) REVERT: A 624 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8817 (m-80) REVERT: F 83 ASP cc_start: 0.9002 (p0) cc_final: 0.8460 (p0) REVERT: F 106 LEU cc_start: 0.9096 (tt) cc_final: 0.8683 (tt) outliers start: 49 outliers final: 24 residues processed: 113 average time/residue: 0.2467 time to fit residues: 45.9065 Evaluate side-chains 89 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 102 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 60 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 142 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 96 optimal weight: 0.0040 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 50.0000 chunk 217 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 overall best weight: 4.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** 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 = 0.3087 r_free = 0.3087 target = 0.032321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.022535 restraints weight = 190994.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.023082 restraints weight = 102596.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.023419 restraints weight = 69724.678| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 16639 Z= 0.276 Angle : 0.583 5.877 22877 Z= 0.315 Chirality : 0.041 0.171 2792 Planarity : 0.004 0.041 2952 Dihedral : 4.247 18.959 2468 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.75 % Favored : 92.21 % Rotamer: Outliers : 4.48 % Allowed : 28.34 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.18), residues: 2310 helix: 2.64 (0.32), residues: 270 sheet: 0.23 (0.20), residues: 741 loop : -1.70 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 36 HIS 0.008 0.001 HIS A 593 PHE 0.032 0.002 PHE B 77 TYR 0.018 0.001 TYR L 37 ARG 0.009 0.001 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 482) hydrogen bonds : angle 4.83190 ( 1266) SS BOND : bond 0.00452 ( 15) SS BOND : angle 1.25820 ( 30) covalent geometry : bond 0.00590 (16624) covalent geometry : angle 0.58147 (22847) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 61 time to evaluate : 1.884 Fit side-chains REVERT: C 325 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8447 (mmm-85) REVERT: L 51 ASP cc_start: 0.9607 (t0) cc_final: 0.8920 (t0) REVERT: L 54 LYS cc_start: 0.9748 (mmmm) cc_final: 0.9235 (mmmm) REVERT: A 325 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8540 (mmm-85) REVERT: F 83 ASP cc_start: 0.9135 (p0) cc_final: 0.8426 (p0) REVERT: F 106 LEU cc_start: 0.9124 (tt) cc_final: 0.8537 (tt) REVERT: B 566 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9332 (mm) outliers start: 67 outliers final: 42 residues processed: 125 average time/residue: 0.2174 time to fit residues: 44.5695 Evaluate side-chains 101 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 56 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 528 CYS Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 103 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 6.9990 chunk 164 optimal weight: 30.0000 chunk 132 optimal weight: 0.0070 chunk 86 optimal weight: 40.0000 chunk 102 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 16 optimal weight: 30.0000 chunk 152 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 GLN ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** 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 = 0.3093 r_free = 0.3093 target = 0.032397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.022584 restraints weight = 191559.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.023144 restraints weight = 101543.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.023489 restraints weight = 68497.604| |-----------------------------------------------------------------------------| r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16639 Z= 0.178 Angle : 0.508 7.582 22877 Z= 0.271 Chirality : 0.041 0.180 2792 Planarity : 0.003 0.046 2952 Dihedral : 3.987 18.332 2468 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.28 % Favored : 93.68 % Rotamer: Outliers : 3.74 % Allowed : 29.21 % Favored : 67.05 % 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: -0.79 (0.18), residues: 2310 helix: 2.41 (0.32), residues: 288 sheet: -0.17 (0.19), residues: 807 loop : -1.55 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 36 HIS 0.003 0.001 HIS A 593 PHE 0.018 0.001 PHE B 77 TYR 0.009 0.001 TYR G 37 ARG 0.006 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 482) hydrogen bonds : angle 4.55016 ( 1266) SS BOND : bond 0.00314 ( 15) SS BOND : angle 1.21564 ( 30) covalent geometry : bond 0.00385 (16624) covalent geometry : angle 0.50618 (22847) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 56 time to evaluate : 2.039 Fit side-chains revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8434 (mmm-85) REVERT: A 325 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8536 (mmm-85) REVERT: F 83 ASP cc_start: 0.9197 (p0) cc_final: 0.8440 (p0) REVERT: F 106 LEU cc_start: 0.9153 (tt) cc_final: 0.8446 (tt) outliers start: 56 outliers final: 39 residues processed: 109 average time/residue: 0.2303 time to fit residues: 41.6084 Evaluate side-chains 96 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 55 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 528 CYS Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 83 optimal weight: 50.0000 chunk 210 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 27 optimal weight: 0.0770 chunk 173 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 overall best weight: 4.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.032013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.022241 restraints weight = 192357.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.022782 restraints weight = 102594.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.023113 restraints weight = 69746.865| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16639 Z= 0.261 Angle : 0.571 6.479 22877 Z= 0.307 Chirality : 0.041 0.140 2792 Planarity : 0.004 0.046 2952 Dihedral : 4.366 20.108 2468 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.31 % Favored : 91.65 % Rotamer: Outliers : 5.28 % Allowed : 27.41 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 2310 helix: 2.13 (0.31), residues: 288 sheet: -0.19 (0.19), residues: 777 loop : -1.76 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 36 HIS 0.006 0.001 HIS F 40 PHE 0.021 0.001 PHE B 77 TYR 0.014 0.001 TYR B 101 ARG 0.006 0.001 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 482) hydrogen bonds : angle 4.81567 ( 1266) SS BOND : bond 0.00441 ( 15) SS BOND : angle 1.39258 ( 30) covalent geometry : bond 0.00558 (16624) covalent geometry : angle 0.56908 (22847) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 52 time to evaluate : 2.025 Fit side-chains REVERT: C 325 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8437 (mmm-85) REVERT: A 97 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9091 (mp) REVERT: A 325 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8546 (mmm-85) REVERT: B 383 VAL cc_start: 0.9485 (OUTLIER) cc_final: 0.9259 (p) outliers start: 79 outliers final: 56 residues processed: 129 average time/residue: 0.2193 time to fit residues: 48.0455 Evaluate side-chains 110 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 50 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 528 CYS Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN A 221 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.032197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.022414 restraints weight = 191320.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.022962 restraints weight = 100969.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.023302 restraints weight = 68287.994| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16639 Z= 0.165 Angle : 0.513 9.730 22877 Z= 0.272 Chirality : 0.041 0.142 2792 Planarity : 0.003 0.046 2952 Dihedral : 4.075 18.035 2468 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.81 % Allowed : 29.28 % Favored : 66.91 % 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: -1.00 (0.18), residues: 2310 helix: 2.38 (0.32), residues: 288 sheet: -0.29 (0.19), residues: 783 loop : -1.72 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 55 HIS 0.003 0.001 HIS A 593 PHE 0.012 0.001 PHE B 77 TYR 0.008 0.001 TYR B 101 ARG 0.006 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 482) hydrogen bonds : angle 4.53771 ( 1266) SS BOND : bond 0.00294 ( 15) SS BOND : angle 1.12576 ( 30) covalent geometry : bond 0.00358 (16624) covalent geometry : angle 0.51188 (22847) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 54 time to evaluate : 1.870 Fit side-chains revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8423 (mmm-85) REVERT: A 325 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8503 (mmm-85) outliers start: 57 outliers final: 50 residues processed: 109 average time/residue: 0.2168 time to fit residues: 40.0599 Evaluate side-chains 103 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 51 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 528 CYS Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 65 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 207 optimal weight: 0.0070 chunk 162 optimal weight: 50.0000 chunk 214 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.031968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.022214 restraints weight = 191616.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.022746 restraints weight = 102328.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.023080 restraints weight = 69623.624| |-----------------------------------------------------------------------------| r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16639 Z= 0.272 Angle : 0.587 7.841 22877 Z= 0.312 Chirality : 0.041 0.136 2792 Planarity : 0.004 0.046 2952 Dihedral : 4.377 21.491 2468 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.61 % Favored : 91.34 % Rotamer: Outliers : 4.88 % Allowed : 28.14 % Favored : 66.98 % 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 (0.18), residues: 2310 helix: 2.08 (0.31), residues: 291 sheet: -0.37 (0.19), residues: 780 loop : -1.83 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 36 HIS 0.005 0.001 HIS A 593 PHE 0.016 0.001 PHE B 77 TYR 0.014 0.001 TYR B 101 ARG 0.005 0.001 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 482) hydrogen bonds : angle 4.80594 ( 1266) SS BOND : bond 0.00429 ( 15) SS BOND : angle 1.34096 ( 30) covalent geometry : bond 0.00581 (16624) covalent geometry : angle 0.58543 (22847) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 50 time to evaluate : 1.874 Fit side-chains REVERT: C 325 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8413 (mmm-85) REVERT: A 97 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9077 (mp) REVERT: A 325 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8538 (mmm-85) REVERT: F 15 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.9059 (tt0) REVERT: B 383 VAL cc_start: 0.9489 (OUTLIER) cc_final: 0.9260 (p) REVERT: B 480 SER cc_start: 0.9829 (OUTLIER) cc_final: 0.9574 (p) REVERT: E 67 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.8898 (mmm160) outliers start: 73 outliers final: 65 residues processed: 120 average time/residue: 0.2232 time to fit residues: 44.6607 Evaluate side-chains 120 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 48 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 528 CYS Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 188 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 173 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.032291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.022521 restraints weight = 189681.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.023079 restraints weight = 98958.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.023433 restraints weight = 66394.598| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16639 Z= 0.108 Angle : 0.503 7.995 22877 Z= 0.263 Chirality : 0.042 0.140 2792 Planarity : 0.003 0.048 2952 Dihedral : 3.893 19.730 2468 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.37 % Rotamer: Outliers : 3.28 % Allowed : 30.01 % Favored : 66.71 % 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: -0.98 (0.18), residues: 2310 helix: 2.48 (0.33), residues: 288 sheet: -0.33 (0.19), residues: 783 loop : -1.68 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.002 0.000 HIS C 276 PHE 0.012 0.001 PHE A 238 TYR 0.006 0.001 TYR A 495 ARG 0.006 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 482) hydrogen bonds : angle 4.33993 ( 1266) SS BOND : bond 0.00229 ( 15) SS BOND : angle 0.99075 ( 30) covalent geometry : bond 0.00234 (16624) covalent geometry : angle 0.50179 (22847) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 50 time to evaluate : 1.839 Fit side-chains REVERT: C 325 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8368 (mmm-85) REVERT: H 83 LEU cc_start: 0.9497 (mp) cc_final: 0.8808 (tp) REVERT: A 325 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8501 (mmm-85) REVERT: B 383 VAL cc_start: 0.9486 (OUTLIER) cc_final: 0.9264 (p) outliers start: 49 outliers final: 41 residues processed: 97 average time/residue: 0.2180 time to fit residues: 36.1015 Evaluate side-chains 93 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 49 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 528 CYS Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 45 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 22 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 159 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 chunk 123 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 145 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.032338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.022594 restraints weight = 190725.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.023164 restraints weight = 99006.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.023514 restraints weight = 66284.300| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16639 Z= 0.100 Angle : 0.497 10.847 22877 Z= 0.256 Chirality : 0.041 0.148 2792 Planarity : 0.003 0.045 2952 Dihedral : 3.692 20.235 2468 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.07 % Allowed : 30.35 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.95 (0.18), residues: 2310 helix: 2.47 (0.32), residues: 288 sheet: -0.34 (0.18), residues: 804 loop : -1.65 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.002 0.000 HIS B 93 PHE 0.012 0.001 PHE A 238 TYR 0.008 0.001 TYR B 101 ARG 0.007 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 482) hydrogen bonds : angle 4.20715 ( 1266) SS BOND : bond 0.00209 ( 15) SS BOND : angle 0.96259 ( 30) covalent geometry : bond 0.00221 (16624) covalent geometry : angle 0.49625 (22847) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 50 time to evaluate : 1.870 Fit side-chains REVERT: C 325 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8362 (mmm-85) REVERT: H 83 LEU cc_start: 0.9483 (mp) cc_final: 0.8767 (tp) REVERT: A 325 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8523 (mmm-85) REVERT: B 383 VAL cc_start: 0.9489 (OUTLIER) cc_final: 0.9270 (p) outliers start: 46 outliers final: 42 residues processed: 95 average time/residue: 0.2871 time to fit residues: 46.4215 Evaluate side-chains 94 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 49 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 528 CYS Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 146 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 166 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 174 optimal weight: 30.0000 chunk 140 optimal weight: 8.9990 chunk 172 optimal weight: 20.0000 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.032203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.022474 restraints weight = 189762.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.023031 restraints weight = 99275.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.023375 restraints weight = 66683.873| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16639 Z= 0.134 Angle : 0.500 8.510 22877 Z= 0.260 Chirality : 0.041 0.141 2792 Planarity : 0.003 0.046 2952 Dihedral : 3.715 19.915 2468 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.28 % Allowed : 30.15 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.95 (0.18), residues: 2310 helix: 2.40 (0.32), residues: 291 sheet: -0.42 (0.18), residues: 840 loop : -1.60 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 36 HIS 0.002 0.001 HIS A 593 PHE 0.013 0.001 PHE B 77 TYR 0.009 0.001 TYR B 101 ARG 0.006 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 482) hydrogen bonds : angle 4.20706 ( 1266) SS BOND : bond 0.00274 ( 15) SS BOND : angle 1.05081 ( 30) covalent geometry : bond 0.00294 (16624) covalent geometry : angle 0.49884 (22847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5411.85 seconds wall clock time: 96 minutes 29.99 seconds (5789.99 seconds total)