Starting phenix.real_space_refine on Sat Mar 7 01:44:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v5k_31726/03_2026/7v5k_31726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v5k_31726/03_2026/7v5k_31726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v5k_31726/03_2026/7v5k_31726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v5k_31726/03_2026/7v5k_31726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v5k_31726/03_2026/7v5k_31726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v5k_31726/03_2026/7v5k_31726.map" } resolution = 2.8 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 192 5.16 5 C 23063 2.51 5 N 6010 2.21 5 O 7104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s 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: 36369 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8836 Classifications: {'peptide': 1141} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 8836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8836 Classifications: {'peptide': 1141} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 8836 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8830 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 1141, 8830 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 9023 Chain: "D" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain: "E" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1668 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "F" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain: "G" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1668 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "H" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain: "I" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1668 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Residues with excluded nonbonded symmetry interactions: 1 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: 9.42, per 1000 atoms: 0.26 Number of scatterers: 36369 At special positions: 0 Unit cell: (214.335, 231.655, 182.942, 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 192 16.00 O 7104 8.00 N 6010 7.00 C 23063 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=2.05 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=2.03 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 503 " - pdb=" SG CYS A 526 " 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.02 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.06 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 185 " - pdb=" SG CYS C 237 " distance=2.02 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.05 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 151 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 151 " - pdb=" SG CYS I 207 " distance=2.01 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: 2.86 Conformation dependent library (CDL) restraints added in 1.9 seconds 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8786 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 83 sheets defined 19.1% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.520A pdb=" N ASP A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.995A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.000A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (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: 4.035A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 390' Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.854A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.563A pdb=" N MET A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.798A pdb=" N GLN A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.220A pdb=" N SER A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 825 through 854 removed outlier: 3.673A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 removed outlier: 3.557A pdb=" N VAL A 898 " --> pdb=" O LEU A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 925 through 929 Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.825A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 Processing helix chain 'A' and resid 987 through 994 removed outlier: 3.592A pdb=" N GLN A 994 " --> pdb=" O LEU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 removed outlier: 3.573A pdb=" N GLY A1011 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1041 removed outlier: 3.852A pdb=" N SER A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 3.855A pdb=" N ALA A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.804A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.576A pdb=" N LYS B 52 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.952A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.980A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 4.107A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.516A pdb=" N GLN B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 825 through 854 removed outlier: 3.616A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 867 removed outlier: 4.173A pdb=" N GLY B 866 " --> pdb=" O ILE B 862 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY B 867 " --> pdb=" O PRO B 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 862 through 867' Processing helix chain 'B' and resid 888 through 898 removed outlier: 3.901A pdb=" N VAL B 898 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 915 Processing helix chain 'B' and resid 925 through 930 Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.670A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 removed outlier: 3.608A pdb=" N GLY B 984 " --> pdb=" O LEU B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 Processing helix chain 'B' and resid 996 through 1011 removed outlier: 3.748A pdb=" N GLY B1011 " --> pdb=" O ALA B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1040 removed outlier: 3.886A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 3.659A pdb=" N ALA B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.506A pdb=" N SER C 106 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.716A pdb=" N SER C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.869A 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 449 through 456 removed outlier: 3.763A pdb=" N MET C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 453 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 588 through 588 No H-bonds generated for 'chain 'C' and resid 588 through 588' Processing helix chain 'C' and resid 595 through 598 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 825 through 854 Processing helix chain 'C' and resid 888 through 898 removed outlier: 3.539A pdb=" N VAL C 898 " --> pdb=" O LEU C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 915 Processing helix chain 'C' and resid 940 through 960 removed outlier: 4.807A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 Processing helix chain 'C' and resid 987 through 994 removed outlier: 3.953A pdb=" N GLN C 994 " --> pdb=" O LEU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1011 Processing helix chain 'C' and resid 1018 through 1040 removed outlier: 3.558A pdb=" N LYS C1035 " --> pdb=" O GLN C1031 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.044A pdb=" N ALA C1065 " --> pdb=" O LEU C1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 197 through 203 removed outlier: 4.332A pdb=" N GLY E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR E 202 " --> pdb=" O SER E 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.196A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 removed outlier: 3.577A pdb=" N GLY F 128 " --> pdb=" O GLN F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'G' and resid 197 through 203 removed outlier: 4.332A pdb=" N GLY G 201 " --> pdb=" O SER G 197 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR G 202 " --> pdb=" O SER G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.143A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 removed outlier: 3.577A pdb=" N GLY H 128 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'I' and resid 197 through 203 removed outlier: 4.332A pdb=" N GLY I 201 " --> pdb=" O SER I 197 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR I 202 " --> pdb=" O SER I 198 " (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: 6.499A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN C 647 " --> pdb=" O SER C 643 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR C 648 " --> pdb=" O CYS C 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 75 removed outlier: 4.173A 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: 6.210A pdb=" N VAL A 263 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR A 283 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 265 " --> pdb=" O PHE A 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.336A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.951A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 232 through 235 Processing sheet with id=AA8, first strand: chain 'A' and resid 232 through 235 removed outlier: 3.545A pdb=" N CYS A 185 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 367 removed outlier: 3.983A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.518A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 477 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N CYS A 425 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 479 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 423 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 481 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=AB4, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.389A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AB6, first strand: chain 'A' and resid 630 through 632 Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.927A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 778 through 782 Processing sheet with id=AB9, first strand: chain 'A' and resid 802 through 803 Processing sheet with id=AC1, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC2, first strand: chain 'A' and resid 967 through 969 removed outlier: 4.234A pdb=" N LYS C 779 " --> pdb=" O ALA A 969 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1121 through 1130 removed outlier: 6.508A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 33 through 35 removed outlier: 5.623A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.438A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.327A pdb=" N VAL B 263 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR B 283 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 265 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.043A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.524A pdb=" N GLU B 188 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AD1, first strand: chain 'B' and resid 127 through 129 removed outlier: 4.312A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD3, first strand: chain 'B' and resid 360 through 367 removed outlier: 4.436A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.818A pdb=" N SER B 440 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 444 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 567 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR B 477 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N CYS B 425 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 479 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE B 423 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 481 " --> pdb=" O ASN B 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 407 through 409 removed outlier: 6.555A pdb=" N CYS B 407 " --> pdb=" O CYS B 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.325A 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: 5.225A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 605 through 607 Processing sheet with id=AD8, first strand: chain 'B' and resid 617 through 618 Processing sheet with id=AD9, first strand: chain 'B' and resid 631 through 632 Processing sheet with id=AE1, first strand: chain 'B' and resid 778 through 782 Processing sheet with id=AE2, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AE3, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 5.888A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1154 through 1156 Processing sheet with id=AE5, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE6, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.210A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.332A pdb=" N VAL C 263 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 283 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU C 265 " --> pdb=" O PHE C 281 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 88 through 90 removed outlier: 7.359A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ARG C 301 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N HIS C 208 " --> pdb=" O ARG C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 127 through 130 removed outlier: 9.102A pdb=" N GLY C 128 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N SER C 135 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C 130 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA C 309 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 139 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 232 through 241 removed outlier: 4.906A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 147 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AF3, first strand: chain 'C' and resid 360 through 367 removed outlier: 5.608A pdb=" N SER C 362 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL C 661 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER C 364 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL C 659 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 374 through 375 removed outlier: 6.235A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 613 " --> pdb=" O TYR C 606 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.808A pdb=" N ILE C 573 " --> pdb=" O CYS C 478 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS C 478 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.785A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 502 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AF8, first strand: chain 'C' and resid 1121 through 1130 removed outlier: 5.834A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.782A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AG2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.558A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 114 through 118 removed outlier: 5.928A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.480A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.709A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.240A pdb=" N GLU E 10 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 131 through 135 removed outlier: 4.294A pdb=" N THR E 146 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 143 " --> pdb=" O THR E 146 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 131 through 135 removed outlier: 5.878A pdb=" N SER E 188 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA E 179 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER E 190 " --> pdb=" O PHE E 177 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 161 through 165 removed outlier: 4.591A pdb=" N TYR E 205 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS E 207 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS E 220 " --> pdb=" O CYS E 207 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.792A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AH3, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.282A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.927A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 153 through 155 removed outlier: 4.480A pdb=" N TRP F 148 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.686A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.238A pdb=" N GLU G 10 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 131 through 135 removed outlier: 4.295A pdb=" N THR G 146 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER G 143 " --> pdb=" O THR G 146 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 131 through 135 removed outlier: 5.879A pdb=" N SER G 188 " --> pdb=" O ALA G 179 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA G 179 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER G 190 " --> pdb=" O PHE G 177 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 162 through 165 removed outlier: 4.590A pdb=" N TYR G 205 " --> pdb=" O VAL G 222 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.817A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AI4, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.280A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.928A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.478A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AI8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.538A pdb=" N ILE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.963A pdb=" N TYR I 112 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 142 through 143 removed outlier: 3.682A pdb=" N SER I 143 " --> pdb=" O THR I 146 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR I 146 " --> pdb=" O SER I 143 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N SER I 188 " --> pdb=" O ALA I 179 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA I 179 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER I 190 " --> pdb=" O PHE I 177 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 162 through 165 removed outlier: 4.590A pdb=" N TYR I 205 " --> pdb=" O VAL I 222 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS I 207 " --> pdb=" O LYS I 220 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS I 220 " --> pdb=" O CYS I 207 " (cutoff:3.500A) 1298 hydrogen bonds defined for protein. 3453 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: 8.96 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7339 1.33 - 1.45: 9861 1.45 - 1.58: 19749 1.58 - 1.70: 0 1.70 - 1.83: 258 Bond restraints: 37207 Sorted by residual: bond pdb=" C MET A 696 " pdb=" N LEU A 697 " ideal model delta sigma weight residual 1.330 1.476 -0.146 1.44e-02 4.82e+03 1.03e+02 bond pdb=" C GLN B 319 " pdb=" N PRO B 320 " ideal model delta sigma weight residual 1.331 1.449 -0.118 1.20e-02 6.94e+03 9.61e+01 bond pdb=" C THR A1175 " pdb=" N ASN A1176 " ideal model delta sigma weight residual 1.328 1.461 -0.133 1.40e-02 5.10e+03 9.04e+01 bond pdb=" C THR C 693 " pdb=" N ARG C 694 " ideal model delta sigma weight residual 1.335 1.457 -0.122 1.31e-02 5.83e+03 8.67e+01 bond pdb=" C VAL H 104 " pdb=" N GLU H 105 " ideal model delta sigma weight residual 1.330 1.220 0.110 1.19e-02 7.06e+03 8.54e+01 ... (remaining 37202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.58: 50511 6.58 - 13.16: 99 13.16 - 19.74: 4 19.74 - 26.32: 1 26.32 - 32.90: 1 Bond angle restraints: 50616 Sorted by residual: angle pdb=" O SER B1144 " pdb=" C SER B1144 " pdb=" N ASN B1145 " ideal model delta sigma weight residual 122.03 95.72 26.31 7.30e-01 1.88e+00 1.30e+03 angle pdb=" C TYR B 641 " pdb=" CA TYR B 641 " pdb=" CB TYR B 641 " ideal model delta sigma weight residual 110.42 77.52 32.90 1.99e+00 2.53e-01 2.73e+02 angle pdb=" N ARG F 142 " pdb=" CA ARG F 142 " pdb=" C ARG F 142 " ideal model delta sigma weight residual 113.19 102.11 11.08 1.19e+00 7.06e-01 8.67e+01 angle pdb=" CA PRO A1161 " pdb=" C PRO A1161 " pdb=" N THR A1162 " ideal model delta sigma weight residual 115.37 126.83 -11.46 1.32e+00 5.74e-01 7.54e+01 angle pdb=" CA SER B1144 " pdb=" C SER B1144 " pdb=" N ASN B1145 " ideal model delta sigma weight residual 118.57 126.10 -7.53 8.80e-01 1.29e+00 7.32e+01 ... (remaining 50611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 20183 17.83 - 35.66: 1599 35.66 - 53.49: 279 53.49 - 71.32: 61 71.32 - 89.15: 31 Dihedral angle restraints: 22153 sinusoidal: 8406 harmonic: 13747 Sorted by residual: dihedral pdb=" C TYR B 641 " pdb=" N TYR B 641 " pdb=" CA TYR B 641 " pdb=" CB TYR B 641 " ideal model delta harmonic sigma weight residual -122.60 -84.88 -37.72 0 2.50e+00 1.60e-01 2.28e+02 dihedral pdb=" C PHE E 157 " pdb=" N PHE E 157 " pdb=" CA PHE E 157 " pdb=" CB PHE E 157 " ideal model delta harmonic sigma weight residual -122.60 -149.08 26.48 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" N TYR B 641 " pdb=" C TYR B 641 " pdb=" CA TYR B 641 " pdb=" CB TYR B 641 " ideal model delta harmonic sigma weight residual 122.80 97.68 25.12 0 2.50e+00 1.60e-01 1.01e+02 ... (remaining 22150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 5530 0.200 - 0.400: 154 0.400 - 0.601: 11 0.601 - 0.801: 1 0.801 - 1.001: 4 Chirality restraints: 5700 Sorted by residual: chirality pdb=" CA PHE E 157 " pdb=" N PHE E 157 " pdb=" C PHE E 157 " pdb=" CB PHE E 157 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA PHE G 157 " pdb=" N PHE G 157 " pdb=" C PHE G 157 " pdb=" CB PHE G 157 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA THR F 94 " pdb=" N THR F 94 " pdb=" C THR F 94 " pdb=" CB THR F 94 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.83 2.00e-01 2.50e+01 1.74e+01 ... (remaining 5697 not shown) Planarity restraints: 6520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B1144 " -0.089 2.00e-02 2.50e+03 1.48e-01 2.20e+02 pdb=" C SER B1144 " 0.257 2.00e-02 2.50e+03 pdb=" O SER B1144 " -0.082 2.00e-02 2.50e+03 pdb=" N ASN B1145 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 640 " -0.058 2.00e-02 2.50e+03 1.15e-01 1.32e+02 pdb=" C GLY B 640 " 0.199 2.00e-02 2.50e+03 pdb=" O GLY B 640 " -0.074 2.00e-02 2.50e+03 pdb=" N TYR B 641 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C1190 " 0.046 2.00e-02 2.50e+03 8.97e-02 8.04e+01 pdb=" C SER C1190 " -0.155 2.00e-02 2.50e+03 pdb=" O SER C1190 " 0.057 2.00e-02 2.50e+03 pdb=" N PHE C1191 " 0.053 2.00e-02 2.50e+03 ... (remaining 6517 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 2 1.81 - 2.59: 319 2.59 - 3.36: 46434 3.36 - 4.13: 91760 4.13 - 4.90: 161795 Nonbonded interactions: 300310 Sorted by model distance: nonbonded pdb=" ND2 ASN A 406 " pdb=" ND2 ASN A 582 " model vdw 1.043 3.200 nonbonded pdb=" CG ASN A 406 " pdb=" ND2 ASN A 582 " model vdw 1.781 3.350 nonbonded pdb=" CB TYR B 641 " pdb=" N TYR B 642 " model vdw 2.008 2.816 nonbonded pdb=" OG1 THR F 109 " pdb=" O ASP F 170 " model vdw 2.091 3.040 nonbonded pdb=" OG1 THR H 109 " pdb=" O ASP H 170 " model vdw 2.091 3.040 ... (remaining 300305 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 50 or resid 52 through 728 or (resid 729 and (n \ ame N or name CA or name C or name O or name CB )) or resid 730 through 739 or ( \ resid 740 and (name N or name CA or name C or name O or name CB )) or resid 741 \ through 1206)) selection = (chain 'B' and (resid 18 through 50 or resid 52 through 728 or (resid 729 and (n \ ame N or name CA or name C or name O or name CB )) or resid 730 through 739 or ( \ resid 740 and (name N or name CA or name C or name O or name CB )) or resid 741 \ through 1206)) selection = (chain 'C' and (resid 18 through 50 or resid 52 through 1206)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 35.890 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.146 37254 Z= 0.675 Angle : 1.254 32.903 50710 Z= 0.861 Chirality : 0.085 1.001 5700 Planarity : 0.007 0.148 6520 Dihedral : 13.498 89.150 13226 Min Nonbonded Distance : 1.043 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 1.43 % Allowed : 8.67 % Favored : 89.90 % Rotamer: Outliers : 2.76 % Allowed : 4.14 % Favored : 93.11 % Cbeta Deviations : 0.73 % 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: -1.38 (0.12), residues: 4674 helix: 0.81 (0.20), residues: 717 sheet: -0.18 (0.15), residues: 1264 loop : -1.86 (0.11), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1179 TYR 0.034 0.002 TYR C1192 PHE 0.047 0.002 PHE B1044 TRP 0.031 0.003 TRP B 553 HIS 0.022 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.01016 (37207) covalent geometry : angle 1.25112 (50616) SS BOND : bond 0.00910 ( 47) SS BOND : angle 2.27698 ( 94) hydrogen bonds : bond 0.16037 ( 1257) hydrogen bonds : angle 8.26947 ( 3453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 353 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8350 (m-40) cc_final: 0.8050 (p0) REVERT: A 988 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6407 (mm-40) REVERT: B 798 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7450 (t) REVERT: B 906 MET cc_start: 0.8476 (ptm) cc_final: 0.6912 (mpp) REVERT: B 1185 SER cc_start: 0.5733 (m) cc_final: 0.5056 (p) REVERT: C 27 LYS cc_start: 0.6037 (mmtm) cc_final: 0.5565 (tttt) REVERT: C 91 HIS cc_start: 0.4972 (t70) cc_final: 0.4499 (t70) REVERT: C 209 THR cc_start: 0.6846 (OUTLIER) cc_final: 0.6240 (m) REVERT: C 240 MET cc_start: 0.7624 (tmm) cc_final: 0.7111 (tmt) REVERT: C 241 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.4505 (p90) REVERT: C 243 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.4753 (p90) REVERT: E 155 ASP cc_start: 0.6452 (t0) cc_final: 0.5989 (p0) REVERT: F 4 MET cc_start: 0.7084 (mtp) cc_final: 0.6878 (mtp) REVERT: F 139 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.5606 (p90) REVERT: G 23 LYS cc_start: 0.9047 (tttm) cc_final: 0.8784 (ttpp) REVERT: G 73 ASP cc_start: 0.7542 (t0) cc_final: 0.7235 (t0) REVERT: G 166 ASN cc_start: 0.2280 (m110) cc_final: 0.1948 (m110) REVERT: H 137 ASN cc_start: 0.5461 (m-40) cc_final: 0.5212 (t0) REVERT: H 208 SER cc_start: 0.6112 (OUTLIER) cc_final: 0.5747 (t) REVERT: I 157 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.5891 (m-10) outliers start: 111 outliers final: 16 residues processed: 448 average time/residue: 0.5993 time to fit residues: 332.4153 Evaluate side-chains 241 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 139 PHE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain I residue 157 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 166 ASN A 167 HIS A 258 GLN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 486 HIS A 519 ASN A 576 GLN A 981 ASN A 993 ASN A 994 GLN A1042 ASN ** A1119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN A1177 ASN B 107 GLN B 208 HIS B 298 HIS B 304 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN B1201 ASN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 244 ASN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN C1020 GLN C1042 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN C1146 HIS ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 ASN G 166 ASN ** G 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.111199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080404 restraints weight = 173329.183| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 4.33 r_work: 0.3431 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37254 Z= 0.164 Angle : 0.750 16.519 50710 Z= 0.395 Chirality : 0.048 0.310 5700 Planarity : 0.005 0.087 6520 Dihedral : 6.530 69.832 5146 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.11 % Favored : 91.44 % Rotamer: Outliers : 2.24 % Allowed : 9.73 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -1.22 (0.12), residues: 4674 helix: 0.99 (0.20), residues: 735 sheet: -0.11 (0.15), residues: 1269 loop : -1.76 (0.11), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 181 TYR 0.031 0.002 TYR B 641 PHE 0.023 0.002 PHE B1044 TRP 0.021 0.002 TRP B1184 HIS 0.008 0.002 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00347 (37207) covalent geometry : angle 0.74940 (50616) SS BOND : bond 0.00295 ( 47) SS BOND : angle 1.04034 ( 94) hydrogen bonds : bond 0.05416 ( 1257) hydrogen bonds : angle 6.49721 ( 3453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 240 time to evaluate : 1.305 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8382 (m-40) cc_final: 0.8046 (p0) REVERT: A 992 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: A 1157 ASP cc_start: 0.2392 (OUTLIER) cc_final: 0.2170 (t0) REVERT: B 563 MET cc_start: 0.5532 (mtp) cc_final: 0.5213 (mtt) REVERT: B 576 GLN cc_start: 0.8109 (mt0) cc_final: 0.7544 (mp10) REVERT: B 642 TYR cc_start: 0.4141 (OUTLIER) cc_final: 0.3367 (p90) REVERT: B 764 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.4787 (p90) REVERT: B 786 PHE cc_start: 0.7611 (m-80) cc_final: 0.7403 (m-10) REVERT: B 906 MET cc_start: 0.8637 (ptm) cc_final: 0.6662 (mpp) REVERT: B 1039 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7618 (mm-30) REVERT: B 1179 ARG cc_start: 0.5375 (ttp80) cc_final: 0.5119 (ttp80) REVERT: B 1183 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: C 27 LYS cc_start: 0.6039 (mmtm) cc_final: 0.5522 (pttt) REVERT: C 193 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8258 (t0) REVERT: C 241 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.5234 (p90) REVERT: C 243 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.4827 (p90) REVERT: D 28 ASP cc_start: 0.8502 (t0) cc_final: 0.8277 (t0) REVERT: D 138 ASN cc_start: 0.6522 (m110) cc_final: 0.6124 (t0) REVERT: E 10 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7041 (mm-30) REVERT: F 24 ARG cc_start: 0.7904 (mmm160) cc_final: 0.7617 (mmp80) REVERT: F 137 ASN cc_start: 0.7272 (m-40) cc_final: 0.7007 (t0) REVERT: F 173 TYR cc_start: 0.6937 (m-80) cc_final: 0.6215 (m-80) REVERT: G 10 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7667 (mm-30) REVERT: G 23 LYS cc_start: 0.9059 (tttm) cc_final: 0.8803 (ttpp) REVERT: G 73 ASP cc_start: 0.8159 (t0) cc_final: 0.7773 (t0) REVERT: G 81 MET cc_start: 0.7902 (tmt) cc_final: 0.7607 (tmt) REVERT: H 137 ASN cc_start: 0.5445 (m-40) cc_final: 0.5187 (t0) REVERT: I 157 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6333 (m-10) outliers start: 90 outliers final: 38 residues processed: 306 average time/residue: 0.6227 time to fit residues: 234.2370 Evaluate side-chains 254 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1157 ASP Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1039 GLU Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 244 ASN Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain I residue 157 PHE Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 366 optimal weight: 9.9990 chunk 125 optimal weight: 0.0370 chunk 220 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 360 optimal weight: 30.0000 chunk 111 optimal weight: 0.6980 chunk 452 optimal weight: 9.9990 chunk 432 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN A 994 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B1110 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.110285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.079329 restraints weight = 174423.721| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.27 r_work: 0.3419 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37254 Z= 0.142 Angle : 0.684 11.782 50710 Z= 0.358 Chirality : 0.046 0.307 5700 Planarity : 0.005 0.067 6520 Dihedral : 5.913 66.589 5128 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.46 % Favored : 91.14 % Rotamer: Outliers : 2.19 % Allowed : 11.15 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.12 (0.12), residues: 4674 helix: 1.26 (0.20), residues: 723 sheet: -0.09 (0.15), residues: 1264 loop : -1.72 (0.12), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1057 TYR 0.024 0.002 TYR C 207 PHE 0.019 0.001 PHE C 164 TRP 0.036 0.002 TRP B 553 HIS 0.023 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00310 (37207) covalent geometry : angle 0.68286 (50616) SS BOND : bond 0.00713 ( 47) SS BOND : angle 1.00804 ( 94) hydrogen bonds : bond 0.04903 ( 1257) hydrogen bonds : angle 6.00847 ( 3453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 232 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8367 (m-40) cc_final: 0.8014 (p0) REVERT: A 563 MET cc_start: 0.6619 (ttm) cc_final: 0.6361 (ttt) REVERT: A 994 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: B 433 ILE cc_start: 0.8375 (tp) cc_final: 0.7950 (pp) REVERT: B 442 ILE cc_start: 0.8337 (mt) cc_final: 0.7981 (mm) REVERT: B 563 MET cc_start: 0.5272 (mtp) cc_final: 0.4984 (mtt) REVERT: B 576 GLN cc_start: 0.8072 (mt0) cc_final: 0.7862 (mp10) REVERT: B 642 TYR cc_start: 0.4100 (OUTLIER) cc_final: 0.3403 (p90) REVERT: B 764 PHE cc_start: 0.6360 (OUTLIER) cc_final: 0.4919 (p90) REVERT: B 786 PHE cc_start: 0.7706 (m-80) cc_final: 0.7338 (m-10) REVERT: B 1183 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: C 27 LYS cc_start: 0.6253 (mmtm) cc_final: 0.5713 (ttpt) REVERT: C 178 THR cc_start: 0.6040 (OUTLIER) cc_final: 0.5739 (m) REVERT: C 220 ASN cc_start: 0.4154 (p0) cc_final: 0.3519 (p0) REVERT: C 241 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.5527 (p90) REVERT: C 243 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.6105 (p90) REVERT: C 563 MET cc_start: 0.4168 (mmm) cc_final: 0.3504 (tpt) REVERT: C 765 ASN cc_start: 0.8342 (t0) cc_final: 0.8137 (t0) REVERT: C 985 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6717 (mm) REVERT: D 4 MET cc_start: 0.5592 (mtm) cc_final: 0.5005 (mtm) REVERT: D 138 ASN cc_start: 0.6591 (m110) cc_final: 0.6149 (t0) REVERT: E 10 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7192 (mm-30) REVERT: E 154 LYS cc_start: 0.5850 (tptt) cc_final: 0.5422 (tptt) REVERT: E 155 ASP cc_start: 0.7069 (t0) cc_final: 0.6425 (t70) REVERT: E 157 PHE cc_start: 0.6602 (m-80) cc_final: 0.5868 (m-80) REVERT: F 137 ASN cc_start: 0.7117 (m-40) cc_final: 0.6911 (t0) REVERT: F 173 TYR cc_start: 0.6903 (m-80) cc_final: 0.6181 (m-80) REVERT: G 10 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7697 (mm-30) REVERT: G 73 ASP cc_start: 0.8296 (t0) cc_final: 0.7931 (t0) REVERT: H 24 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6483 (tpp-160) REVERT: H 137 ASN cc_start: 0.5378 (m-40) cc_final: 0.5165 (t0) REVERT: I 73 ASP cc_start: 0.7995 (t0) cc_final: 0.7558 (t0) outliers start: 88 outliers final: 30 residues processed: 296 average time/residue: 0.6143 time to fit residues: 225.7124 Evaluate side-chains 244 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 994 GLN Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 244 ASN Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain I residue 104 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 233 optimal weight: 3.9990 chunk 455 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 444 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 453 optimal weight: 0.6980 chunk 457 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN A1023 GLN A1138 HIS B 280 GLN B 304 GLN B 410 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN C 733 GLN ** C 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN H 6 GLN I 175 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.107260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.077659 restraints weight = 163746.447| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.89 r_work: 0.3347 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37254 Z= 0.194 Angle : 0.715 12.078 50710 Z= 0.375 Chirality : 0.047 0.276 5700 Planarity : 0.005 0.081 6520 Dihedral : 6.033 61.961 5121 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.78 % Favored : 90.84 % Rotamer: Outliers : 2.59 % Allowed : 11.92 % Favored : 85.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.16 (0.12), residues: 4674 helix: 1.13 (0.20), residues: 735 sheet: -0.15 (0.15), residues: 1277 loop : -1.71 (0.12), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1179 TYR 0.030 0.002 TYR B 77 PHE 0.066 0.002 PHE C 101 TRP 0.022 0.002 TRP B 553 HIS 0.011 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00440 (37207) covalent geometry : angle 0.71472 (50616) SS BOND : bond 0.00351 ( 47) SS BOND : angle 1.03825 ( 94) hydrogen bonds : bond 0.05176 ( 1257) hydrogen bonds : angle 5.84988 ( 3453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 221 time to evaluate : 1.341 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 193 ASN cc_start: 0.8386 (m-40) cc_final: 0.7981 (p0) REVERT: A 295 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8816 (mp) REVERT: A 626 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.6879 (mmp-170) REVERT: A 729 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7184 (mm) REVERT: B 433 ILE cc_start: 0.8441 (tp) cc_final: 0.8035 (pp) REVERT: B 553 TRP cc_start: 0.5585 (t-100) cc_final: 0.4919 (m100) REVERT: B 563 MET cc_start: 0.5351 (mtp) cc_final: 0.5049 (mtt) REVERT: B 642 TYR cc_start: 0.4631 (OUTLIER) cc_final: 0.3775 (p90) REVERT: B 645 ASP cc_start: 0.6756 (m-30) cc_final: 0.6485 (m-30) REVERT: B 764 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.5185 (p90) REVERT: B 786 PHE cc_start: 0.7597 (m-80) cc_final: 0.7332 (m-10) REVERT: B 1177 ASN cc_start: 0.8541 (m-40) cc_final: 0.8224 (t0) REVERT: B 1183 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: C 78 GLN cc_start: 0.9546 (OUTLIER) cc_final: 0.8158 (tp40) REVERT: C 91 HIS cc_start: 0.5078 (t-90) cc_final: 0.4737 (t70) REVERT: C 241 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.5494 (p90) REVERT: C 243 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.6142 (p90) REVERT: C 985 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.6805 (mm) REVERT: C 1012 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: D 138 ASN cc_start: 0.6573 (m110) cc_final: 0.6112 (t0) REVERT: E 10 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7075 (mm-30) REVERT: E 155 ASP cc_start: 0.6979 (t0) cc_final: 0.6663 (t70) REVERT: E 157 PHE cc_start: 0.6453 (m-80) cc_final: 0.5629 (m-80) REVERT: F 137 ASN cc_start: 0.7129 (m-40) cc_final: 0.6882 (t0) REVERT: G 73 ASP cc_start: 0.8296 (t0) cc_final: 0.7928 (t0) REVERT: H 137 ASN cc_start: 0.5441 (m-40) cc_final: 0.5131 (t0) REVERT: I 73 ASP cc_start: 0.7913 (t0) cc_final: 0.7389 (t0) outliers start: 104 outliers final: 49 residues processed: 303 average time/residue: 0.5916 time to fit residues: 222.9827 Evaluate side-chains 249 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1116 PHE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 213 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 246 optimal weight: 0.0170 chunk 93 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 214 optimal weight: 0.9980 chunk 342 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 412 optimal weight: 5.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN B 304 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN C 796 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN I 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.108289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.078354 restraints weight = 206978.715| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 5.06 r_work: 0.3310 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37254 Z= 0.136 Angle : 0.665 12.898 50710 Z= 0.345 Chirality : 0.045 0.256 5700 Planarity : 0.005 0.073 6520 Dihedral : 5.713 61.574 5120 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.71 % Favored : 90.92 % Rotamer: Outliers : 2.39 % Allowed : 13.17 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.12 (0.12), residues: 4674 helix: 1.22 (0.20), residues: 738 sheet: -0.18 (0.15), residues: 1277 loop : -1.67 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 24 TYR 0.028 0.001 TYR A 642 PHE 0.028 0.001 PHE G 133 TRP 0.021 0.001 TRP A 553 HIS 0.007 0.001 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00297 (37207) covalent geometry : angle 0.66495 (50616) SS BOND : bond 0.00275 ( 47) SS BOND : angle 0.89731 ( 94) hydrogen bonds : bond 0.04634 ( 1257) hydrogen bonds : angle 5.67775 ( 3453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 200 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8378 (m-40) cc_final: 0.7993 (p0) REVERT: A 626 ARG cc_start: 0.7137 (tpp-160) cc_final: 0.6852 (mmp-170) REVERT: A 757 MET cc_start: 0.6278 (mtt) cc_final: 0.5966 (mmt) REVERT: A 994 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8209 (tm-30) REVERT: A 1169 ASN cc_start: 0.5374 (p0) cc_final: 0.5042 (p0) REVERT: B 433 ILE cc_start: 0.8354 (tp) cc_final: 0.7947 (pp) REVERT: B 553 TRP cc_start: 0.5604 (t-100) cc_final: 0.4922 (m100) REVERT: B 563 MET cc_start: 0.5202 (mtp) cc_final: 0.4966 (mtt) REVERT: B 576 GLN cc_start: 0.8588 (mt0) cc_final: 0.8289 (mp10) REVERT: B 642 TYR cc_start: 0.4468 (OUTLIER) cc_final: 0.3673 (p90) REVERT: B 645 ASP cc_start: 0.6666 (m-30) cc_final: 0.6436 (m-30) REVERT: B 664 ASP cc_start: 0.7107 (t0) cc_final: 0.6886 (t0) REVERT: B 764 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.5253 (p90) REVERT: B 1179 ARG cc_start: 0.6837 (tpp-160) cc_final: 0.6577 (tpp-160) REVERT: C 240 MET cc_start: 0.8386 (tmm) cc_final: 0.7200 (tmm) REVERT: C 241 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.5476 (p90) REVERT: C 243 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.6150 (p90) REVERT: D 138 ASN cc_start: 0.6784 (m110) cc_final: 0.6411 (t0) REVERT: E 10 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7271 (mm-30) REVERT: E 157 PHE cc_start: 0.5924 (m-80) cc_final: 0.5686 (m-80) REVERT: E 187 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7377 (t80) REVERT: G 73 ASP cc_start: 0.8359 (t0) cc_final: 0.8016 (t0) REVERT: H 1 ASP cc_start: 0.7406 (t0) cc_final: 0.6873 (m-30) REVERT: H 18 ARG cc_start: 0.8053 (pmt-80) cc_final: 0.7840 (ttp80) REVERT: H 70 ASP cc_start: 0.8069 (m-30) cc_final: 0.7820 (p0) REVERT: H 125 LEU cc_start: 0.3982 (OUTLIER) cc_final: 0.3782 (tp) REVERT: H 137 ASN cc_start: 0.5637 (m-40) cc_final: 0.5415 (t0) REVERT: I 73 ASP cc_start: 0.7910 (t0) cc_final: 0.7408 (t0) REVERT: I 101 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8311 (p) outliers start: 96 outliers final: 42 residues processed: 279 average time/residue: 0.6481 time to fit residues: 223.4622 Evaluate side-chains 240 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 6 optimal weight: 0.8980 chunk 391 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 280 optimal weight: 30.0000 chunk 422 optimal weight: 9.9990 chunk 338 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 371 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN A1177 ASN B 167 HIS B 304 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN I 99 GLN I 175 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.105306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.074637 restraints weight = 195949.816| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 4.62 r_work: 0.3249 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 37254 Z= 0.209 Angle : 0.730 14.403 50710 Z= 0.380 Chirality : 0.048 0.297 5700 Planarity : 0.005 0.075 6520 Dihedral : 6.047 60.646 5120 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.21 % Favored : 90.47 % Rotamer: Outliers : 2.41 % Allowed : 13.89 % Favored : 83.70 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.20 (0.12), residues: 4674 helix: 1.06 (0.20), residues: 742 sheet: -0.30 (0.14), residues: 1351 loop : -1.69 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1057 TYR 0.055 0.002 TYR I 105 PHE 0.039 0.002 PHE C1172 TRP 0.026 0.002 TRP A1184 HIS 0.008 0.001 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00477 (37207) covalent geometry : angle 0.72915 (50616) SS BOND : bond 0.00348 ( 47) SS BOND : angle 1.05620 ( 94) hydrogen bonds : bond 0.05259 ( 1257) hydrogen bonds : angle 5.70112 ( 3453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 204 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8511 (m-40) cc_final: 0.8148 (p0) REVERT: A 295 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8820 (mp) REVERT: A 734 SER cc_start: 0.6874 (m) cc_final: 0.6460 (t) REVERT: B 398 ASN cc_start: 0.8140 (m-40) cc_final: 0.7932 (t0) REVERT: B 553 TRP cc_start: 0.5507 (t-100) cc_final: 0.4774 (m100) REVERT: B 563 MET cc_start: 0.5245 (mtp) cc_final: 0.5006 (mtt) REVERT: B 642 TYR cc_start: 0.4653 (OUTLIER) cc_final: 0.3763 (p90) REVERT: B 645 ASP cc_start: 0.6865 (m-30) cc_final: 0.6470 (m-30) REVERT: B 764 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.4995 (p90) REVERT: B 1047 ILE cc_start: 0.3952 (OUTLIER) cc_final: 0.3502 (tp) REVERT: B 1177 ASN cc_start: 0.8798 (m-40) cc_final: 0.8585 (t0) REVERT: C 78 GLN cc_start: 0.9568 (OUTLIER) cc_final: 0.8229 (tp40) REVERT: C 161 MET cc_start: 0.8371 (mmm) cc_final: 0.8069 (mmm) REVERT: C 241 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.5642 (p90) REVERT: C 243 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.6051 (p90) REVERT: C 563 MET cc_start: 0.4307 (tpt) cc_final: 0.3955 (tpp) REVERT: C 1113 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8470 (tpt90) REVERT: D 138 ASN cc_start: 0.6809 (m110) cc_final: 0.6434 (t0) REVERT: E 10 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7307 (mm-30) REVERT: E 187 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7475 (t80) REVERT: F 24 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7412 (mmm160) REVERT: F 105 GLU cc_start: 0.5717 (tp30) cc_final: 0.5110 (mm-30) REVERT: G 73 ASP cc_start: 0.8510 (t0) cc_final: 0.8224 (t0) REVERT: G 81 MET cc_start: 0.8157 (tmm) cc_final: 0.7829 (tmm) REVERT: H 1 ASP cc_start: 0.7413 (t0) cc_final: 0.6900 (m-30) REVERT: H 70 ASP cc_start: 0.8072 (m-30) cc_final: 0.7857 (p0) REVERT: H 125 LEU cc_start: 0.3974 (OUTLIER) cc_final: 0.3721 (tp) REVERT: H 137 ASN cc_start: 0.5588 (m-40) cc_final: 0.5199 (t0) REVERT: I 73 ASP cc_start: 0.7982 (t0) cc_final: 0.7350 (t0) REVERT: I 101 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.7793 (p) REVERT: I 104 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8164 (p0) REVERT: I 105 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8325 (m-80) outliers start: 97 outliers final: 50 residues processed: 288 average time/residue: 0.6076 time to fit residues: 216.1520 Evaluate side-chains 253 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 190 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1113 ARG Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 121 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 315 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 433 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN B 167 HIS B 304 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN C 987 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN I 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.106846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.076621 restraints weight = 205270.295| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 4.89 r_work: 0.3266 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37254 Z= 0.137 Angle : 0.674 14.416 50710 Z= 0.348 Chirality : 0.046 0.315 5700 Planarity : 0.005 0.082 6520 Dihedral : 5.772 60.992 5120 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.71 % Favored : 91.01 % Rotamer: Outliers : 2.07 % Allowed : 14.73 % Favored : 83.21 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.07 (0.12), residues: 4674 helix: 1.26 (0.20), residues: 738 sheet: -0.20 (0.14), residues: 1318 loop : -1.63 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 221 TYR 0.025 0.001 TYR A 642 PHE 0.029 0.002 PHE C1172 TRP 0.023 0.001 TRP A1184 HIS 0.009 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00305 (37207) covalent geometry : angle 0.67368 (50616) SS BOND : bond 0.00272 ( 47) SS BOND : angle 0.88931 ( 94) hydrogen bonds : bond 0.04620 ( 1257) hydrogen bonds : angle 5.53001 ( 3453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 196 time to evaluate : 1.376 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: A 193 ASN cc_start: 0.8483 (m-40) cc_final: 0.8081 (p0) REVERT: A 295 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8846 (mp) REVERT: A 734 SER cc_start: 0.7036 (m) cc_final: 0.6581 (t) REVERT: A 1117 CYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8311 (m) REVERT: A 1169 ASN cc_start: 0.5229 (p0) cc_final: 0.5014 (p0) REVERT: B 553 TRP cc_start: 0.5458 (t-100) cc_final: 0.4640 (m100) REVERT: B 645 ASP cc_start: 0.6717 (m-30) cc_final: 0.6459 (m-30) REVERT: B 764 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.4895 (p90) REVERT: C 78 GLN cc_start: 0.9560 (OUTLIER) cc_final: 0.8192 (tp40) REVERT: C 161 MET cc_start: 0.8313 (mmm) cc_final: 0.7982 (mmm) REVERT: C 241 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.5704 (p90) REVERT: C 243 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.6432 (p90) REVERT: C 563 MET cc_start: 0.4467 (tpt) cc_final: 0.4180 (tpp) REVERT: D 4 MET cc_start: 0.5480 (mtm) cc_final: 0.4951 (mtm) REVERT: D 24 ARG cc_start: 0.7693 (mmp-170) cc_final: 0.7373 (mmp-170) REVERT: D 138 ASN cc_start: 0.6942 (m110) cc_final: 0.6589 (t0) REVERT: E 10 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7376 (mm-30) REVERT: E 154 LYS cc_start: 0.5850 (tppt) cc_final: 0.5364 (tmtt) REVERT: F 105 GLU cc_start: 0.5684 (tp30) cc_final: 0.5086 (mm-30) REVERT: G 73 ASP cc_start: 0.8552 (t0) cc_final: 0.8234 (t0) REVERT: G 81 MET cc_start: 0.8191 (tmm) cc_final: 0.7842 (tmm) REVERT: G 159 GLU cc_start: 0.6868 (tp30) cc_final: 0.5979 (tp30) REVERT: H 1 ASP cc_start: 0.7250 (t0) cc_final: 0.6726 (m-30) REVERT: H 125 LEU cc_start: 0.4002 (OUTLIER) cc_final: 0.3794 (tp) REVERT: H 137 ASN cc_start: 0.5671 (m-40) cc_final: 0.5338 (t0) REVERT: I 73 ASP cc_start: 0.7967 (t0) cc_final: 0.7325 (t0) outliers start: 83 outliers final: 46 residues processed: 264 average time/residue: 0.6056 time to fit residues: 197.3267 Evaluate side-chains 240 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 311 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 444 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 318 optimal weight: 1.9990 chunk 407 optimal weight: 20.0000 chunk 312 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN A 907 GLN B 167 HIS B 304 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 37 GLN I 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.105456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.074420 restraints weight = 189916.838| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 4.79 r_work: 0.3204 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37254 Z= 0.196 Angle : 0.721 14.324 50710 Z= 0.375 Chirality : 0.048 0.317 5700 Planarity : 0.005 0.085 6520 Dihedral : 6.010 59.587 5118 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.16 % Favored : 90.56 % Rotamer: Outliers : 2.07 % Allowed : 15.07 % Favored : 82.86 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.15 (0.12), residues: 4674 helix: 1.14 (0.20), residues: 741 sheet: -0.23 (0.14), residues: 1327 loop : -1.68 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 626 TYR 0.073 0.002 TYR I 105 PHE 0.035 0.002 PHE C1172 TRP 0.024 0.002 TRP A1184 HIS 0.008 0.001 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00449 (37207) covalent geometry : angle 0.72033 (50616) SS BOND : bond 0.00330 ( 47) SS BOND : angle 1.05039 ( 94) hydrogen bonds : bond 0.05078 ( 1257) hydrogen bonds : angle 5.57334 ( 3453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 193 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8476 (m-40) cc_final: 0.8081 (p0) REVERT: A 295 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8835 (mp) REVERT: A 734 SER cc_start: 0.7650 (m) cc_final: 0.7266 (p) REVERT: A 757 MET cc_start: 0.7022 (mmt) cc_final: 0.6811 (mmm) REVERT: A 1117 CYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8510 (m) REVERT: B 553 TRP cc_start: 0.5278 (t-100) cc_final: 0.4570 (m100) REVERT: B 645 ASP cc_start: 0.7149 (m-30) cc_final: 0.6737 (m-30) REVERT: B 764 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.4907 (p90) REVERT: B 1047 ILE cc_start: 0.4081 (OUTLIER) cc_final: 0.3548 (tp) REVERT: C 78 GLN cc_start: 0.9576 (OUTLIER) cc_final: 0.8259 (tp40) REVERT: C 161 MET cc_start: 0.8326 (mmm) cc_final: 0.8073 (mmm) REVERT: C 241 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.5818 (p90) REVERT: C 243 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.6107 (p90) REVERT: C 563 MET cc_start: 0.4622 (tpt) cc_final: 0.4344 (tpp) REVERT: C 928 TYR cc_start: 0.4874 (m-80) cc_final: 0.4552 (m-80) REVERT: C 1012 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: D 4 MET cc_start: 0.5585 (mtm) cc_final: 0.4964 (mtm) REVERT: D 24 ARG cc_start: 0.7768 (mmp-170) cc_final: 0.7348 (mmp-170) REVERT: E 10 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7463 (mm-30) REVERT: F 105 GLU cc_start: 0.5738 (tp30) cc_final: 0.5187 (mm-30) REVERT: G 73 ASP cc_start: 0.8484 (t0) cc_final: 0.8196 (t0) REVERT: G 81 MET cc_start: 0.8254 (tmm) cc_final: 0.7846 (tmm) REVERT: G 159 GLU cc_start: 0.6974 (tp30) cc_final: 0.6142 (tp30) REVERT: H 1 ASP cc_start: 0.7309 (t0) cc_final: 0.6832 (m-30) REVERT: H 137 ASN cc_start: 0.5795 (m-40) cc_final: 0.5483 (t0) REVERT: I 73 ASP cc_start: 0.7924 (t0) cc_final: 0.7271 (t0) REVERT: I 101 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8227 (p) REVERT: I 105 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: I 155 ASP cc_start: 0.7555 (t0) cc_final: 0.6934 (p0) outliers start: 83 outliers final: 50 residues processed: 263 average time/residue: 0.6422 time to fit residues: 206.9860 Evaluate side-chains 244 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 339 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 457 optimal weight: 9.9990 chunk 162 optimal weight: 50.0000 chunk 415 optimal weight: 0.9990 chunk 462 optimal weight: 9.9990 chunk 195 optimal weight: 0.5980 chunk 159 optimal weight: 6.9990 chunk 367 optimal weight: 10.0000 chunk 311 optimal weight: 0.7980 chunk 414 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN B1129 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 37 GLN I 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.106318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.073543 restraints weight = 163955.067| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.37 r_work: 0.3329 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37254 Z= 0.135 Angle : 0.688 14.373 50710 Z= 0.354 Chirality : 0.046 0.311 5700 Planarity : 0.005 0.085 6520 Dihedral : 5.790 60.354 5118 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.78 % Favored : 91.01 % Rotamer: Outliers : 1.97 % Allowed : 15.39 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.06 (0.12), residues: 4674 helix: 1.28 (0.20), residues: 742 sheet: -0.13 (0.14), residues: 1324 loop : -1.67 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1057 TYR 0.026 0.001 TYR B 641 PHE 0.028 0.001 PHE C1172 TRP 0.026 0.001 TRP A 553 HIS 0.006 0.001 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00301 (37207) covalent geometry : angle 0.68611 (50616) SS BOND : bond 0.00378 ( 47) SS BOND : angle 1.34694 ( 94) hydrogen bonds : bond 0.04512 ( 1257) hydrogen bonds : angle 5.44228 ( 3453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 196 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8492 (m-40) cc_final: 0.8003 (p0) REVERT: A 295 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 734 SER cc_start: 0.7213 (m) cc_final: 0.6890 (p) REVERT: A 1117 CYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8124 (m) REVERT: B 433 ILE cc_start: 0.8393 (tp) cc_final: 0.7957 (pp) REVERT: B 553 TRP cc_start: 0.5205 (t-100) cc_final: 0.4364 (m100) REVERT: B 645 ASP cc_start: 0.6891 (m-30) cc_final: 0.6524 (m-30) REVERT: B 764 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.5053 (p90) REVERT: B 1047 ILE cc_start: 0.3888 (OUTLIER) cc_final: 0.3389 (tp) REVERT: C 78 GLN cc_start: 0.9493 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: C 161 MET cc_start: 0.8219 (mmm) cc_final: 0.7967 (mmm) REVERT: C 240 MET cc_start: 0.8461 (tpp) cc_final: 0.7442 (tmm) REVERT: C 241 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.5755 (p90) REVERT: C 243 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.6182 (p90) REVERT: C 563 MET cc_start: 0.4168 (tpt) cc_final: 0.3801 (tpp) REVERT: C 928 TYR cc_start: 0.4895 (m-80) cc_final: 0.4636 (m-80) REVERT: D 4 MET cc_start: 0.5651 (mtm) cc_final: 0.5000 (mtm) REVERT: E 10 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7490 (mm-30) REVERT: E 154 LYS cc_start: 0.5292 (tppt) cc_final: 0.4603 (tmtt) REVERT: E 155 ASP cc_start: 0.7189 (t0) cc_final: 0.6719 (t70) REVERT: F 105 GLU cc_start: 0.6228 (tp30) cc_final: 0.5814 (mm-30) REVERT: G 73 ASP cc_start: 0.8528 (t0) cc_final: 0.8207 (t0) REVERT: G 81 MET cc_start: 0.8160 (tmm) cc_final: 0.7695 (tmm) REVERT: H 1 ASP cc_start: 0.7193 (t0) cc_final: 0.6748 (m-30) REVERT: H 125 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4805 (tp) REVERT: H 137 ASN cc_start: 0.5683 (m-40) cc_final: 0.5327 (t0) REVERT: I 73 ASP cc_start: 0.7810 (t0) cc_final: 0.7112 (t0) REVERT: I 155 ASP cc_start: 0.7483 (t0) cc_final: 0.6840 (p0) outliers start: 79 outliers final: 49 residues processed: 263 average time/residue: 0.6435 time to fit residues: 207.4939 Evaluate side-chains 244 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1129 ASN Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 328 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 445 optimal weight: 7.9990 chunk 375 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 402 optimal weight: 30.0000 chunk 461 optimal weight: 30.0000 chunk 202 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 chunk 427 optimal weight: 0.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN A 544 GLN A1063 GLN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1063 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN H 6 GLN H 37 GLN I 3 GLN I 175 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.103250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.070900 restraints weight = 177649.198| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.29 r_work: 0.3156 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 37254 Z= 0.313 Angle : 0.845 13.887 50710 Z= 0.443 Chirality : 0.052 0.387 5700 Planarity : 0.006 0.092 6520 Dihedral : 6.536 57.505 5118 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.70 % Favored : 89.96 % Rotamer: Outliers : 1.92 % Allowed : 15.61 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.36 % 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: -1.32 (0.12), residues: 4674 helix: 0.91 (0.20), residues: 736 sheet: -0.29 (0.14), residues: 1342 loop : -1.80 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 18 TYR 0.044 0.002 TYR A 642 PHE 0.035 0.003 PHE A 764 TRP 0.032 0.002 TRP A 553 HIS 0.009 0.002 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00727 (37207) covalent geometry : angle 0.84277 (50616) SS BOND : bond 0.00507 ( 47) SS BOND : angle 1.56350 ( 94) hydrogen bonds : bond 0.05855 ( 1257) hydrogen bonds : angle 5.76367 ( 3453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 196 time to evaluate : 0.939 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 193 ASN cc_start: 0.8408 (m-40) cc_final: 0.7997 (p0) REVERT: A 295 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8824 (mp) REVERT: B 645 ASP cc_start: 0.7040 (m-30) cc_final: 0.6512 (m-30) REVERT: B 764 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.6066 (p90) REVERT: B 782 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8927 (tt) REVERT: B 1047 ILE cc_start: 0.3908 (OUTLIER) cc_final: 0.3370 (tp) REVERT: C 78 GLN cc_start: 0.9615 (OUTLIER) cc_final: 0.8239 (tp40) REVERT: C 563 MET cc_start: 0.4656 (tpt) cc_final: 0.4326 (tpp) REVERT: C 928 TYR cc_start: 0.5211 (m-80) cc_final: 0.4888 (m-80) REVERT: C 1053 ASP cc_start: 0.7815 (m-30) cc_final: 0.7589 (m-30) REVERT: C 1113 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8362 (tpt90) REVERT: D 4 MET cc_start: 0.5614 (mtm) cc_final: 0.5041 (mtm) REVERT: D 116 PHE cc_start: 0.2900 (m-10) cc_final: 0.2698 (m-10) REVERT: D 148 TRP cc_start: 0.1524 (m100) cc_final: 0.1174 (m100) REVERT: E 10 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7422 (mm-30) REVERT: E 154 LYS cc_start: 0.5354 (tppt) cc_final: 0.4683 (tmtt) REVERT: E 155 ASP cc_start: 0.7287 (t0) cc_final: 0.6899 (t70) REVERT: F 24 ARG cc_start: 0.8212 (mmm160) cc_final: 0.7927 (mmm160) REVERT: F 105 GLU cc_start: 0.6015 (tp30) cc_final: 0.5555 (mm-30) REVERT: G 73 ASP cc_start: 0.8558 (t0) cc_final: 0.8286 (t0) REVERT: G 81 MET cc_start: 0.8172 (tmm) cc_final: 0.7935 (tmm) REVERT: G 187 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7249 (t80) REVERT: H 1 ASP cc_start: 0.7230 (t0) cc_final: 0.6816 (m-30) REVERT: H 125 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.5098 (tp) REVERT: H 137 ASN cc_start: 0.5726 (m-40) cc_final: 0.5339 (t0) REVERT: I 73 ASP cc_start: 0.7949 (t0) cc_final: 0.7275 (t0) REVERT: I 101 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8649 (p) REVERT: I 155 ASP cc_start: 0.7483 (t0) cc_final: 0.6879 (p0) outliers start: 77 outliers final: 54 residues processed: 260 average time/residue: 0.5868 time to fit residues: 189.0626 Evaluate side-chains 247 residues out of total 4061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1141 TYR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1113 ARG Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain C residue 1197 ILE Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 187 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 153 optimal weight: 7.9990 chunk 434 optimal weight: 30.0000 chunk 38 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 355 optimal weight: 10.0000 chunk 410 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 48 optimal weight: 30.0000 chunk 203 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN A 544 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 ASN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 37 GLN I 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.104584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.073569 restraints weight = 137353.765| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.50 r_work: 0.3283 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37254 Z= 0.175 Angle : 0.728 13.568 50710 Z= 0.378 Chirality : 0.047 0.276 5700 Planarity : 0.005 0.090 6520 Dihedral : 6.177 58.002 5118 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.23 % Favored : 90.52 % Rotamer: Outliers : 1.67 % Allowed : 16.23 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 4674 helix: 1.15 (0.20), residues: 731 sheet: -0.33 (0.14), residues: 1362 loop : -1.73 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 18 TYR 0.029 0.002 TYR B 641 PHE 0.030 0.002 PHE C1172 TRP 0.031 0.002 TRP A 553 HIS 0.008 0.001 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00394 (37207) covalent geometry : angle 0.72644 (50616) SS BOND : bond 0.00410 ( 47) SS BOND : angle 1.32324 ( 94) hydrogen bonds : bond 0.04961 ( 1257) hydrogen bonds : angle 5.57574 ( 3453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18626.52 seconds wall clock time: 316 minutes 32.42 seconds (18992.42 seconds total)