Starting phenix.real_space_refine on Thu Sep 18 11:42:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lld_63198/09_2025/9lld_63198.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lld_63198/09_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_63198/09_2025/9lld_63198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lld_63198/09_2025/9lld_63198.map" model { file = "/net/cci-nas-00/data/ceres_data/9lld_63198/09_2025/9lld_63198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lld_63198/09_2025/9lld_63198.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 18, 'GLU:plan': 21, 'TYR:plan': 12, 'HIS:plan': 4, 'ARG:plan': 11, 'ASN:plan1': 9, 'GLN:plan1': 7, 'PHE:plan': 4} 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, 'ASP:plan': 2, 'PHE:plan': 1} 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: {'ASP:plan': 15, 'GLU:plan': 19, 'TYR:plan': 12, 'HIS:plan': 4, 'GLN:plan1': 9, 'ARG:plan': 13, 'ASN:plan1': 10, 'PHE:plan': 4} 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, 'ASP:plan': 2, 'ARG:plan': 1} 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: {'ASP:plan': 14, 'GLU:plan': 19, 'TYR:plan': 12, 'ARG:plan': 10, 'HIS:plan': 3, 'ASN:plan1': 8, 'GLN:plan1': 7, 'PHE:plan': 4} 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: {'GLU:plan': 3, 'ASP:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 4.35, per 1000 atoms: 0.27 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: 1.36 Conformation dependent library (CDL) restraints added in 939.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.58 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: 2.92 Time building geometry restraints manager: 1.82 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: 8.620 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.400 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- 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 : 8.66 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG H 98 TYR 0.011 0.001 TYR A 197 PHE 0.011 0.001 PHE A 624 TRP 0.009 0.001 TRP A 483 HIS 0.003 0.000 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00334 (16624) covalent geometry : angle 0.55442 (22847) SS BOND : bond 0.00287 ( 15) SS BOND : angle 0.99144 ( 30) hydrogen bonds : bond 0.15929 ( 482) hydrogen bonds : angle 5.69052 ( 1266) *********************** 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 : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 VAL cc_start: 0.7894 (t) cc_final: 0.7606 (t) 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: 1 residues processed: 129 average time/residue: 0.1180 time to fit residues: 24.2385 Evaluate side-chains 68 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 491 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.033064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.023378 restraints weight = 190354.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.023946 restraints weight = 101208.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.024305 restraints weight = 68149.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.024517 restraints weight = 53017.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.024652 restraints weight = 45556.640| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 16639 Z= 0.243 Angle : 0.599 7.538 22877 Z= 0.324 Chirality : 0.043 0.346 2792 Planarity : 0.004 0.047 2952 Dihedral : 4.275 36.469 2472 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.53 % Favored : 92.38 % Rotamer: Outliers : 4.68 % Allowed : 28.54 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.18), residues: 2310 helix: 2.36 (0.31), residues: 270 sheet: 0.27 (0.20), residues: 762 loop : -1.59 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 66 TYR 0.017 0.002 TYR G 50 PHE 0.013 0.002 PHE A 595 TRP 0.012 0.002 TRP F 36 HIS 0.020 0.002 HIS L 40 Details of bonding type rmsd covalent geometry : bond 0.00522 (16624) covalent geometry : angle 0.59757 (22847) SS BOND : bond 0.01058 ( 15) SS BOND : angle 1.20991 ( 30) hydrogen bonds : bond 0.04540 ( 482) hydrogen bonds : angle 4.74095 ( 1266) *********************** 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 144 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 74 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8453 (mmm-85) REVERT: H 83 LEU cc_start: 0.9264 (mp) cc_final: 0.8550 (tp) REVERT: L 51 ASP cc_start: 0.9489 (OUTLIER) cc_final: 0.8970 (t0) REVERT: A 325 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8483 (mmm-85) REVERT: A 407 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9137 (mp) REVERT: F 83 ASP cc_start: 0.8849 (p0) cc_final: 0.8470 (p0) REVERT: F 106 LEU cc_start: 0.8911 (tt) cc_final: 0.8679 (tp) REVERT: E 12 LYS cc_start: 0.8900 (mttp) cc_final: 0.8675 (mtpp) outliers start: 70 outliers final: 29 residues processed: 137 average time/residue: 0.1190 time to fit residues: 25.8293 Evaluate side-chains 94 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 264 ASN Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 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 407 ILE Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain B residue 231 SER 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 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 E residue 6 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 50 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 105 optimal weight: 0.0000 chunk 28 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 overall best weight: 3.7190 ------------------------------------------------------------------------------- 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 39 GLN A 221 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.032399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.022600 restraints weight = 191934.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.023150 restraints weight = 102242.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.023483 restraints weight = 69247.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.023697 restraints weight = 54593.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.023823 restraints weight = 46893.453| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16639 Z= 0.234 Angle : 0.561 8.301 22877 Z= 0.300 Chirality : 0.042 0.213 2792 Planarity : 0.004 0.041 2952 Dihedral : 4.162 19.147 2468 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.71 % Favored : 93.25 % Rotamer: Outliers : 4.61 % Allowed : 28.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.18), residues: 2310 helix: 2.63 (0.32), residues: 270 sheet: -0.04 (0.19), residues: 789 loop : -1.58 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 38 TYR 0.016 0.001 TYR G 37 PHE 0.013 0.001 PHE C 77 TRP 0.015 0.001 TRP E 36 HIS 0.005 0.001 HIS L 40 Details of bonding type rmsd covalent geometry : bond 0.00506 (16624) covalent geometry : angle 0.55926 (22847) SS BOND : bond 0.00437 ( 15) SS BOND : angle 1.33468 ( 30) hydrogen bonds : bond 0.04906 ( 482) hydrogen bonds : angle 4.86499 ( 1266) *********************** 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 132 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 63 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8461 (mmm-85) REVERT: H 83 LEU cc_start: 0.9339 (mp) cc_final: 0.8617 (tp) REVERT: A 325 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8539 (mmm-85) REVERT: F 83 ASP cc_start: 0.9050 (p0) cc_final: 0.8677 (p0) REVERT: F 106 LEU cc_start: 0.9065 (tt) cc_final: 0.8485 (tt) outliers start: 69 outliers final: 46 residues processed: 127 average time/residue: 0.0954 time to fit residues: 20.3001 Evaluate side-chains 106 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 58 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 289 THR Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 503 THR 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 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 231 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 273 VAL 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 525 VAL Chi-restraints excluded: chain A residue 556 VAL 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 18 THR Chi-restraints excluded: chain F residue 47 LEU 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 245 THR Chi-restraints excluded: chain B residue 246 VAL 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 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 627 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 217 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 223 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 491 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.032095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.022320 restraints weight = 191282.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.022861 restraints weight = 101806.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.023202 restraints weight = 68993.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.023402 restraints weight = 54107.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.023541 restraints weight = 46784.099| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16639 Z= 0.237 Angle : 0.550 6.399 22877 Z= 0.297 Chirality : 0.041 0.142 2792 Planarity : 0.004 0.041 2952 Dihedral : 4.253 19.211 2468 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.10 % Favored : 91.86 % Rotamer: Outliers : 5.41 % Allowed : 27.47 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.18), residues: 2310 helix: 2.27 (0.32), residues: 288 sheet: 0.15 (0.20), residues: 747 loop : -1.78 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 38 TYR 0.012 0.001 TYR B 101 PHE 0.010 0.001 PHE B 624 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00509 (16624) covalent geometry : angle 0.54891 (22847) SS BOND : bond 0.00356 ( 15) SS BOND : angle 1.14046 ( 30) hydrogen bonds : bond 0.04621 ( 482) hydrogen bonds : angle 4.73047 ( 1266) *********************** 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 137 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 56 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8446 (mmm-85) REVERT: A 97 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9080 (mp) REVERT: A 325 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8534 (mmm-85) REVERT: B 480 SER cc_start: 0.9832 (OUTLIER) cc_final: 0.9567 (p) REVERT: E 67 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8832 (mmm160) outliers start: 81 outliers final: 56 residues processed: 133 average time/residue: 0.1089 time to fit residues: 23.8704 Evaluate side-chains 114 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 53 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 289 THR 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 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 220 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 248 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 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 525 VAL Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 556 VAL 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 47 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 107 THR 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 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 322 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 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 11 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 67 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 6 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** 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 = 0.3083 r_free = 0.3083 target = 0.032211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.022442 restraints weight = 190783.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.022987 restraints weight = 100835.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.023334 restraints weight = 68127.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.023535 restraints weight = 53336.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.023672 restraints weight = 46094.264| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16639 Z= 0.166 Angle : 0.505 10.485 22877 Z= 0.269 Chirality : 0.041 0.182 2792 Planarity : 0.003 0.045 2952 Dihedral : 4.073 19.011 2468 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.62 % Favored : 93.33 % Rotamer: Outliers : 5.08 % Allowed : 27.54 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.18), residues: 2310 helix: 2.38 (0.32), residues: 288 sheet: 0.14 (0.20), residues: 738 loop : -1.76 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.009 0.001 TYR B 101 PHE 0.012 0.001 PHE B 77 TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00360 (16624) covalent geometry : angle 0.50388 (22847) SS BOND : bond 0.00302 ( 15) SS BOND : angle 1.19885 ( 30) hydrogen bonds : bond 0.04392 ( 482) hydrogen bonds : angle 4.54266 ( 1266) *********************** 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 132 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 56 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8411 (mmm-85) REVERT: L 48 MET cc_start: 0.9219 (pmm) cc_final: 0.8666 (pmm) REVERT: A 97 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9128 (mp) REVERT: A 325 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8528 (mmm-85) outliers start: 76 outliers final: 56 residues processed: 130 average time/residue: 0.1011 time to fit residues: 21.6745 Evaluate side-chains 112 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 53 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 329 THR 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 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 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 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 347 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 96 ASN 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 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 627 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain E residue 51 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 9 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 175 optimal weight: 0.0980 chunk 105 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 143 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** 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 = 0.3089 r_free = 0.3089 target = 0.032327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.022559 restraints weight = 190641.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.023122 restraints weight = 99256.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.023472 restraints weight = 66476.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.023686 restraints weight = 51811.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.023818 restraints weight = 44611.414| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16639 Z= 0.123 Angle : 0.491 8.786 22877 Z= 0.258 Chirality : 0.041 0.154 2792 Planarity : 0.003 0.044 2952 Dihedral : 3.856 18.313 2468 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.80 % Favored : 93.16 % Rotamer: Outliers : 4.61 % Allowed : 28.28 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.18), residues: 2310 helix: 2.42 (0.32), residues: 291 sheet: -0.22 (0.19), residues: 822 loop : -1.58 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.009 0.001 TYR G 37 PHE 0.011 0.001 PHE A 238 TRP 0.008 0.001 TRP L 55 HIS 0.002 0.000 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00269 (16624) covalent geometry : angle 0.48951 (22847) SS BOND : bond 0.00246 ( 15) SS BOND : angle 0.99288 ( 30) hydrogen bonds : bond 0.04062 ( 482) hydrogen bonds : angle 4.33932 ( 1266) *********************** 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 125 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 56 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8418 (mmm-85) REVERT: H 83 LEU cc_start: 0.9393 (mp) cc_final: 0.8674 (tp) REVERT: L 48 MET cc_start: 0.9113 (pmm) cc_final: 0.8621 (pmm) REVERT: A 97 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9063 (tp) REVERT: A 325 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8505 (mmm-85) REVERT: B 480 SER cc_start: 0.9823 (OUTLIER) cc_final: 0.9557 (p) outliers start: 69 outliers final: 54 residues processed: 121 average time/residue: 0.1063 time to fit residues: 21.3715 Evaluate side-chains 113 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 55 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 325 ARG Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 528 CYS 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 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 322 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain B residue 184 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 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 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 556 VAL Chi-restraints excluded: chain B residue 629 LEU 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 G residue 96 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 51 optimal weight: 3.9990 chunk 138 optimal weight: 0.1980 chunk 220 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** G 38 GLN ** 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 = 0.3081 r_free = 0.3081 target = 0.032181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.022459 restraints weight = 189782.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.022995 restraints weight = 100010.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.023334 restraints weight = 67443.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.023542 restraints weight = 52882.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.023671 restraints weight = 45663.962| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16639 Z= 0.158 Angle : 0.503 10.773 22877 Z= 0.265 Chirality : 0.041 0.169 2792 Planarity : 0.003 0.042 2952 Dihedral : 3.868 17.827 2468 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.49 % Favored : 93.46 % Rotamer: Outliers : 5.41 % Allowed : 27.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.18), residues: 2310 helix: 2.39 (0.32), residues: 291 sheet: -0.24 (0.19), residues: 807 loop : -1.57 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 553 TYR 0.010 0.001 TYR B 101 PHE 0.012 0.001 PHE A 238 TRP 0.009 0.001 TRP L 36 HIS 0.003 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00344 (16624) covalent geometry : angle 0.50153 (22847) SS BOND : bond 0.00311 ( 15) SS BOND : angle 1.07593 ( 30) hydrogen bonds : bond 0.04153 ( 482) hydrogen bonds : angle 4.37478 ( 1266) *********************** 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 136 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 55 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8410 (mmm-85) REVERT: H 83 LEU cc_start: 0.9404 (mp) cc_final: 0.8673 (tp) REVERT: A 97 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9048 (tp) REVERT: A 325 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8517 (mmm-85) REVERT: B 480 SER cc_start: 0.9826 (OUTLIER) cc_final: 0.9557 (p) outliers start: 81 outliers final: 69 residues processed: 131 average time/residue: 0.0910 time to fit residues: 20.3515 Evaluate side-chains 125 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 52 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 325 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 347 THR 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 C residue 556 VAL 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 294 ILE 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 334 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain B residue 184 LEU 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 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 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 B residue 650 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain G residue 48 MET 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 190 optimal weight: 4.9990 chunk 165 optimal weight: 0.0270 chunk 44 optimal weight: 10.0000 chunk 10 optimal weight: 40.0000 chunk 159 optimal weight: 50.0000 chunk 27 optimal weight: 0.0670 chunk 182 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.2180 ------------------------------------------------------------------------------- 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** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.032353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.022609 restraints weight = 190265.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.023177 restraints weight = 98480.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.023530 restraints weight = 65776.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.023747 restraints weight = 51235.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.023885 restraints weight = 43912.534| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16639 Z= 0.101 Angle : 0.490 10.459 22877 Z= 0.253 Chirality : 0.041 0.154 2792 Planarity : 0.003 0.042 2952 Dihedral : 3.670 17.384 2468 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.15 % Favored : 93.81 % Rotamer: Outliers : 4.81 % Allowed : 28.88 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.18), residues: 2310 helix: 2.46 (0.32), residues: 291 sheet: -0.12 (0.19), residues: 807 loop : -1.55 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.008 0.001 TYR G 37 PHE 0.012 0.001 PHE A 238 TRP 0.008 0.001 TRP E 47 HIS 0.002 0.000 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00224 (16624) covalent geometry : angle 0.48950 (22847) SS BOND : bond 0.00236 ( 15) SS BOND : angle 0.92889 ( 30) hydrogen bonds : bond 0.03880 ( 482) hydrogen bonds : angle 4.20264 ( 1266) *********************** 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 128 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 56 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 325 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8348 (mmm-85) REVERT: H 83 LEU cc_start: 0.9396 (mp) cc_final: 0.8651 (tp) REVERT: L 48 MET cc_start: 0.9037 (pmm) cc_final: 0.8617 (pmm) REVERT: A 325 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8486 (mmm-85) REVERT: B 480 SER cc_start: 0.9820 (OUTLIER) cc_final: 0.9554 (p) outliers start: 72 outliers final: 64 residues processed: 123 average time/residue: 0.0971 time to fit residues: 19.9253 Evaluate side-chains 120 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 53 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 325 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 347 THR 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 C residue 556 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 114 VAL 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 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 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 325 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain B residue 184 LEU 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 294 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 362 CYS 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 556 VAL 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 G residue 48 MET 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 221 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 533 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** ** B 221 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 = 0.3074 r_free = 0.3074 target = 0.032033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.022316 restraints weight = 191209.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.022859 restraints weight = 100893.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.023198 restraints weight = 68244.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.023403 restraints weight = 53505.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.023532 restraints weight = 46189.833| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16639 Z= 0.198 Angle : 0.525 9.407 22877 Z= 0.276 Chirality : 0.041 0.152 2792 Planarity : 0.003 0.041 2952 Dihedral : 3.883 17.559 2468 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.45 % Favored : 92.51 % Rotamer: Outliers : 4.81 % Allowed : 28.81 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.18), residues: 2310 helix: 2.39 (0.32), residues: 291 sheet: -0.24 (0.19), residues: 798 loop : -1.58 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 553 TYR 0.011 0.001 TYR B 101 PHE 0.010 0.001 PHE A 238 TRP 0.011 0.001 TRP L 36 HIS 0.007 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00427 (16624) covalent geometry : angle 0.52359 (22847) SS BOND : bond 0.00358 ( 15) SS BOND : angle 1.08573 ( 30) hydrogen bonds : bond 0.04239 ( 482) hydrogen bonds : angle 4.40237 ( 1266) *********************** 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 124 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 52 time to evaluate : 0.513 Fit side-chains REVERT: C 325 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8385 (mmm-85) REVERT: H 83 LEU cc_start: 0.9444 (mp) cc_final: 0.8694 (tp) REVERT: L 48 MET cc_start: 0.9114 (pmm) cc_final: 0.8732 (pmm) REVERT: A 97 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.9059 (tp) REVERT: A 325 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8520 (mmm-85) REVERT: B 480 SER cc_start: 0.9827 (OUTLIER) cc_final: 0.9560 (p) outliers start: 72 outliers final: 61 residues processed: 120 average time/residue: 0.0982 time to fit residues: 19.5084 Evaluate side-chains 116 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 51 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 325 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 347 THR 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 529 ILE Chi-restraints excluded: chain C residue 556 VAL 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 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 347 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 564 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 47 LEU Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain B residue 184 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 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 347 THR Chi-restraints excluded: chain B residue 362 CYS 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 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 B residue 650 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 51 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 66 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 213 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 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 = 0.3093 r_free = 0.3093 target = 0.032404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.022676 restraints weight = 187959.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.023244 restraints weight = 97879.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.023594 restraints weight = 65549.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.023813 restraints weight = 51151.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.023941 restraints weight = 43850.781| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16639 Z= 0.091 Angle : 0.492 9.930 22877 Z= 0.252 Chirality : 0.042 0.155 2792 Planarity : 0.003 0.042 2952 Dihedral : 3.598 16.957 2468 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.68 % Allowed : 30.21 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.18), residues: 2310 helix: 2.54 (0.33), residues: 291 sheet: -0.19 (0.19), residues: 801 loop : -1.49 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.007 0.001 TYR G 37 PHE 0.012 0.001 PHE A 238 TRP 0.011 0.001 TRP E 47 HIS 0.002 0.000 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00199 (16624) covalent geometry : angle 0.49088 (22847) SS BOND : bond 0.00205 ( 15) SS BOND : angle 0.89538 ( 30) hydrogen bonds : bond 0.03779 ( 482) hydrogen bonds : angle 4.13441 ( 1266) ********************** 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 109 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 54 time to evaluate : 0.495 Fit side-chains REVERT: C 325 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8326 (mmm-85) REVERT: H 83 LEU cc_start: 0.9411 (mp) cc_final: 0.8668 (tp) REVERT: L 48 MET cc_start: 0.9061 (pmm) cc_final: 0.8641 (pmm) REVERT: A 325 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8493 (mmm-85) REVERT: B 480 SER cc_start: 0.9820 (OUTLIER) cc_final: 0.9551 (p) outliers start: 55 outliers final: 52 residues processed: 107 average time/residue: 0.0860 time to fit residues: 15.6077 Evaluate side-chains 106 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 51 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 325 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 528 CYS Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 114 VAL 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 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 325 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain B residue 184 LEU 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 362 CYS 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 556 VAL 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 51 ILE Chi-restraints excluded: chain G residue 48 MET 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 46 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.032093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.022382 restraints weight = 190869.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.022920 restraints weight = 100692.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.023264 restraints weight = 68038.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.023474 restraints weight = 53278.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.023597 restraints weight = 45874.056| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16639 Z= 0.172 Angle : 0.512 8.991 22877 Z= 0.266 Chirality : 0.041 0.141 2792 Planarity : 0.003 0.042 2952 Dihedral : 3.737 17.042 2468 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.01 % Allowed : 29.95 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.18), residues: 2310 helix: 2.46 (0.32), residues: 291 sheet: -0.25 (0.19), residues: 816 loop : -1.48 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 38 TYR 0.011 0.001 TYR B 101 PHE 0.011 0.001 PHE A 238 TRP 0.009 0.001 TRP L 36 HIS 0.003 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00374 (16624) covalent geometry : angle 0.51121 (22847) SS BOND : bond 0.00323 ( 15) SS BOND : angle 1.05236 ( 30) hydrogen bonds : bond 0.04061 ( 482) hydrogen bonds : angle 4.26061 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.48 seconds wall clock time: 55 minutes 46.80 seconds (3346.80 seconds total)