Starting phenix.real_space_refine on Fri Mar 6 21:56:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v6o_31744/03_2026/7v6o_31744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6o_31744/03_2026/7v6o_31744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v6o_31744/03_2026/7v6o_31744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6o_31744/03_2026/7v6o_31744.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v6o_31744/03_2026/7v6o_31744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6o_31744/03_2026/7v6o_31744.map" } resolution = 4.56 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 179 5.16 5 C 21873 2.51 5 N 5852 2.21 5 O 6912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34816 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 8325 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 49, 'TRANS': 1087} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 507 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'TYR:plan': 13, 'HIS:plan': 2, 'GLN:plan1': 11, 'PHE:plan': 14, 'ARG:plan': 10, 'GLU:plan': 7, 'ASN:plan1': 7, 'ASP:plan': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 358 Chain: "B" Number of atoms: 8446 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8440 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TYR:plan': 13, 'ARG:plan': 10, 'HIS:plan': 5, 'ASN:plan1': 5, 'GLU:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 8, 'PHE:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 280 Conformer: "B" Number of residues, atoms: 1141, 8440 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TYR:plan': 13, 'ARG:plan': 10, 'HIS:plan': 5, 'ASN:plan1': 5, 'GLU:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 8, 'PHE:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 280 bond proxies already assigned to first conformer: 8608 Chain: "C" Number of atoms: 8401 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1137, 8395 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 50, 'TRANS': 1086} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 437 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 386 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'TRP:plan': 3, 'TYR:plan': 11, 'ASP:plan': 5, 'PHE:plan': 8, 'HIS:plan': 3, 'ASN:plan1': 10, 'ARG:plan': 8, 'GLU:plan': 6, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 304 Conformer: "B" Number of residues, atoms: 1137, 8395 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 50, 'TRANS': 1086} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 437 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 386 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'TRP:plan': 3, 'TYR:plan': 11, 'ASP:plan': 5, 'PHE:plan': 8, 'HIS:plan': 3, 'ASN:plan1': 10, 'ARG:plan': 8, 'GLU:plan': 6, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 304 bond proxies already assigned to first conformer: 8559 Chain: "D" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1574 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1615 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TRP:plan': 4, 'TYR:plan': 3, 'ARG:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "F" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1602 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1644 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1600 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1609 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 3, 'ASP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 80 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER B 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER B 51 " occ=0.54 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 11.26, per 1000 atoms: 0.32 Number of scatterers: 34816 At special positions: 0 Unit cell: (208.601, 219.58, 205.307, 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 179 16.00 O 6912 8.00 N 5852 7.00 C 21873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.02 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.04 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.04 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.04 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.02 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 199 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 91 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 156 " - pdb=" SG CYS G 212 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 156 " - pdb=" SG CYS I 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 2.4 seconds 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8822 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 75 sheets defined 19.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 222 through 231 removed outlier: 4.005A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.677A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.823A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.532A pdb=" N VAL A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 Processing helix chain 'A' and resid 925 through 930 Processing helix chain 'A' and resid 940 through 959 removed outlier: 3.762A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 987 through 994 Processing helix chain 'A' and resid 996 through 1011 Processing helix chain 'A' and resid 1016 through 1041 removed outlier: 3.559A pdb=" N SER A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1106 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.898A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.063A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.532A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.847A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.535A pdb=" N SER B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 529 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.520A pdb=" N LEU B 820 " --> pdb=" O LYS B 816 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 823 " --> pdb=" O GLN B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 915 Processing helix chain 'B' and resid 940 through 958 removed outlier: 4.055A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 987 through 994 Processing helix chain 'B' and resid 996 through 1011 Processing helix chain 'B' and resid 1016 through 1042 Processing helix chain 'B' and resid 1058 through 1106 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.615A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.765A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 removed outlier: 4.173A pdb=" N LEU C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.573A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.994A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 809 through 813 Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.603A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 854 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 915 Processing helix chain 'C' and resid 940 through 958 removed outlier: 3.545A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 984 Processing helix chain 'C' and resid 987 through 992 Processing helix chain 'C' and resid 996 through 1011 Processing helix chain 'C' and resid 1017 through 1041 Processing helix chain 'C' and resid 1059 through 1106 Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'E' and resid 203 through 208 removed outlier: 4.510A pdb=" N THR E 207 " --> pdb=" O SER E 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 187 through 194 Processing helix chain 'G' and resid 144 through 149 removed outlier: 4.249A pdb=" N GLY G 149 " --> pdb=" O LYS G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 208 removed outlier: 4.429A pdb=" N THR G 207 " --> pdb=" O SER G 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 187 through 194 Processing helix chain 'I' and resid 144 through 149 removed outlier: 4.155A pdb=" N GLY I 149 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 208 removed outlier: 4.521A pdb=" N THR I 207 " --> pdb=" O SER I 203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 5.969A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 75 removed outlier: 3.579A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.562A pdb=" N VAL A 263 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR A 283 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 265 " --> pdb=" O PHE A 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.409A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 367 removed outlier: 5.615A pdb=" N SER A 362 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 661 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER A 364 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL A 659 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 671 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.542A pdb=" N LYS A 400 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.870A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N CYS A 503 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TRP A 553 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 618 through 619 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 782 Processing sheet with id=AB4, first strand: chain 'A' and resid 790 through 791 removed outlier: 4.012A pdb=" N HIS A1138 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB6, first strand: chain 'B' and resid 33 through 35 removed outlier: 5.894A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N HIS B 91 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 75 removed outlier: 4.219A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 86 removed outlier: 5.765A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.490A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.506A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 126 through 129 removed outlier: 4.144A pdb=" N SER B 126 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AC4, first strand: chain 'B' and resid 360 through 361 removed outlier: 3.515A pdb=" N VAL B 661 " --> pdb=" O TYR B 361 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 662 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B 671 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 400 through 405 removed outlier: 7.083A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.040A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 605 through 607 removed outlier: 3.559A pdb=" N TYR B 606 " --> pdb=" O GLY B 613 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 613 " --> pdb=" O TYR B 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 618 through 619 removed outlier: 3.523A pdb=" N GLN B 618 " --> pdb=" O CYS B 650 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 650 " --> pdb=" O GLN B 618 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 778 through 782 Processing sheet with id=AD1, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD2, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 6.296A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AD4, first strand: chain 'C' and resid 69 through 76 removed outlier: 5.960A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.767A pdb=" N LEU C 324 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.300A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 185 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 184 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C 239 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 186 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS C 237 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU C 188 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG C 235 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AD8, first strand: chain 'C' and resid 206 through 208 removed outlier: 6.163A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 360 through 367 removed outlier: 5.729A pdb=" N SER C 362 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL C 661 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER C 364 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL C 659 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA C 671 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 400 through 405 removed outlier: 6.893A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.343A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 606 through 607 Processing sheet with id=AE4, first strand: chain 'C' and resid 778 through 783 Processing sheet with id=AE5, first strand: chain 'C' and resid 802 through 803 Processing sheet with id=AE6, first strand: chain 'C' and resid 1121 through 1124 removed outlier: 7.239A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1127 through 1130 Processing sheet with id=AE8, first strand: chain 'D' and resid 8 through 9 Processing sheet with id=AE9, first strand: chain 'D' and resid 13 through 16 Processing sheet with id=AF1, first strand: chain 'D' and resid 48 through 51 removed outlier: 6.624A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 88 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 119 through 123 removed outlier: 5.621A pdb=" N LEU D 140 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER D 182 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASN D 142 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU D 180 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AF4, first strand: chain 'D' and resid 158 through 159 Processing sheet with id=AF5, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AF6, first strand: chain 'E' and resid 58 through 60 removed outlier: 7.263A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.651A pdb=" N GLY E 155 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 194 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP E 160 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR E 192 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 197 " --> pdb=" O HIS E 180 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.651A pdb=" N GLY E 155 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 194 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP E 160 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR E 192 " --> pdb=" O ASP E 160 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AG1, first strand: chain 'F' and resid 8 through 9 Processing sheet with id=AG2, first strand: chain 'F' and resid 13 through 15 Processing sheet with id=AG3, first strand: chain 'F' and resid 48 through 51 removed outlier: 6.528A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 119 through 123 removed outlier: 5.958A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 158 through 159 Processing sheet with id=AG6, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'G' and resid 58 through 60 removed outlier: 5.609A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 103 through 104 Processing sheet with id=AG9, first strand: chain 'G' and resid 138 through 140 removed outlier: 3.888A pdb=" N GLY G 155 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 194 " --> pdb=" O VAL G 158 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL G 197 " --> pdb=" O HIS G 180 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 138 through 140 removed outlier: 3.888A pdb=" N GLY G 155 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 194 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 167 through 170 removed outlier: 3.713A pdb=" N HIS G 216 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR G 221 " --> pdb=" O HIS G 216 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 8 through 9 Processing sheet with id=AH4, first strand: chain 'H' and resid 13 through 16 Processing sheet with id=AH5, first strand: chain 'H' and resid 48 through 51 removed outlier: 6.520A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR H 88 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.558A pdb=" N ASN H 143 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 158 through 159 Processing sheet with id=AH8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.705A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 37 through 39 removed outlier: 3.573A pdb=" N ALA I 92 " --> pdb=" O VAL I 126 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 49 through 51 Processing sheet with id=AI2, first strand: chain 'I' and resid 138 through 140 removed outlier: 3.831A pdb=" N GLY I 155 " --> pdb=" O LEU I 140 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP I 160 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR I 192 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 167 through 170 1247 hydrogen bonds defined for protein. 3312 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: 9.55 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6657 1.33 - 1.45: 8769 1.45 - 1.57: 19861 1.57 - 1.69: 0 1.69 - 1.82: 226 Bond restraints: 35513 Sorted by residual: bond pdb=" N THR C1013 " pdb=" CA THR C1013 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.55e+01 bond pdb=" N THR B 741 " pdb=" CA THR B 741 " ideal model delta sigma weight residual 1.458 1.495 -0.037 7.40e-03 1.83e+04 2.52e+01 bond pdb=" N CYS A 195 " pdb=" CA CYS A 195 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 2.02e+01 bond pdb=" N VAL B 514 " pdb=" CA VAL B 514 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.70e-03 1.32e+04 1.90e+01 bond pdb=" N THR C 741 " pdb=" CA THR C 741 " ideal model delta sigma weight residual 1.457 1.496 -0.039 9.10e-03 1.21e+04 1.88e+01 ... (remaining 35508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 44790 2.71 - 5.42: 3547 5.42 - 8.14: 50 8.14 - 10.85: 12 10.85 - 13.56: 5 Bond angle restraints: 48404 Sorted by residual: angle pdb=" C THR C 741 " pdb=" CA THR C 741 " pdb=" CB THR C 741 " ideal model delta sigma weight residual 110.71 119.26 -8.55 9.40e-01 1.13e+00 8.27e+01 angle pdb=" N ASN B 602 " pdb=" CA ASN B 602 " pdb=" C ASN B 602 " ideal model delta sigma weight residual 113.19 103.05 10.14 1.19e+00 7.06e-01 7.26e+01 angle pdb=" C ASP C 510 " pdb=" CA ASP C 510 " pdb=" CB ASP C 510 " ideal model delta sigma weight residual 109.83 117.77 -7.94 9.90e-01 1.02e+00 6.43e+01 angle pdb=" C THR B 741 " pdb=" CA THR B 741 " pdb=" CB THR B 741 " ideal model delta sigma weight residual 111.00 117.83 -6.83 8.70e-01 1.32e+00 6.17e+01 angle pdb=" CA PRO G 163 " pdb=" N PRO G 163 " pdb=" CD PRO G 163 " ideal model delta sigma weight residual 112.00 101.89 10.11 1.40e+00 5.10e-01 5.22e+01 ... (remaining 48399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 19236 16.76 - 33.52: 1427 33.52 - 50.28: 473 50.28 - 67.04: 98 67.04 - 83.80: 14 Dihedral angle restraints: 21248 sinusoidal: 7499 harmonic: 13749 Sorted by residual: dihedral pdb=" CB CYS B 679 " pdb=" SG CYS B 679 " pdb=" SG CYS B 713 " pdb=" CB CYS B 713 " ideal model delta sinusoidal sigma weight residual -86.00 -154.22 68.22 1 1.00e+01 1.00e-02 6.04e+01 dihedral pdb=" C GLU G 164 " pdb=" N GLU G 164 " pdb=" CA GLU G 164 " pdb=" CB GLU G 164 " ideal model delta harmonic sigma weight residual -122.60 -141.24 18.64 0 2.50e+00 1.60e-01 5.56e+01 dihedral pdb=" C THR C 741 " pdb=" N THR C 741 " pdb=" CA THR C 741 " pdb=" CB THR C 741 " ideal model delta harmonic sigma weight residual -122.00 -138.56 16.56 0 2.50e+00 1.60e-01 4.39e+01 ... (remaining 21245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 4593 0.146 - 0.291: 1000 0.291 - 0.437: 16 0.437 - 0.582: 4 0.582 - 0.728: 2 Chirality restraints: 5615 Sorted by residual: chirality pdb=" CA PRO G 163 " pdb=" N PRO G 163 " pdb=" C PRO G 163 " pdb=" CB PRO G 163 " both_signs ideal model delta sigma weight residual False 2.72 1.99 0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA GLU G 164 " pdb=" N GLU G 164 " pdb=" C GLU G 164 " pdb=" CB GLU G 164 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.83e+00 chirality pdb=" CA VAL B 604 " pdb=" N VAL B 604 " pdb=" C VAL B 604 " pdb=" CB VAL B 604 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.92e+00 ... (remaining 5612 not shown) Planarity restraints: 6304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 928 " -0.038 2.00e-02 2.50e+03 7.65e-02 5.85e+01 pdb=" C TYR C 928 " 0.132 2.00e-02 2.50e+03 pdb=" O TYR C 928 " -0.049 2.00e-02 2.50e+03 pdb=" N VAL C 929 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BSER B 51 " 0.034 2.00e-02 2.50e+03 7.05e-02 4.97e+01 pdb=" C BSER B 51 " -0.122 2.00e-02 2.50e+03 pdb=" O BSER B 51 " 0.046 2.00e-02 2.50e+03 pdb=" N LYS B 52 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BSER C 51 " -0.034 2.00e-02 2.50e+03 7.02e-02 4.93e+01 pdb=" C BSER C 51 " 0.121 2.00e-02 2.50e+03 pdb=" O BSER C 51 " -0.045 2.00e-02 2.50e+03 pdb=" N LYS C 52 " -0.042 2.00e-02 2.50e+03 ... (remaining 6301 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 15 2.35 - 2.99: 17591 2.99 - 3.62: 51785 3.62 - 4.26: 79484 4.26 - 4.90: 129428 Nonbonded interactions: 278303 Sorted by model distance: nonbonded pdb=" O LYS I 217 " pdb=" OD1 ASN I 220 " model vdw 1.712 3.040 nonbonded pdb=" OD1 ASP B 664 " pdb=" OG1 THR B 667 " model vdw 1.763 3.040 nonbonded pdb=" CG ASP B 664 " pdb=" OG1 THR B 667 " model vdw 1.908 3.270 nonbonded pdb=" O GLY B 359 " pdb=" CE2 TYR B 361 " model vdw 2.135 3.340 nonbonded pdb=" OD2 ASP B 330 " pdb=" NH2 ARG B 334 " model vdw 2.171 3.120 ... (remaining 278298 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 18 through 19 and (name N or name CA or name C or name O \ or name CB )) or resid 20 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 43 or (resid 44 and (name N or na \ me CA or name C or name O or name CB )) or resid 45 through 47 or (resid 48 and \ (name N or name CA or name C or name O or name CB )) or resid 49 through 50 or r \ esid 52 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB )) or resid 58 through 61 or (resid 62 and (name N or name CA or name C or \ name O or name CB )) or resid 63 through 76 or (resid 77 and (name N or name CA \ or name C or name O or name CB )) or resid 78 through 79 or (resid 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 through 128 or (resi \ d 129 and (name N or name CA or name C or name O or name CB )) or resid 130 thro \ ugh 141 or (resid 142 and (name N or name CA or name C or name O or name CB )) o \ r resid 143 through 166 or (resid 167 through 168 and (name N or name CA or name \ C or name O or name CB )) or resid 169 through 200 or (resid 201 and (name N or \ name CA or name C or name O or name CB )) or resid 202 through 234 or (resid 23 \ 5 through 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 246 or (resid 247 through 249 and (name N or name CA or name C or na \ me O or name CB )) or resid 250 through 268 or (resid 269 and (name N or name CA \ or name C or name O or name CB )) or resid 270 through 279 or (resid 280 and (n \ ame N or name CA or name C or name O or name CB )) or resid 281 through 303 or ( \ resid 304 and (name N or name CA or name C or name O or name CB )) or resid 305 \ through 306 or (resid 307 through 309 and (name N or name CA or name C or name O \ or name CB )) or resid 310 through 313 or (resid 314 and (name N or name CA or \ name C or name O or name CB )) or resid 315 through 340 or (resid 341 and (name \ N or name CA or name C or name O or name CB )) or resid 342 through 343 or (resi \ d 344 through 345 and (name N or name CA or name C or name O or name CB )) or re \ sid 346 through 362 or (resid 363 and (name N or name CA or name C or name O or \ name CB )) or resid 364 through 365 or (resid 366 and (name N or name CA or name \ C or name O or name CB )) or resid 367 through 368 or (resid 369 and (name N or \ name CA or name C or name O or name CB )) or resid 370 through 373 or (resid 37 \ 4 through 375 and (name N or name CA or name C or name O or name CB )) or resid \ 376 through 377 or resid 382 through 387 or (resid 388 and (name N or name CA or \ name C or name O or name CB )) or resid 389 through 396 or (resid 397 and (name \ N or name CA or name C or name O or name CB )) or resid 398 through 405 or (res \ id 406 and (name N or name CA or name C or name O or name CB )) or resid 407 thr \ ough 408 or (resid 409 through 410 and (name N or name CA or name C or name O or \ name CB )) or resid 411 through 463 or (resid 464 through 466 and (name N or na \ me CA or name C or name O or name CB )) or resid 467 or (resid 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 through 482 or (resid 4 \ 83 through 484 and (name N or name CA or name C or name O or name CB )) or resid \ 485 through 496 or (resid 497 and (name N or name CA or name C or name O or nam \ e CB )) or resid 498 through 539 or (resid 540 and (name N or name CA or name C \ or name O or name CB )) or resid 541 or (resid 542 through 543 and (name N or na \ me CA or name C or name O or name CB )) or resid 544 through 558 or (resid 559 a \ nd (name N or name CA or name C or name O or name CB )) or resid 560 through 562 \ or (resid 563 through 567 and (name N or name CA or name C or name O or name CB \ )) or resid 568 through 581 or (resid 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 or (resid 584 and (name N or name CA or name C \ or name O or name CB )) or resid 585 through 586 or (resid 595 and (name N or na \ me CA or name C or name O or name CB )) or resid 597 through 598 or (resid 599 t \ hrough 600 and (name N or name CA or name C or name O or name CB )) or resid 601 \ through 643 or (resid 644 and (name N or name CA or name C or name O or name CB \ )) or resid 645 through 646 or (resid 647 and (name N or name CA or name C or n \ ame O or name CB )) or resid 648 through 656 or (resid 657 and (name N or name C \ A or name C or name O or name CB )) or resid 658 through 659 or (resid 660 and ( \ name N or name CA or name C or name O or name CB )) or resid 661 through 662 or \ (resid 663 through 666 and (name N or name CA or name C or name O or name CB )) \ or resid 667 through 690 or (resid 691 and (name N or name CA or name C or name \ O or name CB )) or resid 692 through 693 or (resid 694 and (name N or name CA or \ name C or name O or name CB )) or resid 695 through 714 or (resid 715 and (name \ N or name CA or name C or name O or name CB )) or resid 716 through 739 or (res \ id 740 and (name N or name CA or name C or name O or name CB )) or resid 741 thr \ ough 779 or (resid 780 and (name N or name CA or name C or name O or name CB )) \ or resid 781 through 784 or (resid 785 through 786 and (name N or name CA or nam \ e C or name O or name CB )) or resid 787 through 798 or (resid 799 and (name N o \ r name CA or name C or name O or name CB )) or resid 800 through 808 or (resid 8 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 810 through \ 841 or (resid 842 and (name N or name CA or name C or name O or name CB )) or r \ esid 843 through 844 or (resid 845 and (name N or name CA or name C or name O or \ name CB )) or resid 846 through 848 or (resid 849 and (name N or name CA or nam \ e C or name O or name CB )) or resid 850 through 851 or (resid 852 and (name N o \ r name CA or name C or name O or name CB )) or resid 853 or (resid 854 and (name \ N or name CA or name C or name O or name CB )) or resid 855 or (resid 856 and ( \ name N or name CA or name C or name O or name CB )) or resid 857 through 868 or \ (resid 869 through 871 and (name N or name CA or name C or name O or name CB )) \ or resid 872 or (resid 873 and (name N or name CA or name C or name O or name CB \ )) or resid 874 through 886 or (resid 887 and (name N or name CA or name C or n \ ame O or name CB )) or resid 888 through 889 or (resid 890 and (name N or name C \ A or name C or name O or name CB )) or resid 891 through 892 or (resid 893 and ( \ name N or name CA or name C or name O or name CB )) or resid 894 through 896 or \ (resid 897 and (name N or name CA or name C or name O or name CB )) or resid 898 \ through 908 or (resid 909 and (name N or name CA or name C or name O or name CB \ )) or resid 910 through 912 or (resid 913 through 914 and (name N or name CA or \ name C or name O or name CB )) or resid 915 through 938 or (resid 939 and (name \ N or name CA or name C or name O or name CB )) or resid 940 through 949 or (res \ id 950 and (name N or name CA or name C or name O or name CB )) or resid 951 thr \ ough 959 or (resid 960 and (name N or name CA or name C or name O or name CB )) \ or resid 961 through 963 or (resid 964 and (name N or name CA or name C or name \ O or name CB )) or resid 965 through 973 or (resid 974 and (name N or name CA or \ name C or name O or name CB )) or resid 975 through 984 or (resid 985 through 9 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 988 through \ 989 or (resid 990 and (name N or name CA or name C or name O or name CB )) or r \ esid 991 through 992 or (resid 993 and (name N or name CA or name C or name O or \ name CB )) or resid 994 through 1008 or (resid 1009 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1010 through 1016 or (resid 1017 through \ 1018 and (name N or name CA or name C or name O or name CB )) or resid 1019 or ( \ resid 1020 and (name N or name CA or name C or name O or name CB )) or resid 102 \ 1 through 1030 or (resid 1031 through 1032 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1033 through 1034 or (resid 1035 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1036 through 1039 or (resid 1040 \ and (name N or name CA or name C or name O or name CB )) or resid 1041 through \ 1053 or (resid 1054 and (name N or name CA or name C or name O or name CB )) or \ resid 1055 through 1073 or (resid 1074 and (name N or name CA or name C or name \ O or name CB )) or resid 1075 through 1076 or (resid 1077 and (name N or name CA \ or name C or name O or name CB )) or resid 1078 through 1083 or (resid 1084 and \ (name N or name CA or name C or name O or name CB )) or resid 1085 through 1087 \ or (resid 1088 and (name N or name CA or name C or name O or name CB )) or resi \ d 1089 through 1096 or (resid 1097 and (name N or name CA or name C or name O or \ name CB )) or resid 1098 through 1099 or (resid 1100 and (name N or name CA or \ name C or name O or name CB )) or resid 1101 or (resid 1102 and (name N or name \ CA or name C or name O or name CB )) or resid 1103 through 1109 or resid 1111 th \ rough 1112 or (resid 1113 and (name N or name CA or name C or name O or name CB \ )) or resid 1114 through 1115 or (resid 1116 and (name N or name CA or name C or \ name O or name CB )) or resid 1117 through 1121 or (resid 1122 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1123 through 1124 or (resid 11 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 1126 throug \ h 1135 or (resid 1136 through 1139 and (name N or name CA or name C or name O or \ name CB )) or resid 1140 through 1150 or (resid 1151 through 1153 and (name N o \ r name CA or name C or name O or name CB )) or resid 1154 through 1176 or (resid \ 1177 and (name N or name CA or name C or name O or name CB )) or resid 1178 or \ (resid 1179 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 80 through 1181 or (resid 1182 through 1184 and (name N or name CA or name C or \ name O or name CB )) or resid 1185 through 1191 or (resid 1192 through 1193 and \ (name N or name CA or name C or name O or name CB )) or resid 1194 through 1206) \ ) selection = (chain 'B' and (resid 18 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 43 or (resid 44 and (name N or nam \ e CA or name C or name O or name CB )) or resid 45 through 47 or (resid 48 and ( \ name N or name CA or name C or name O or name CB )) or resid 49 through 50 or re \ sid 52 through 63 or (resid 64 and (name N or name CA or name C or name O or nam \ e CB )) or resid 65 through 76 or (resid 77 and (name N or name CA or name C or \ name O or name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA \ or name C or name O or name CB )) or resid 81 through 96 or (resid 98 through 10 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 102 through \ 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or re \ sid 106 through 111 or (resid 112 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 114 through 125 or (resid 126 and (name N or nam \ e CA or name C or name O or name CB )) or resid 127 through 128 or (resid 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 139 \ or (resid 140 and (name N or name CA or name C or name O or name CB )) or resid \ 141 through 143 or (resid 144 and (name N or name CA or name C or name O or name \ CB )) or resid 145 through 147 or (resid 148 through 149 and (name N or name CA \ or name C or name O or name CB )) or resid 150 through 163 or (resid 164 and (n \ ame N or name CA or name C or name O or name CB )) or resid 165 through 180 or ( \ resid 181 through 184 and (name N or name CA or name C or name O or name CB )) o \ r resid 185 through 187 or (resid 188 and (name N or name CA or name C or name O \ or name CB )) or resid 189 or (resid 190 and (name N or name CA or name C or na \ me O or name CB )) or resid 191 through 198 or (resid 199 and (name N or name CA \ or name C or name O or name CB )) or resid 200 through 203 or (resid 204 throug \ h 205 and (name N or name CA or name C or name O or name CB )) or resid 206 thro \ ugh 221 or (resid 222 through 223 and (name N or name CA or name C or name O or \ name CB )) or resid 224 through 228 or (resid 229 and (name N or name CA or name \ C or name O or name CB )) or resid 230 through 233 or (resid 234 through 236 an \ d (name N or name CA or name C or name O or name CB )) or resid 237 through 244 \ or (resid 245 and (name N or name CA or name C or name O or name CB )) or resid \ 246 through 248 or (resid 249 and (name N or name CA or name C or name O or name \ CB )) or resid 250 through 257 or (resid 258 and (name N or name CA or name C o \ r name O or name CB )) or resid 259 through 262 or (resid 263 and (name N or nam \ e CA or name C or name O or name CB )) or resid 264 through 279 or (resid 280 an \ d (name N or name CA or name C or name O or name CB )) or resid 281 through 283 \ or (resid 284 and (name N or name CA or name C or name O or name CB )) or resid \ 285 through 288 or (resid 289 through 291 and (name N or name CA or name C or na \ me O or name CB )) or resid 292 through 300 or (resid 301 and (name N or name CA \ or name C or name O or name CB )) or resid 302 through 307 or (resid 308 throug \ h 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thro \ ugh 312 or (resid 313 through 314 and (name N or name CA or name C or name O or \ name CB )) or resid 315 through 316 or (resid 317 and (name N or name CA or name \ C or name O or name CB )) or resid 318 through 325 or (resid 326 and (name N or \ name CA or name C or name O or name CB )) or resid 327 through 340 or (resid 34 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 342 or (resi \ d 343 through 345 and (name N or name CA or name C or name O or name CB )) or re \ sid 346 through 353 or (resid 354 and (name N or name CA or name C or name O or \ name CB )) or resid 355 through 373 or (resid 374 through 375 and (name N or nam \ e CA or name C or name O or name CB )) or resid 376 through 377 or (resid 382 an \ d (name N or name CA or name C or name O or name CB )) or resid 383 through 400 \ or (resid 401 and (name N or name CA or name C or name O or name CB )) or resid \ 402 through 405 or (resid 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 or (resid 408 through 410 and (name N or name CA or name C o \ r name O or name CB )) or resid 411 through 437 or (resid 438 and (name N or nam \ e CA or name C or name O or name CB )) or resid 439 through 441 or (resid 442 an \ d (name N or name CA or name C or name O or name CB )) or resid 443 or (resid 44 \ 4 through 446 and (name N or name CA or name C or name O or name CB )) or resid \ 447 through 464 or (resid 465 through 466 and (name N or name CA or name C or na \ me O or name CB )) or resid 467 through 470 or (resid 471 and (name N or name CA \ or name C or name O or name CB )) or resid 472 through 474 or (resid 475 and (n \ ame N or name CA or name C or name O or name CB )) or resid 476 through 482 or ( \ resid 483 through 484 and (name N or name CA or name C or name O or name CB )) o \ r resid 485 through 490 or (resid 491 and (name N or name CA or name C or name O \ or name CB )) or resid 492 through 504 or (resid 505 and (name N or name CA or \ name C or name O or name CB )) or resid 506 through 520 or (resid 521 and (name \ N or name CA or name C or name O or name CB )) or resid 522 through 523 or (resi \ d 524 and (name N or name CA or name C or name O or name CB )) or resid 525 or ( \ resid 526 through 527 and (name N or name CA or name C or name O or name CB )) o \ r resid 528 through 558 or (resid 559 and (name N or name CA or name C or name O \ or name CB )) or resid 560 through 565 or (resid 566 through 567 and (name N or \ name CA or name C or name O or name CB )) or resid 568 or (resid 569 and (name \ N or name CA or name C or name O or name CB )) or resid 570 or (resid 571 and (n \ ame N or name CA or name C or name O or name CB )) or resid 572 through 575 or ( \ resid 576 through 577 and (name N or name CA or name C or name O or name CB )) o \ r resid 578 through 581 or (resid 582 and (name N or name CA or name C or name O \ or name CB )) or resid 583 through 586 or (resid 587 and (name N or name CA or \ name C or name O or name CB )) or resid 597 through 598 or (resid 599 through 60 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 601 through \ 606 or (resid 607 and (name N or name CA or name C or name O or name CB )) or re \ sid 608 through 631 or (resid 632 and (name N or name CA or name C or name O or \ name CB )) or resid 633 through 635 or (resid 636 and (name N or name CA or name \ C or name O or name CB )) or resid 637 through 659 or (resid 660 and (name N or \ name CA or name C or name O or name CB )) or resid 661 through 662 or (resid 66 \ 3 through 666 and (name N or name CA or name C or name O or name CB )) or resid \ 667 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 690 or (resid 691 and (name N or name CA or name C o \ r name O or name CB )) or resid 692 through 693 or (resid 694 and (name N or nam \ e CA or name C or name O or name CB )) or resid 695 through 776 or resid 778 thr \ ough 779 or (resid 780 and (name N or name CA or name C or name O or name CB )) \ or resid 781 through 784 or (resid 785 through 786 and (name N or name CA or nam \ e C or name O or name CB )) or resid 787 through 792 or (resid 793 and (name N o \ r name CA or name C or name O or name CB )) or resid 794 through 806 or (resid 8 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 808 through \ 840 or (resid 841 through 842 and (name N or name CA or name C or name O or nam \ e CB )) or resid 843 through 853 or (resid 854 and (name N or name CA or name C \ or name O or name CB )) or resid 855 or (resid 856 and (name N or name CA or nam \ e C or name O or name CB )) or resid 857 through 868 or (resid 869 through 871 a \ nd (name N or name CA or name C or name O or name CB )) or resid 872 through 924 \ or (resid 925 through 926 and (name N or name CA or name C or name O or name CB \ )) or resid 927 through 938 or (resid 939 and (name N or name CA or name C or n \ ame O or name CB )) or resid 940 through 949 or (resid 950 and (name N or name C \ A or name C or name O or name CB )) or resid 951 through 959 or (resid 960 and ( \ name N or name CA or name C or name O or name CB )) or resid 961 through 966 or \ (resid 967 through 969 and (name N or name CA or name C or name O or name CB )) \ or resid 970 through 973 or (resid 974 and (name N or name CA or name C or name \ O or name CB )) or resid 975 through 976 or (resid 977 and (name N or name CA or \ name C or name O or name CB )) or resid 978 through 984 or (resid 985 through 9 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 988 through \ 989 or (resid 990 and (name N or name CA or name C or name O or name CB )) or r \ esid 991 through 992 or (resid 993 and (name N or name CA or name C or name O or \ name CB )) or resid 994 through 1011 or (resid 1012 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1013 through 1015 or (resid 1016 through \ 1018 and (name N or name CA or name C or name O or name CB )) or resid 1019 thro \ ugh 1039 or (resid 1040 and (name N or name CA or name C or name O or name CB )) \ or resid 1041 through 1052 or (resid 1053 through 1054 and (name N or name CA o \ r name C or name O or name CB )) or resid 1055 through 1056 or (resid 1057 and ( \ name N or name CA or name C or name O or name CB )) or resid 1058 through 1061 o \ r (resid 1062 through 1063 and (name N or name CA or name C or name O or name CB \ )) or resid 1064 through 1065 or (resid 1066 and (name N or name CA or name C o \ r name O or name CB )) or resid 1067 or (resid 1068 through 1069 and (name N or \ name CA or name C or name O or name CB )) or resid 1070 through 1096 or (resid 1 \ 097 and (name N or name CA or name C or name O or name CB )) or resid 1098 throu \ gh 1099 or (resid 1100 and (name N or name CA or name C or name O or name CB )) \ or resid 1101 or (resid 1102 and (name N or name CA or name C or name O or name \ CB )) or resid 1103 through 1104 or (resid 1105 and (name N or name CA or name C \ or name O or name CB )) or resid 1106 through 1109 or resid 1111 or (resid 1112 \ through 1113 and (name N or name CA or name C or name O or name CB )) or resid \ 1114 through 1124 or (resid 1125 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1126 through 1150 or (resid 1151 through 1153 and (name N or \ name CA or name C or name O or name CB )) or resid 1154 or (resid 1155 through 1 \ 156 and (name N or name CA or name C or name O or name CB )) or resid 1157 throu \ gh 1170 or (resid 1171 through 1172 and (name N or name CA or name C or name O o \ r name CB )) or resid 1173 through 1181 or (resid 1182 through 1184 and (name N \ or name CA or name C or name O or name CB )) or resid 1185 or (resid 1186 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1187 through 1191 or \ (resid 1192 through 1193 and (name N or name CA or name C or name O or name CB \ )) or resid 1194 through 1197 or (resid 1198 and (name N or name CA or name C or \ name O or name CB )) or resid 1199 through 1206)) selection = (chain 'C' and ((resid 18 through 19 and (name N or name CA or name C or name O \ or name CB )) or resid 20 through 50 or resid 52 through 56 or (resid 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 61 or (res \ id 62 and (name N or name CA or name C or name O or name CB )) or resid 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 90 or (resid 91 through 92 and (name N or name CA or name C or name O or na \ me CB )) or resid 93 through 96 or (resid 98 through 101 and (name N or name CA \ or name C or name O or name CB )) or resid 102 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 111 or (r \ esid 112 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 125 or (resid 126 and (name N or name CA or name C or name O \ or name CB )) or resid 127 through 139 or (resid 140 and (name N or name CA or n \ ame C or name O or name CB )) or resid 141 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 145 through 148 or (resid \ 149 and (name N or name CA or name C or name O or name CB )) or resid 150 throu \ gh 166 or (resid 167 through 168 and (name N or name CA or name C or name O or n \ ame CB )) or resid 169 through 179 or (resid 180 through 184 and (name N or name \ CA or name C or name O or name CB )) or resid 185 through 187 or (resid 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 or (resid 190 \ and (name N or name CA or name C or name O or name CB )) or resid 191 through 2 \ 19 or (resid 220 through 223 and (name N or name CA or name C or name O or name \ CB )) or resid 224 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 through 235 or (resid 236 and (name N or name \ CA or name C or name O or name CB )) or resid 237 through 244 or (resid 245 and \ (name N or name CA or name C or name O or name CB )) or resid 246 or (resid 247 \ through 249 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 50 through 262 or (resid 263 and (name N or name CA or name C or name O or name \ CB )) or resid 264 through 283 or (resid 284 and (name N or name CA or name C or \ name O or name CB )) or resid 285 through 288 or (resid 289 through 291 and (na \ me N or name CA or name C or name O or name CB )) or resid 292 through 300 or (r \ esid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 t \ hrough 303 or (resid 304 and (name N or name CA or name C or name O or name CB ) \ ) or resid 305 through 306 or (resid 307 through 309 and (name N or name CA or n \ ame C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 \ and (name N or name CA or name C or name O or name CB )) or resid 315 through 3 \ 16 or (resid 317 and (name N or name CA or name C or name O or name CB )) or res \ id 318 through 325 or (resid 326 and (name N or name CA or name C or name O or n \ ame CB )) or resid 327 through 342 or (resid 343 through 345 and (name N or name \ CA or name C or name O or name CB )) or resid 346 through 353 or (resid 354 and \ (name N or name CA or name C or name O or name CB )) or resid 355 through 362 o \ r (resid 363 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 64 through 368 or (resid 369 and (name N or name CA or name C or name O or name \ CB )) or resid 370 through 374 or (resid 375 and (name N or name CA or name C or \ name O or name CB )) or resid 376 through 387 or (resid 388 and (name N or name \ CA or name C or name O or name CB )) or resid 389 through 396 or (resid 397 and \ (name N or name CA or name C or name O or name CB )) or resid 398 through 399 o \ r (resid 400 through 401 and (name N or name CA or name C or name O or name CB ) \ ) or resid 402 through 441 or (resid 442 and (name N or name CA or name C or nam \ e O or name CB )) or resid 443 or (resid 444 through 446 and (name N or name CA \ or name C or name O or name CB )) or resid 447 through 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 467 or (r \ esid 468 and (name N or name CA or name C or name O or name CB )) or resid 469 t \ hrough 470 or (resid 471 and (name N or name CA or name C or name O or name CB ) \ ) or resid 472 through 474 or (resid 475 and (name N or name CA or name C or nam \ e O or name CB )) or resid 476 through 492 or (resid 493 and (name N or name CA \ or name C or name O or name CB )) or resid 494 through 496 or (resid 497 and (na \ me N or name CA or name C or name O or name CB )) or resid 498 through 504 or (r \ esid 505 and (name N or name CA or name C or name O or name CB )) or resid 506 t \ hrough 522 or (resid 523 through 524 and (name N or name CA or name C or name O \ or name CB )) or resid 525 or (resid 526 through 527 and (name N or name CA or n \ ame C or name O or name CB )) or resid 528 through 539 or (resid 540 and (name N \ or name CA or name C or name O or name CB )) or resid 541 or (resid 542 through \ 543 and (name N or name CA or name C or name O or name CB )) or resid 544 throu \ gh 552 or (resid 553 and (name N or name CA or name C or name O or name CB )) or \ resid 554 through 562 or (resid 563 through 567 and (name N or name CA or name \ C or name O or name CB )) or resid 568 or (resid 569 and (name N or name CA or n \ ame C or name O or name CB )) or resid 570 or (resid 571 and (name N or name CA \ or name C or name O or name CB )) or resid 572 through 575 or (resid 576 through \ 577 and (name N or name CA or name C or name O or name CB )) or resid 578 throu \ gh 587 or resid 597 through 604 or (resid 605 through 607 and (name N or name CA \ or name C or name O or name CB )) or resid 608 through 631 or (resid 632 and (n \ ame N or name CA or name C or name O or name CB )) or resid 633 through 635 or ( \ resid 636 and (name N or name CA or name C or name O or name CB )) or resid 637 \ through 643 or (resid 644 and (name N or name CA or name C or name O or name CB \ )) or resid 645 through 646 or (resid 647 and (name N or name CA or name C or na \ me O or name CB )) or resid 648 through 656 or (resid 657 and (name N or name CA \ or name C or name O or name CB )) or resid 658 through 685 or (resid 686 and (n \ ame N or name CA or name C or name O or name CB )) or resid 687 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 739 or (resid 740 and (name N or name CA or name C or name O or name CB \ )) or resid 741 through 776 or resid 778 through 785 or (resid 786 and (name N o \ r name CA or name C or name O or name CB )) or resid 787 through 798 or (resid 7 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 800 through \ 806 or (resid 807 and (name N or name CA or name C or name O or name CB )) or r \ esid 808 or (resid 809 and (name N or name CA or name C or name O or name CB )) \ or resid 810 through 840 or (resid 841 through 842 and (name N or name CA or nam \ e C or name O or name CB )) or resid 843 through 844 or (resid 845 and (name N o \ r name CA or name C or name O or name CB )) or resid 846 through 848 or (resid 8 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 850 through \ 851 or (resid 852 and (name N or name CA or name C or name O or name CB )) or r \ esid 853 through 872 or (resid 873 and (name N or name CA or name C or name O or \ name CB )) or resid 874 through 886 or (resid 887 and (name N or name CA or nam \ e C or name O or name CB )) or resid 888 through 889 or (resid 890 and (name N o \ r name CA or name C or name O or name CB )) or resid 891 through 892 or (resid 8 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 894 through \ 896 or (resid 897 and (name N or name CA or name C or name O or name CB )) or r \ esid 898 through 908 or (resid 909 and (name N or name CA or name C or name O or \ name CB )) or resid 910 through 912 or (resid 913 through 914 and (name N or na \ me CA or name C or name O or name CB )) or resid 915 through 924 or (resid 925 t \ hrough 926 and (name N or name CA or name C or name O or name CB )) or resid 927 \ through 963 or (resid 964 and (name N or name CA or name C or name O or name CB \ )) or resid 965 through 976 or (resid 977 and (name N or name CA or name C or n \ ame O or name CB )) or resid 978 through 986 or (resid 987 and (name N or name C \ A or name C or name O or name CB )) or resid 988 through 1008 or (resid 1009 and \ (name N or name CA or name C or name O or name CB )) or resid 1010 through 1011 \ or (resid 1012 and (name N or name CA or name C or name O or name CB )) or resi \ d 1013 through 1015 or (resid 1016 through 1018 and (name N or name CA or name C \ or name O or name CB )) or resid 1019 or (resid 1020 and (name N or name CA or \ name C or name O or name CB )) or resid 1021 through 1030 or (resid 1031 through \ 1032 and (name N or name CA or name C or name O or name CB )) or resid 1033 thr \ ough 1034 or (resid 1035 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1036 through 1052 or (resid 1053 through 1054 and (name N or name CA \ or name C or name O or name CB )) or resid 1055 through 1056 or (resid 1057 and \ (name N or name CA or name C or name O or name CB )) or resid 1058 through 1061 \ or (resid 1062 through 1063 and (name N or name CA or name C or name O or name C \ B )) or resid 1064 through 1065 or (resid 1066 and (name N or name CA or name C \ or name O or name CB )) or resid 1067 or (resid 1068 through 1069 and (name N or \ name CA or name C or name O or name CB )) or resid 1070 through 1083 or (resid \ 1084 and (name N or name CA or name C or name O or name CB )) or resid 1085 thro \ ugh 1087 or (resid 1088 and (name N or name CA or name C or name O or name CB )) \ or resid 1089 through 1104 or (resid 1105 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1106 through 1111 or (resid 1112 through 1113 and ( \ name N or name CA or name C or name O or name CB )) or resid 1114 through 1135 o \ r (resid 1136 through 1139 and (name N or name CA or name C or name O or name CB \ )) or resid 1140 through 1154 or (resid 1155 through 1156 and (name N or name C \ A or name C or name O or name CB )) or resid 1157 through 1197 or (resid 1198 an \ d (name N or name CA or name C or name O or name CB )) or resid 1199 through 120 \ 6)) } ncs_group { reference = (chain 'D' and (resid 4 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 13 or (resid 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 88 or (resid 89 and (nam \ e N or name CA or name C or name O or name CB )) or resid 90 through 98 or (resi \ d 99 and (name N or name CA or name C or name O or name CB )) or resid 100 throu \ gh 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) or \ resid 108 through 136 or (resid 137 through 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 140 or (resid 141 and (name N or \ name CA or name C or name O or name CB )) or resid 142 through 150 or (resid 151 \ and (name N or name CA or name C or name O or name CB )) or resid 152 through 1 \ 68 or (resid 169 and (name N or name CA or name C or name O or name CB )) or res \ id 170 through 177 or (resid 178 through 179 and (name N or name CA or name C or \ name O or name CB )) or resid 180 through 186 or (resid 187 and (name N or name \ CA or name C or name O or name CB )) or resid 188 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 200 o \ r (resid 201 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 02 through 213 or (resid 214 and (name N or name CA or name C or name O or name \ CB )) or resid 215 through 219)) selection = (chain 'F' and (resid 4 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 13 or (resid 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 19 or (resid 20 through \ 21 and (name N or name CA or name C or name O or name CB )) or resid 22 through \ 36 or (resid 37 through 40 and (name N or name CA or name C or name O or name CB \ )) or resid 41 through 80 or (resid 81 and (name N or name CA or name C or name \ O or name CB )) or resid 82 through 85 or (resid 86 through 87 and (name N or n \ ame CA or name C or name O or name CB )) or resid 88 or (resid 89 and (name N or \ name CA or name C or name O or name CB )) or resid 90 through 100 or (resid 101 \ and (name N or name CA or name C or name O or name CB )) or resid 102 through 1 \ 06 or (resid 107 and (name N or name CA or name C or name O or name CB )) or res \ id 108 through 112 or (resid 113 and (name N or name CA or name C or name O or n \ ame CB )) or resid 114 through 140 or (resid 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 175 or (resid 176 through 179 and \ (name N or name CA or name C or name O or name CB )) or resid 180 through 190 o \ r (resid 191 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 92 through 219)) selection = (chain 'H' and (resid 4 through 19 or (resid 20 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 36 or (resid 37 through \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 through 85 or (resid 86 through 87 and (name N or name CA or name C or name \ O or name CB )) or resid 88 through 98 or (resid 99 and (name N or name CA or n \ ame C or name O or name CB )) or resid 100 or (resid 101 and (name N or name CA \ or name C or name O or name CB )) or resid 102 through 112 or (resid 113 and (na \ me N or name CA or name C or name O or name CB )) or resid 114 through 136 or (r \ esid 137 through 138 and (name N or name CA or name C or name O or name CB )) or \ resid 139 through 150 or (resid 151 and (name N or name CA or name C or name O \ or name CB )) or resid 152 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 175 or (resid 176 through 179 \ and (name N or name CA or name C or name O or name CB )) or resid 180 through 2 \ 13 or (resid 214 and (name N or name CA or name C or name O or name CB )) or res \ id 215 through 219)) } ncs_group { reference = (chain 'E' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 45 or (resid 46 through 52 and (nam \ e N or name CA or name C or name O or name CB )) or resid 53 through 61 or resid \ 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or res \ id 65 through 72 or (resid 73 and (name N or name CA or name C or name O or name \ CB )) or resid 74 through 78 or (resid 79 and (name N or name CA or name C or n \ ame O or name CB )) or resid 80 or (resid 81 and (name N or name CA or name C or \ name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 97 or (resid 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 102 or (resid 103 throu \ gh 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thr \ ough 109 or (resid 110 through 111 and (name N or name CA or name C or name O or \ name CB )) or resid 112 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB )) or resid 117 through 227)) selection = (chain 'G' and (resid 3 or (resid 4 and (name N or name CA or name C or name O o \ r 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 45 or (resid 46 through 52 and (nam \ e N or name CA or name C or name O or name CB )) or resid 53 through 56 or (resi \ d 57 and (name N or name CA or name C or name O or name CB )) or resid 58 throug \ h 59 or (resid 60 through 61 and (name N or name CA or name C or name O or name \ CB )) or resid 63 through 66 or (resid 67 through 68 and (name N or name CA or n \ ame C or name O or name CB )) or resid 69 through 82 or (resid 83 and (name N or \ name CA or name C or name O or name CB )) or resid 84 through 101 or (resid 102 \ through 105 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 06 through 110 or (resid 111 and (name N or name CA or name C or name O or name \ CB )) or resid 112 through 139 or (resid 140 through 141 and (name N or name CA \ or name C or name O or name CB )) or resid 142 through 227)) selection = (chain 'I' and (resid 3 through 19 or resid 21 through 49 or (resid 50 through 5 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 53 through 5 \ 6 or (resid 57 and (name N or name CA or name C or name O or name CB )) or resid \ 58 through 59 or (resid 60 through 61 and (name N or name CA or name C or name \ O or name CB )) or resid 63 or (resid 64 and (name N or name CA or name C or nam \ e O or name CB )) or resid 65 through 78 or (resid 79 and (name N or name CA or \ name C or name O or name CB )) or resid 80 through 97 or (resid 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 102 or (resid 10 \ 3 through 105 and (name N or name CA or name C or name O or name CB )) or resid \ 106 through 109 or (resid 110 through 111 and (name N or name CA or name C or na \ me O or name CB )) or resid 112 through 115 or (resid 116 and (name N or name CA \ or name C or name O or name CB )) or resid 117 through 136 or (resid 137 and (n \ ame N or name CA or name C or name O or name CB )) or resid 138 through 139 or ( \ resid 140 through 141 and (name N or name CA or name C or name O or name CB )) o \ r resid 142 through 227)) } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 40.940 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.130 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 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 : 0.013 0.049 35560 Z= 1.021 Angle : 1.539 13.559 48498 Z= 1.187 Chirality : 0.107 0.728 5615 Planarity : 0.004 0.083 6304 Dihedral : 13.449 83.799 12285 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.90 % Allowed : 4.04 % Favored : 95.06 % Rotamer: Outliers : 7.18 % Allowed : 9.71 % Favored : 83.10 % Cbeta Deviations : 0.54 % 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 are not related in a simple way. whole: 1.49 (0.12), residues: 4679 helix: 4.15 (0.17), residues: 776 sheet: 1.88 (0.15), residues: 1196 loop : -0.42 (0.11), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1057 TYR 0.031 0.002 TYR B 794 PHE 0.016 0.002 PHE C 156 TRP 0.010 0.001 TRP G 120 HIS 0.020 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.01325 (35513) covalent geometry : angle 1.53983 (48404) SS BOND : bond 0.00634 ( 47) SS BOND : angle 1.07961 ( 94) hydrogen bonds : bond 0.18990 ( 1225) hydrogen bonds : angle 8.25806 ( 3312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 374 time to evaluate : 1.306 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 THR cc_start: 0.6306 (OUTLIER) cc_final: 0.5284 (m) REVERT: A 794 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.6129 (p90) REVERT: A 985 ILE cc_start: 0.5467 (OUTLIER) cc_final: 0.4830 (tt) REVERT: A 1036 LEU cc_start: 0.8315 (mt) cc_final: 0.7864 (mt) REVERT: A 1042 ASN cc_start: 0.7748 (m110) cc_final: 0.7543 (t0) REVERT: A 1117 CYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7349 (p) REVERT: A 1124 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8933 (p) REVERT: A 1180 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.6055 (mp) REVERT: B 32 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5675 (pm20) REVERT: B 232 PHE cc_start: 0.6892 (m-80) cc_final: 0.6330 (m-80) REVERT: B 234 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7084 (mm) REVERT: B 324 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6714 (tp) REVERT: B 694 ARG cc_start: 0.6792 (tpm170) cc_final: 0.6296 (tmt170) REVERT: B 759 LEU cc_start: 0.5021 (OUTLIER) cc_final: 0.4804 (mp) REVERT: B 1005 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8943 (mp) REVERT: B 1047 ILE cc_start: 0.6685 (tt) cc_final: 0.6434 (tt) REVERT: B 1123 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8376 (mm) REVERT: C 290 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8193 (mm) REVERT: C 363 VAL cc_start: 0.7043 (OUTLIER) cc_final: 0.6783 (t) REVERT: C 786 PHE cc_start: 0.7786 (m-80) cc_final: 0.7426 (m-80) REVERT: C 817 CYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6495 (p) REVERT: C 894 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8865 (pp) REVERT: C 1047 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.5101 (tp) REVERT: C 1187 THR cc_start: 0.6227 (OUTLIER) cc_final: 0.6002 (p) REVERT: D 22 VAL cc_start: 0.6238 (OUTLIER) cc_final: 0.6005 (t) REVERT: D 24 ILE cc_start: 0.4280 (OUTLIER) cc_final: 0.3776 (mt) REVERT: D 103 PHE cc_start: 0.7986 (p90) cc_final: 0.7697 (p90) REVERT: D 128 GLU cc_start: 0.3088 (OUTLIER) cc_final: 0.2702 (pp20) REVERT: D 173 SER cc_start: 0.4604 (m) cc_final: 0.4356 (t) REVERT: E 34 MET cc_start: 0.8196 (tpp) cc_final: 0.7564 (ttt) REVERT: E 38 ARG cc_start: 0.6923 (ttm170) cc_final: 0.6644 (tmm160) REVERT: E 100 ASN cc_start: 0.4737 (m110) cc_final: 0.3668 (m110) REVERT: F 5 ILE cc_start: 0.5169 (OUTLIER) cc_final: 0.4609 (mm) REVERT: F 18 VAL cc_start: 0.8137 (t) cc_final: 0.7887 (t) REVERT: G 35 HIS cc_start: 0.8533 (m-70) cc_final: 0.8030 (m90) REVERT: H 7 MET cc_start: 0.4852 (tmm) cc_final: 0.3145 (mpp) REVERT: H 128 GLU cc_start: -0.1984 (OUTLIER) cc_final: -0.2590 (pt0) REVERT: I 35 HIS cc_start: 0.3560 (OUTLIER) cc_final: 0.2065 (m-70) REVERT: I 118 ASP cc_start: 0.6207 (t0) cc_final: 0.5961 (t0) REVERT: I 211 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.6966 (tt) outliers start: 264 outliers final: 48 residues processed: 602 average time/residue: 0.2080 time to fit residues: 208.4480 Evaluate side-chains 248 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 175 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.4980 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 280 GLN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 HIS A 398 ASN A 765 ASN A 785 ASN A 839 ASN A 993 ASN A 999 ASN A1079 ASN A1085 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 ASN B 261 GLN B 277 ASN B 319 GLN B 521 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 ASN B1201 ASN C 98 GLN C 111 GLN C 114 ASN C 226 ASN C 681 HIS C1042 ASN ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN F 37 ASN F 40 GLN F 157 ASN G 187 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN H 157 ASN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.086559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.063646 restraints weight = 626335.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.062091 restraints weight = 388377.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.062377 restraints weight = 324925.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.062310 restraints weight = 266010.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.062517 restraints weight = 232211.091| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35560 Z= 0.155 Angle : 0.699 10.912 48498 Z= 0.372 Chirality : 0.048 0.303 5615 Planarity : 0.005 0.148 6304 Dihedral : 4.910 45.478 5052 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.38 % Favored : 96.30 % Rotamer: Outliers : 0.16 % Allowed : 2.53 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 0.66 (0.12), residues: 4679 helix: 2.41 (0.18), residues: 787 sheet: 1.50 (0.15), residues: 1204 loop : -0.71 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 19 TYR 0.041 0.002 TYR H 145 PHE 0.027 0.002 PHE C 228 TRP 0.020 0.002 TRP A 960 HIS 0.012 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00324 (35513) covalent geometry : angle 0.69637 (48404) SS BOND : bond 0.00719 ( 47) SS BOND : angle 1.55360 ( 94) hydrogen bonds : bond 0.06054 ( 1225) hydrogen bonds : angle 6.53519 ( 3312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 217 time to evaluate : 1.285 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: A 641 TYR cc_start: 0.5179 (p90) cc_final: 0.4332 (p90) REVERT: A 913 MET cc_start: 0.7695 (mpp) cc_final: 0.7238 (mpp) REVERT: B 686 MET cc_start: 0.6178 (ttp) cc_final: 0.5841 (ttp) REVERT: B 694 ARG cc_start: 0.7641 (tpm170) cc_final: 0.7418 (mmm160) REVERT: B 939 MET cc_start: 0.8145 (tpt) cc_final: 0.7647 (tpp) REVERT: C 147 PHE cc_start: 0.8393 (m-80) cc_final: 0.8147 (m-80) REVERT: C 786 PHE cc_start: 0.7969 (m-80) cc_final: 0.7668 (m-80) REVERT: C 932 TYR cc_start: 0.5240 (p90) cc_final: 0.4965 (p90) REVERT: D 173 SER cc_start: 0.4497 (m) cc_final: 0.4189 (t) REVERT: E 83 MET cc_start: 0.6880 (mpp) cc_final: 0.5610 (tpp) REVERT: E 86 LEU cc_start: 0.6850 (tt) cc_final: 0.5863 (pp) REVERT: G 163 PRO cc_start: 0.5731 (OUTLIER) cc_final: 0.5471 (Cg_endo) REVERT: H 111 ILE cc_start: 0.7164 (mp) cc_final: 0.6601 (mm) REVERT: I 34 MET cc_start: 0.6310 (tpp) cc_final: 0.5825 (tpp) outliers start: 6 outliers final: 1 residues processed: 223 average time/residue: 0.2245 time to fit residues: 81.8743 Evaluate side-chains 141 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 438 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 456 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 181 optimal weight: 0.0770 chunk 278 optimal weight: 50.0000 chunk 221 optimal weight: 30.0000 chunk 178 optimal weight: 0.8980 chunk 279 optimal weight: 30.0000 overall best weight: 3.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 627 GLN A 670 HIS ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN F 129 GLN ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS G 82 GLN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 GLN H 37 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.082825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.059442 restraints weight = 534057.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.058183 restraints weight = 429235.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.057873 restraints weight = 423550.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.058116 restraints weight = 313209.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.057899 restraints weight = 286532.725| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 35560 Z= 0.203 Angle : 0.721 10.090 48498 Z= 0.387 Chirality : 0.047 0.235 5615 Planarity : 0.005 0.126 6304 Dihedral : 5.236 45.685 5052 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.99 % Favored : 94.71 % Rotamer: Outliers : 0.14 % Allowed : 2.91 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.05 (0.12), residues: 4679 helix: 1.52 (0.18), residues: 793 sheet: 0.77 (0.15), residues: 1173 loop : -0.90 (0.11), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 226 TYR 0.035 0.003 TYR H 145 PHE 0.034 0.002 PHE H 86 TRP 0.040 0.002 TRP B 44 HIS 0.009 0.002 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00430 (35513) covalent geometry : angle 0.71950 (48404) SS BOND : bond 0.00660 ( 47) SS BOND : angle 1.39333 ( 94) hydrogen bonds : bond 0.05296 ( 1225) hydrogen bonds : angle 6.20188 ( 3312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 1.404 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: A 441 LEU cc_start: 0.8668 (mt) cc_final: 0.8464 (tp) REVERT: A 641 TYR cc_start: 0.5174 (p90) cc_final: 0.4518 (p90) REVERT: A 913 MET cc_start: 0.7891 (mpp) cc_final: 0.7246 (mpp) REVERT: B 906 MET cc_start: 0.1737 (mtt) cc_final: 0.1352 (mtt) REVERT: C 84 MET cc_start: 0.6916 (mmm) cc_final: 0.6400 (mmm) REVERT: C 1137 MET cc_start: 0.8284 (mpp) cc_final: 0.7964 (mpp) REVERT: E 34 MET cc_start: 0.8135 (ttm) cc_final: 0.7238 (tmm) REVERT: E 83 MET cc_start: 0.7236 (mpp) cc_final: 0.6052 (tpp) REVERT: E 86 LEU cc_start: 0.6647 (tt) cc_final: 0.6155 (pp) REVERT: H 111 ILE cc_start: 0.7551 (mp) cc_final: 0.6966 (mm) REVERT: I 34 MET cc_start: 0.6082 (tpp) cc_final: 0.5759 (tpp) outliers start: 5 outliers final: 0 residues processed: 184 average time/residue: 0.2326 time to fit residues: 70.3200 Evaluate side-chains 126 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 277 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 278 optimal weight: 50.0000 chunk 395 optimal weight: 0.2980 chunk 213 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.082509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.059669 restraints weight = 628693.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.057765 restraints weight = 480330.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.057673 restraints weight = 488183.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.058075 restraints weight = 327485.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.058003 restraints weight = 256610.641| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35560 Z= 0.161 Angle : 0.622 9.395 48498 Z= 0.331 Chirality : 0.045 0.297 5615 Planarity : 0.005 0.140 6304 Dihedral : 5.026 46.432 5052 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.64 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.18 (0.12), residues: 4679 helix: 1.62 (0.18), residues: 788 sheet: 0.59 (0.15), residues: 1165 loop : -1.00 (0.11), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 691 TYR 0.033 0.002 TYR C 794 PHE 0.015 0.002 PHE C 786 TRP 0.017 0.002 TRP F 38 HIS 0.007 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00338 (35513) covalent geometry : angle 0.62026 (48404) SS BOND : bond 0.00884 ( 47) SS BOND : angle 1.13886 ( 94) hydrogen bonds : bond 0.04684 ( 1225) hydrogen bonds : angle 5.87791 ( 3312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.6983 (tpt) cc_final: 0.6679 (tmm) REVERT: A 441 LEU cc_start: 0.8670 (mt) cc_final: 0.8431 (tp) REVERT: A 641 TYR cc_start: 0.5086 (p90) cc_final: 0.4206 (p90) REVERT: A 913 MET cc_start: 0.7738 (mpp) cc_final: 0.7154 (mpp) REVERT: B 148 MET cc_start: 0.8402 (tpt) cc_final: 0.8167 (tpp) REVERT: B 161 MET cc_start: 0.6309 (mmp) cc_final: 0.6010 (ptt) REVERT: B 786 PHE cc_start: 0.7302 (m-10) cc_final: 0.6862 (m-10) REVERT: B 906 MET cc_start: 0.1996 (mtt) cc_final: 0.1430 (mtt) REVERT: B 939 MET cc_start: 0.7892 (tpt) cc_final: 0.7613 (tpp) REVERT: B 967 PHE cc_start: 0.4412 (p90) cc_final: 0.3987 (p90) REVERT: C 84 MET cc_start: 0.6916 (mmm) cc_final: 0.6472 (mmm) REVERT: E 34 MET cc_start: 0.8141 (ttm) cc_final: 0.7872 (ttm) REVERT: E 80 TYR cc_start: 0.8826 (m-10) cc_final: 0.8589 (m-80) REVERT: E 83 MET cc_start: 0.7194 (mpp) cc_final: 0.5867 (tpp) REVERT: E 86 LEU cc_start: 0.6873 (tt) cc_final: 0.6163 (pp) REVERT: G 68 PHE cc_start: 0.6691 (m-80) cc_final: 0.6331 (m-80) REVERT: H 111 ILE cc_start: 0.7251 (mp) cc_final: 0.6956 (mm) REVERT: I 34 MET cc_start: 0.6157 (tpp) cc_final: 0.5884 (tpp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2174 time to fit residues: 67.0319 Evaluate side-chains 126 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 293 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 468 optimal weight: 0.9990 chunk 408 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 272 optimal weight: 20.0000 chunk 383 optimal weight: 20.0000 chunk 292 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN ** A 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN F 129 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS I 3 GLN I 180 HIS ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.081234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.058577 restraints weight = 596379.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.056646 restraints weight = 477942.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.056923 restraints weight = 400301.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.056877 restraints weight = 310512.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.057011 restraints weight = 253269.554| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35560 Z= 0.168 Angle : 0.647 10.476 48498 Z= 0.343 Chirality : 0.046 0.271 5615 Planarity : 0.005 0.124 6304 Dihedral : 5.126 44.181 5052 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.12 % Favored : 93.64 % Rotamer: Outliers : 0.03 % Allowed : 2.59 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.38 (0.12), residues: 4679 helix: 1.51 (0.19), residues: 788 sheet: 0.30 (0.15), residues: 1220 loop : -1.09 (0.11), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 87 TYR 0.026 0.002 TYR A 794 PHE 0.031 0.002 PHE H 86 TRP 0.015 0.002 TRP B1184 HIS 0.015 0.001 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.00356 (35513) covalent geometry : angle 0.64597 (48404) SS BOND : bond 0.00468 ( 47) SS BOND : angle 1.05076 ( 94) hydrogen bonds : bond 0.04660 ( 1225) hydrogen bonds : angle 5.81889 ( 3312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 TYR cc_start: 0.5454 (p90) cc_final: 0.4626 (p90) REVERT: A 913 MET cc_start: 0.8012 (mpp) cc_final: 0.7379 (mpp) REVERT: B 786 PHE cc_start: 0.7352 (m-10) cc_final: 0.6967 (m-10) REVERT: B 906 MET cc_start: 0.2368 (mtt) cc_final: 0.1997 (mtt) REVERT: B 939 MET cc_start: 0.7884 (tpt) cc_final: 0.7679 (tpp) REVERT: B 967 PHE cc_start: 0.4324 (p90) cc_final: 0.3700 (p90) REVERT: C 84 MET cc_start: 0.7131 (mmm) cc_final: 0.6863 (mmm) REVERT: C 161 MET cc_start: 0.7686 (tpt) cc_final: 0.7323 (tpp) REVERT: C 397 TYR cc_start: 0.5973 (p90) cc_final: 0.5595 (p90) REVERT: E 34 MET cc_start: 0.8244 (ttm) cc_final: 0.7367 (tmm) REVERT: E 80 TYR cc_start: 0.8792 (m-10) cc_final: 0.8539 (m-80) REVERT: E 83 MET cc_start: 0.7048 (mpp) cc_final: 0.5666 (tpp) REVERT: E 86 LEU cc_start: 0.6884 (tt) cc_final: 0.6195 (pp) REVERT: G 68 PHE cc_start: 0.6637 (m-80) cc_final: 0.6142 (m-80) REVERT: G 163 PRO cc_start: 0.6294 (OUTLIER) cc_final: 0.5942 (Cg_endo) REVERT: I 34 MET cc_start: 0.6226 (tpp) cc_final: 0.5941 (tpp) REVERT: I 215 ASN cc_start: 0.7318 (t0) cc_final: 0.7083 (p0) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2243 time to fit residues: 62.7866 Evaluate side-chains 129 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 132 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 432 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 327 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 182 optimal weight: 0.0670 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.080498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.057726 restraints weight = 544100.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.055623 restraints weight = 398522.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.056060 restraints weight = 352180.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.055689 restraints weight = 321149.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.055268 restraints weight = 327822.343| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35560 Z= 0.183 Angle : 0.662 14.027 48498 Z= 0.351 Chirality : 0.045 0.306 5615 Planarity : 0.005 0.132 6304 Dihedral : 5.293 45.952 5052 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.84 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.56 (0.12), residues: 4679 helix: 1.43 (0.19), residues: 785 sheet: 0.13 (0.15), residues: 1230 loop : -1.20 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 626 TYR 0.031 0.002 TYR E 59 PHE 0.017 0.002 PHE C 630 TRP 0.013 0.002 TRP B 960 HIS 0.019 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00387 (35513) covalent geometry : angle 0.66079 (48404) SS BOND : bond 0.00428 ( 47) SS BOND : angle 1.16145 ( 94) hydrogen bonds : bond 0.04618 ( 1225) hydrogen bonds : angle 5.90651 ( 3312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.262 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: A 240 MET cc_start: 0.7178 (tpt) cc_final: 0.6642 (tmm) REVERT: A 452 MET cc_start: 0.6747 (ptp) cc_final: 0.6529 (ptt) REVERT: A 641 TYR cc_start: 0.5532 (p90) cc_final: 0.4611 (p90) REVERT: B 148 MET cc_start: 0.8605 (tpt) cc_final: 0.8290 (tpp) REVERT: B 786 PHE cc_start: 0.7611 (m-10) cc_final: 0.7218 (m-10) REVERT: B 906 MET cc_start: 0.2825 (mtt) cc_final: 0.2368 (mtt) REVERT: B 939 MET cc_start: 0.7890 (tpp) cc_final: 0.7458 (tpp) REVERT: B 967 PHE cc_start: 0.4443 (p90) cc_final: 0.3990 (p90) REVERT: C 84 MET cc_start: 0.7209 (mmm) cc_final: 0.6888 (mmm) REVERT: C 161 MET cc_start: 0.7831 (tpt) cc_final: 0.7625 (tpp) REVERT: E 34 MET cc_start: 0.8427 (ttm) cc_final: 0.7986 (ttt) REVERT: E 80 TYR cc_start: 0.8883 (m-10) cc_final: 0.8656 (m-80) REVERT: E 83 MET cc_start: 0.6989 (mpp) cc_final: 0.5602 (tpp) REVERT: E 86 LEU cc_start: 0.6748 (tt) cc_final: 0.6282 (pp) REVERT: F 110 GLU cc_start: 0.8041 (pp20) cc_final: 0.7829 (tm-30) REVERT: H 111 ILE cc_start: 0.7111 (mp) cc_final: 0.6768 (mm) REVERT: I 34 MET cc_start: 0.6284 (tpp) cc_final: 0.5916 (tpp) REVERT: I 216 HIS cc_start: 0.1399 (t70) cc_final: 0.1152 (t70) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2208 time to fit residues: 62.4289 Evaluate side-chains 123 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 73 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 288 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 402 optimal weight: 7.9990 chunk 398 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS C 842 GLN ** C 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN F 40 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.079646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.056067 restraints weight = 399340.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.054848 restraints weight = 342013.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.054383 restraints weight = 320887.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.054456 restraints weight = 265577.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.055175 restraints weight = 239588.549| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35560 Z= 0.201 Angle : 0.679 17.996 48498 Z= 0.361 Chirality : 0.045 0.242 5615 Planarity : 0.005 0.108 6304 Dihedral : 5.520 44.657 5052 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.06 % Favored : 92.66 % Rotamer: Outliers : 0.03 % Allowed : 1.41 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.81 (0.12), residues: 4679 helix: 1.17 (0.18), residues: 796 sheet: -0.07 (0.15), residues: 1232 loop : -1.34 (0.12), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 113 TYR 0.033 0.002 TYR B 689 PHE 0.022 0.002 PHE C1044 TRP 0.019 0.002 TRP B 960 HIS 0.013 0.002 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00424 (35513) covalent geometry : angle 0.67784 (48404) SS BOND : bond 0.00453 ( 47) SS BOND : angle 1.08661 ( 94) hydrogen bonds : bond 0.04727 ( 1225) hydrogen bonds : angle 6.03419 ( 3312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.6992 (ptp) cc_final: 0.6784 (ptt) REVERT: A 563 MET cc_start: 0.7676 (tpt) cc_final: 0.7332 (tpp) REVERT: A 641 TYR cc_start: 0.5252 (p90) cc_final: 0.4326 (p90) REVERT: A 682 ILE cc_start: 0.7832 (pt) cc_final: 0.7613 (pt) REVERT: B 786 PHE cc_start: 0.7657 (m-10) cc_final: 0.7256 (m-10) REVERT: B 906 MET cc_start: 0.2800 (mtt) cc_final: 0.2376 (mtt) REVERT: B 939 MET cc_start: 0.7866 (tpp) cc_final: 0.7538 (tpp) REVERT: E 34 MET cc_start: 0.8373 (ttm) cc_final: 0.7909 (ttt) REVERT: E 83 MET cc_start: 0.7155 (mpp) cc_final: 0.5772 (tpp) REVERT: E 86 LEU cc_start: 0.6332 (tt) cc_final: 0.5792 (pp) REVERT: F 110 GLU cc_start: 0.7996 (pp20) cc_final: 0.7693 (tp30) REVERT: F 154 LYS cc_start: 0.5840 (pttt) cc_final: 0.5566 (ttpp) REVERT: G 163 PRO cc_start: 0.6285 (OUTLIER) cc_final: 0.5988 (Cg_endo) REVERT: H 111 ILE cc_start: 0.7607 (mp) cc_final: 0.7235 (mm) REVERT: I 34 MET cc_start: 0.6286 (tpp) cc_final: 0.6010 (tpp) REVERT: I 216 HIS cc_start: 0.1630 (t70) cc_final: 0.1356 (t70) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.2084 time to fit residues: 57.1688 Evaluate side-chains 121 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 97 optimal weight: 9.9990 chunk 207 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 382 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 407 optimal weight: 0.9980 chunk 433 optimal weight: 40.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN B 636 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.079583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.057516 restraints weight = 535136.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.055480 restraints weight = 423944.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.055869 restraints weight = 387263.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.055861 restraints weight = 301309.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055677 restraints weight = 265519.058| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.6476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35560 Z= 0.177 Angle : 0.652 11.861 48498 Z= 0.345 Chirality : 0.045 0.308 5615 Planarity : 0.005 0.140 6304 Dihedral : 5.483 45.354 5052 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.53 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.84 (0.12), residues: 4679 helix: 1.24 (0.18), residues: 794 sheet: -0.07 (0.15), residues: 1249 loop : -1.41 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 301 TYR 0.023 0.002 TYR A 641 PHE 0.021 0.002 PHE C 101 TRP 0.034 0.002 TRP E 120 HIS 0.010 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00375 (35513) covalent geometry : angle 0.65112 (48404) SS BOND : bond 0.00402 ( 47) SS BOND : angle 1.08171 ( 94) hydrogen bonds : bond 0.04597 ( 1225) hydrogen bonds : angle 5.96021 ( 3312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.268 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.6792 (ptp) cc_final: 0.6517 (ptt) REVERT: A 563 MET cc_start: 0.7859 (tpt) cc_final: 0.6945 (mmm) REVERT: A 641 TYR cc_start: 0.5303 (p90) cc_final: 0.4300 (p90) REVERT: A 682 ILE cc_start: 0.7903 (pt) cc_final: 0.7676 (pt) REVERT: A 913 MET cc_start: 0.8152 (mpp) cc_final: 0.7417 (mpp) REVERT: B 148 MET cc_start: 0.8607 (tpt) cc_final: 0.8303 (tpp) REVERT: B 786 PHE cc_start: 0.7708 (m-10) cc_final: 0.7304 (m-10) REVERT: B 906 MET cc_start: 0.2665 (mtt) cc_final: 0.2211 (mtt) REVERT: C 84 MET cc_start: 0.6724 (mmm) cc_final: 0.6378 (mmm) REVERT: E 34 MET cc_start: 0.8032 (ttm) cc_final: 0.7799 (ttm) REVERT: E 83 MET cc_start: 0.7027 (mpp) cc_final: 0.5553 (ttm) REVERT: E 86 LEU cc_start: 0.6888 (tt) cc_final: 0.6277 (pp) REVERT: F 154 LYS cc_start: 0.5811 (pttt) cc_final: 0.5521 (ttpp) REVERT: H 7 MET cc_start: 0.4550 (tmm) cc_final: 0.4291 (tmm) REVERT: H 111 ILE cc_start: 0.7099 (mp) cc_final: 0.6342 (mm) REVERT: I 216 HIS cc_start: 0.1443 (t70) cc_final: 0.1171 (t70) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2177 time to fit residues: 56.2087 Evaluate side-chains 124 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 465 optimal weight: 8.9990 chunk 294 optimal weight: 0.4980 chunk 209 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 417 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 335 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN ** I 74 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 = 0.3911 r_free = 0.3911 target = 0.079576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.057391 restraints weight = 555728.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.054619 restraints weight = 433375.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.054607 restraints weight = 440767.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.054813 restraints weight = 335384.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.054613 restraints weight = 298925.314| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35560 Z= 0.151 Angle : 0.628 10.342 48498 Z= 0.331 Chirality : 0.045 0.317 5615 Planarity : 0.004 0.120 6304 Dihedral : 5.370 43.725 5052 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.13 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.82 (0.12), residues: 4679 helix: 1.41 (0.19), residues: 790 sheet: -0.09 (0.15), residues: 1253 loop : -1.43 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 691 TYR 0.026 0.002 TYR B 641 PHE 0.024 0.002 PHE C 101 TRP 0.033 0.002 TRP E 120 HIS 0.013 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00318 (35513) covalent geometry : angle 0.62671 (48404) SS BOND : bond 0.00350 ( 47) SS BOND : angle 0.98676 ( 94) hydrogen bonds : bond 0.04430 ( 1225) hydrogen bonds : angle 5.81614 ( 3312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.234 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.7063 (ptp) cc_final: 0.6816 (ptt) REVERT: A 563 MET cc_start: 0.7763 (tpt) cc_final: 0.7148 (mmm) REVERT: A 682 ILE cc_start: 0.7940 (pt) cc_final: 0.7710 (pt) REVERT: A 913 MET cc_start: 0.7967 (mpp) cc_final: 0.7284 (mpp) REVERT: B 148 MET cc_start: 0.8601 (tpt) cc_final: 0.8348 (tpp) REVERT: B 786 PHE cc_start: 0.7620 (m-10) cc_final: 0.7242 (m-10) REVERT: B 906 MET cc_start: 0.2642 (mtt) cc_final: 0.2137 (mtt) REVERT: C 563 MET cc_start: 0.5220 (mmt) cc_final: 0.3750 (tpt) REVERT: C 913 MET cc_start: 0.7249 (mpp) cc_final: 0.6631 (mpp) REVERT: E 34 MET cc_start: 0.8303 (ttm) cc_final: 0.8023 (ttm) REVERT: E 83 MET cc_start: 0.7037 (mpp) cc_final: 0.5469 (ttm) REVERT: E 86 LEU cc_start: 0.6192 (tt) cc_final: 0.5337 (pp) REVERT: F 154 LYS cc_start: 0.5643 (pttt) cc_final: 0.5358 (ttpp) REVERT: H 111 ILE cc_start: 0.7600 (mp) cc_final: 0.7232 (mm) REVERT: I 216 HIS cc_start: 0.1625 (t70) cc_final: 0.1335 (t70) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2119 time to fit residues: 55.9544 Evaluate side-chains 127 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 89 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 388 optimal weight: 5.9990 chunk 414 optimal weight: 30.0000 chunk 371 optimal weight: 30.0000 chunk 440 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 329 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 321 optimal weight: 0.0170 chunk 91 optimal weight: 10.0000 overall best weight: 5.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1079 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN F 40 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN H 194 HIS ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.078281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.055850 restraints weight = 477867.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.053043 restraints weight = 419997.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.052930 restraints weight = 366366.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.053399 restraints weight = 278652.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.053073 restraints weight = 236780.586| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.7415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35560 Z= 0.238 Angle : 0.740 12.012 48498 Z= 0.394 Chirality : 0.047 0.268 5615 Planarity : 0.005 0.108 6304 Dihedral : 5.987 40.367 5052 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.17 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.23 (0.12), residues: 4679 helix: 0.86 (0.18), residues: 774 sheet: -0.33 (0.15), residues: 1264 loop : -1.63 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 98 TYR 0.027 0.002 TYR B 641 PHE 0.027 0.002 PHE C 630 TRP 0.056 0.003 TRP I 120 HIS 0.013 0.002 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00501 (35513) covalent geometry : angle 0.73862 (48404) SS BOND : bond 0.00481 ( 47) SS BOND : angle 1.15865 ( 94) hydrogen bonds : bond 0.04980 ( 1225) hydrogen bonds : angle 6.32469 ( 3312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.389 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: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.7067 (ptp) cc_final: 0.6843 (ptt) REVERT: A 641 TYR cc_start: 0.5100 (p90) cc_final: 0.4109 (p90) REVERT: A 913 MET cc_start: 0.8164 (mpp) cc_final: 0.7394 (mpp) REVERT: B 906 MET cc_start: 0.3115 (mtt) cc_final: 0.2568 (mtt) REVERT: C 563 MET cc_start: 0.5376 (mmt) cc_final: 0.3796 (tpt) REVERT: E 34 MET cc_start: 0.8132 (ttm) cc_final: 0.7766 (ttm) REVERT: E 83 MET cc_start: 0.6906 (mpp) cc_final: 0.5380 (ttm) REVERT: E 86 LEU cc_start: 0.5820 (tt) cc_final: 0.4953 (pt) REVERT: F 154 LYS cc_start: 0.5671 (pttt) cc_final: 0.5387 (ttpp) REVERT: H 7 MET cc_start: 0.3298 (tmm) cc_final: 0.2463 (ttp) REVERT: H 111 ILE cc_start: 0.7612 (mp) cc_final: 0.7251 (mm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2140 time to fit residues: 55.5565 Evaluate side-chains 122 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 263 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 338 optimal weight: 0.0050 chunk 31 optimal weight: 6.9990 chunk 436 optimal weight: 0.0070 chunk 94 optimal weight: 10.0000 chunk 222 optimal weight: 0.0570 chunk 98 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 chunk 328 optimal weight: 0.9990 overall best weight: 0.2930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 HIS B 261 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN H 92 GLN H 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.080075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.058448 restraints weight = 549639.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.055715 restraints weight = 389824.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.055866 restraints weight = 342820.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.056005 restraints weight = 263125.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.056236 restraints weight = 227212.211| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.7205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35560 Z= 0.125 Angle : 0.640 10.246 48498 Z= 0.334 Chirality : 0.045 0.242 5615 Planarity : 0.004 0.095 6304 Dihedral : 5.274 48.358 5052 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.02 % 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 are not related in a simple way. whole: -0.81 (0.12), residues: 4679 helix: 1.54 (0.19), residues: 778 sheet: -0.04 (0.15), residues: 1280 loop : -1.49 (0.12), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 691 TYR 0.055 0.002 TYR C 689 PHE 0.027 0.002 PHE G 27 TRP 0.032 0.002 TRP E 120 HIS 0.011 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00254 (35513) covalent geometry : angle 0.63894 (48404) SS BOND : bond 0.00267 ( 47) SS BOND : angle 1.17636 ( 94) hydrogen bonds : bond 0.04355 ( 1225) hydrogen bonds : angle 5.61615 ( 3312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8104.12 seconds wall clock time: 140 minutes 11.49 seconds (8411.49 seconds total)