Starting phenix.real_space_refine on Tue Sep 15 10:22:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6raz_4788/09_2026/6raz_4788.cif Found real_map, /net/cci-nas-00/data/ceres_data/6raz_4788/09_2026/6raz_4788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6raz_4788/09_2026/6raz_4788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6raz_4788/09_2026/6raz_4788.map" model { file = "/net/cci-nas-00/data/ceres_data/6raz_4788/09_2026/6raz_4788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6raz_4788/09_2026/6raz_4788.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6raz_4788/09_2026/6raz_4788.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6raz_4788/09_2026/6raz_4788.cif" } resolution = 4.46 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= 0.001 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: 5 Type Number sf(0) Gaussians P 39 5.49 5 S 209 5.16 5 C 24015 2.51 5 N 6711 2.21 5 O 7320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 235 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38294 Number of models: 1 Model: "" Number of chains: 18 Chain: "X" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Classifications: {'DNA': 2} Link IDs: {'rna3p': 1} Chain: "A" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4190 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 13, 'TRANS': 505} Chain breaks: 1 Chain: "H" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1583 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 14, 'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1259 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1661 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ILE%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4442 Classifications: {'peptide': 559} Link IDs: {'PTRANS': 23, 'TRANS': 535} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "5" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4459 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 26, 'TRANS': 544} Chain breaks: 10 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "6" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4609 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 569} Chain breaks: 4 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "3" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4585 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 567} Chain breaks: 9 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "4" Number of atoms: 4811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4811 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 25, 'TRANS': 580} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "7" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4594 Classifications: {'peptide': 601} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 38} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.13, per 1000 atoms: 0.21 Number of scatterers: 38294 At special positions: 0 Unit cell: (187.92, 183.6, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 209 16.00 P 39 15.00 O 7320 8.00 N 6711 7.00 C 24015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 192 " - pdb=" SG CYS 5 202 " distance=2.04 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 Atom "HETATM38259 O4' ATP 4 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9072 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 32 sheets defined 36.1% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 Processing helix chain 'A' and resid 26 through 43 removed outlier: 4.446A pdb=" N ILE A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A 35 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 63 removed outlier: 4.463A pdb=" N LYS A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.602A pdb=" N LEU A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.961A pdb=" N ALA A 129 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 130' Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.790A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 5.080A pdb=" N GLU A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.632A pdb=" N SER A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 removed outlier: 4.107A pdb=" N GLN A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.841A pdb=" N GLU A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.832A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.822A pdb=" N VAL A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALA A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 422 through 448 removed outlier: 4.233A pdb=" N SER A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE A 440 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.014A pdb=" N ALA A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.714A pdb=" N ALA A 496 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 removed outlier: 4.410A pdb=" N PHE A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.673A pdb=" N ALA A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 17 through 20 Processing helix chain 'H' and resid 34 through 40 Processing helix chain 'H' and resid 44 through 50 Processing helix chain 'H' and resid 60 through 62 No H-bonds generated for 'chain 'H' and resid 60 through 62' Processing helix chain 'H' and resid 63 through 99 removed outlier: 3.635A pdb=" N PHE H 69 " --> pdb=" O PRO H 65 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG H 88 " --> pdb=" O TYR H 84 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 3.922A pdb=" N PHE H 118 " --> pdb=" O PRO H 114 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA H 128 " --> pdb=" O LYS H 124 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR H 129 " --> pdb=" O SER H 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 12 Processing helix chain 'L' and resid 49 through 54 Processing helix chain 'L' and resid 70 through 78 removed outlier: 5.271A pdb=" N GLU L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 94 through 103 removed outlier: 3.564A pdb=" N LEU L 98 " --> pdb=" O VAL L 94 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 106 No H-bonds generated for 'chain 'L' and resid 104 through 106' Processing helix chain 'L' and resid 111 through 131 removed outlier: 3.857A pdb=" N ASP L 122 " --> pdb=" O LYS L 118 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 156 Processing helix chain 'L' and resid 160 through 169 removed outlier: 5.256A pdb=" N HIS L 166 " --> pdb=" O TYR L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 61 removed outlier: 4.149A pdb=" N GLU M 61 " --> pdb=" O TYR M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 86 removed outlier: 4.930A pdb=" N VAL M 84 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 109 removed outlier: 4.119A pdb=" N TYR M 107 " --> pdb=" O GLU M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 126 removed outlier: 4.187A pdb=" N ILE M 121 " --> pdb=" O ILE M 117 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE M 122 " --> pdb=" O GLY M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 131 Processing helix chain 'M' and resid 152 through 172 removed outlier: 4.251A pdb=" N LEU M 156 " --> pdb=" O ILE M 152 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN M 164 " --> pdb=" O GLY M 160 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN M 172 " --> pdb=" O ILE M 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 51 removed outlier: 3.893A pdb=" N GLU N 40 " --> pdb=" O GLN N 36 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE N 42 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU N 43 " --> pdb=" O LEU N 39 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR N 44 " --> pdb=" O GLU N 40 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA N 45 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP N 46 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET N 50 " --> pdb=" O TRP N 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N CYS N 51 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 80 removed outlier: 4.721A pdb=" N VAL N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER N 68 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA N 71 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 115 removed outlier: 3.605A pdb=" N VAL N 88 " --> pdb=" O ASP N 84 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE N 100 " --> pdb=" O ARG N 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET N 101 " --> pdb=" O VAL N 97 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU N 105 " --> pdb=" O MET N 101 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN N 110 " --> pdb=" O ARG N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 127 removed outlier: 3.827A pdb=" N GLN N 122 " --> pdb=" O HIS N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 153 removed outlier: 3.529A pdb=" N THR N 138 " --> pdb=" O SER N 134 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA N 141 " --> pdb=" O GLU N 137 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN N 142 " --> pdb=" O THR N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 223 Processing helix chain '2' and resid 175 through 189 removed outlier: 4.315A pdb=" N GLU 2 179 " --> pdb=" O GLY 2 175 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE 2 180 " --> pdb=" O PRO 2 176 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA 2 181 " --> pdb=" O ARG 2 177 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN 2 182 " --> pdb=" O THR 2 178 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE 2 187 " --> pdb=" O ARG 2 183 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG 2 189 " --> pdb=" O GLN 2 185 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 211 removed outlier: 3.774A pdb=" N ASP 2 202 " --> pdb=" O TYR 2 198 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE 2 204 " --> pdb=" O TYR 2 200 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG 2 205 " --> pdb=" O ARG 2 201 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 227 removed outlier: 3.890A pdb=" N HIS 2 227 " --> pdb=" O ALA 2 223 " (cutoff:3.500A) Processing helix chain '2' and resid 236 through 256 removed outlier: 4.251A pdb=" N VAL 2 247 " --> pdb=" O ILE 2 243 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER 2 254 " --> pdb=" O ASP 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 257 through 260 Processing helix chain '2' and resid 448 through 453 Processing helix chain '2' and resid 457 through 465 removed outlier: 4.443A pdb=" N VAL 2 463 " --> pdb=" O VAL 2 459 " (cutoff:3.500A) Processing helix chain '2' and resid 473 through 484 removed outlier: 4.020A pdb=" N LYS 2 477 " --> pdb=" O HIS 2 473 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG 2 478 " --> pdb=" O ASP 2 474 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU 2 484 " --> pdb=" O LEU 2 480 " (cutoff:3.500A) Processing helix chain '2' and resid 520 through 525 removed outlier: 4.271A pdb=" N VAL 2 524 " --> pdb=" O TYR 2 520 " (cutoff:3.500A) Processing helix chain '2' and resid 573 through 577 Processing helix chain '2' and resid 578 through 588 removed outlier: 4.178A pdb=" N SER 2 584 " --> pdb=" O GLN 2 580 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU 2 587 " --> pdb=" O THR 2 583 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA 2 588 " --> pdb=" O SER 2 584 " (cutoff:3.500A) Processing helix chain '2' and resid 635 through 640 removed outlier: 3.516A pdb=" N LEU 2 639 " --> pdb=" O SER 2 635 " (cutoff:3.500A) Processing helix chain '2' and resid 660 through 668 Processing helix chain '2' and resid 697 through 707 removed outlier: 3.690A pdb=" N ILE 2 701 " --> pdb=" O LEU 2 697 " (cutoff:3.500A) Processing helix chain '2' and resid 716 through 718 No H-bonds generated for 'chain '2' and resid 716 through 718' Processing helix chain '2' and resid 719 through 730 removed outlier: 3.604A pdb=" N MET 2 723 " --> pdb=" O LYS 2 719 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU 2 727 " --> pdb=" O MET 2 723 " (cutoff:3.500A) Processing helix chain '2' and resid 741 through 752 removed outlier: 4.225A pdb=" N VAL 2 747 " --> pdb=" O HIS 2 743 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET 2 750 " --> pdb=" O SER 2 746 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU 2 752 " --> pdb=" O ILE 2 748 " (cutoff:3.500A) Processing helix chain '2' and resid 752 through 759 removed outlier: 3.544A pdb=" N ARG 2 756 " --> pdb=" O GLU 2 752 " (cutoff:3.500A) Processing helix chain '2' and resid 764 through 780 removed outlier: 3.550A pdb=" N VAL 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE 2 780 " --> pdb=" O LEU 2 776 " (cutoff:3.500A) Processing helix chain '2' and resid 781 through 783 No H-bonds generated for 'chain '2' and resid 781 through 783' Processing helix chain '2' and resid 787 through 795 removed outlier: 4.237A pdb=" N MET 2 791 " --> pdb=" O VAL 2 787 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER 2 793 " --> pdb=" O LYS 2 789 " (cutoff:3.500A) Processing helix chain '2' and resid 796 through 798 No H-bonds generated for 'chain '2' and resid 796 through 798' Processing helix chain '5' and resid 27 through 32 Processing helix chain '5' and resid 32 through 39 Processing helix chain '5' and resid 52 through 58 Processing helix chain '5' and resid 78 through 86 removed outlier: 3.801A pdb=" N LYS 5 82 " --> pdb=" O THR 5 78 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS 5 85 " --> pdb=" O ASP 5 81 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN 5 86 " --> pdb=" O LYS 5 82 " (cutoff:3.500A) Processing helix chain '5' and resid 86 through 103 removed outlier: 4.995A pdb=" N GLU 5 92 " --> pdb=" O THR 5 88 " (cutoff:3.500A) Processing helix chain '5' and resid 104 through 107 removed outlier: 3.763A pdb=" N ALA 5 107 " --> pdb=" O GLU 5 104 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 104 through 107' Processing helix chain '5' and resid 211 through 214 Processing helix chain '5' and resid 313 through 324 removed outlier: 4.209A pdb=" N MET 5 322 " --> pdb=" O HIS 5 318 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA 5 323 " --> pdb=" O PHE 5 319 " (cutoff:3.500A) Processing helix chain '5' and resid 331 through 335 removed outlier: 3.622A pdb=" N SER 5 335 " --> pdb=" O LEU 5 332 " (cutoff:3.500A) Processing helix chain '5' and resid 343 through 351 removed outlier: 4.511A pdb=" N LYS 5 348 " --> pdb=" O ASP 5 345 " (cutoff:3.500A) Processing helix chain '5' and resid 383 through 394 removed outlier: 4.067A pdb=" N LEU 5 388 " --> pdb=" O LYS 5 384 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS 5 393 " --> pdb=" O LYS 5 389 " (cutoff:3.500A) Processing helix chain '5' and resid 449 through 452 removed outlier: 3.560A pdb=" N ARG 5 452 " --> pdb=" O GLU 5 449 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 449 through 452' Processing helix chain '5' and resid 453 through 459 Processing helix chain '5' and resid 489 through 495 removed outlier: 3.742A pdb=" N THR 5 495 " --> pdb=" O ARG 5 491 " (cutoff:3.500A) Processing helix chain '5' and resid 522 through 532 removed outlier: 3.703A pdb=" N ILE 5 527 " --> pdb=" O GLU 5 523 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR 5 528 " --> pdb=" O SER 5 524 " (cutoff:3.500A) Processing helix chain '5' and resid 533 through 538 Processing helix chain '5' and resid 554 through 566 Processing helix chain '5' and resid 608 through 613 Processing helix chain '5' and resid 616 through 620 Processing helix chain '5' and resid 621 through 626 Processing helix chain '5' and resid 637 through 648 removed outlier: 3.842A pdb=" N VAL 5 645 " --> pdb=" O ARG 5 641 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER 5 646 " --> pdb=" O LEU 5 642 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 30 removed outlier: 3.680A pdb=" N PHE 6 28 " --> pdb=" O LEU 6 24 " (cutoff:3.500A) Processing helix chain '6' and resid 41 through 47 Processing helix chain '6' and resid 60 through 65 Processing helix chain '6' and resid 69 through 73 Processing helix chain '6' and resid 76 through 94 Proline residue: 6 82 - end of helix removed outlier: 3.646A pdb=" N ASP 6 94 " --> pdb=" O ASN 6 90 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 125 removed outlier: 3.536A pdb=" N LYS 6 124 " --> pdb=" O THR 6 121 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE 6 125 " --> pdb=" O THR 6 122 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 121 through 125' Processing helix chain '6' and resid 325 through 330 Processing helix chain '6' and resid 330 through 335 removed outlier: 3.873A pdb=" N ASP 6 335 " --> pdb=" O GLU 6 331 " (cutoff:3.500A) Processing helix chain '6' and resid 337 through 345 removed outlier: 3.635A pdb=" N ASN 6 341 " --> pdb=" O ASN 6 337 " (cutoff:3.500A) Processing helix chain '6' and resid 355 through 360 Processing helix chain '6' and resid 360 through 365 Processing helix chain '6' and resid 395 through 405 removed outlier: 3.702A pdb=" N SER 6 402 " --> pdb=" O LEU 6 398 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP 6 403 " --> pdb=" O LYS 6 399 " (cutoff:3.500A) Processing helix chain '6' and resid 417 through 421 removed outlier: 3.922A pdb=" N LEU 6 421 " --> pdb=" O ALA 6 418 " (cutoff:3.500A) Processing helix chain '6' and resid 461 through 466 Processing helix chain '6' and resid 507 through 513 removed outlier: 3.789A pdb=" N ILE 6 512 " --> pdb=" O LEU 6 508 " (cutoff:3.500A) Processing helix chain '6' and resid 517 through 522 Processing helix chain '6' and resid 536 through 545 removed outlier: 4.336A pdb=" N ILE 6 540 " --> pdb=" O VAL 6 536 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA 6 541 " --> pdb=" O ASP 6 537 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG 6 542 " --> pdb=" O TYR 6 538 " (cutoff:3.500A) Processing helix chain '6' and resid 560 through 571 removed outlier: 4.391A pdb=" N THR 6 569 " --> pdb=" O LEU 6 565 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE 6 570 " --> pdb=" O ARG 6 566 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA 6 571 " --> pdb=" O TYR 6 567 " (cutoff:3.500A) Processing helix chain '6' and resid 572 through 574 No H-bonds generated for 'chain '6' and resid 572 through 574' Processing helix chain '6' and resid 580 through 585 Processing helix chain '6' and resid 585 through 599 removed outlier: 4.033A pdb=" N GLY 6 599 " --> pdb=" O GLN 6 595 " (cutoff:3.500A) Processing helix chain '6' and resid 609 through 627 removed outlier: 4.022A pdb=" N SER 6 615 " --> pdb=" O ARG 6 611 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 6 620 " --> pdb=" O MET 6 616 " (cutoff:3.500A) Processing helix chain '6' and resid 634 through 650 removed outlier: 3.777A pdb=" N LYS 6 638 " --> pdb=" O GLU 6 634 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE 6 648 " --> pdb=" O LEU 6 644 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE 6 649 " --> pdb=" O ASN 6 645 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 18 removed outlier: 4.421A pdb=" N ASP 3 11 " --> pdb=" O GLN 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 29 removed outlier: 4.020A pdb=" N TYR 3 29 " --> pdb=" O ASP 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 47 through 55 removed outlier: 3.648A pdb=" N LEU 3 51 " --> pdb=" O ASN 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 55 through 64 removed outlier: 3.827A pdb=" N LEU 3 62 " --> pdb=" O ARG 3 58 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU 3 63 " --> pdb=" O ALA 3 59 " (cutoff:3.500A) Processing helix chain '3' and resid 68 through 83 removed outlier: 4.255A pdb=" N ALA 3 72 " --> pdb=" O ASP 3 68 " (cutoff:3.500A) Processing helix chain '3' and resid 201 through 205 Processing helix chain '3' and resid 274 through 284 removed outlier: 3.920A pdb=" N ILE 3 278 " --> pdb=" O SER 3 274 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET 3 279 " --> pdb=" O ARG 3 275 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS 3 283 " --> pdb=" O MET 3 279 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU 3 284 " --> pdb=" O LEU 3 280 " (cutoff:3.500A) Processing helix chain '3' and resid 285 through 287 No H-bonds generated for 'chain '3' and resid 285 through 287' Processing helix chain '3' and resid 289 through 296 removed outlier: 3.848A pdb=" N LEU 3 293 " --> pdb=" O ASP 3 289 " (cutoff:3.500A) Processing helix chain '3' and resid 309 through 318 removed outlier: 3.969A pdb=" N LEU 3 313 " --> pdb=" O LYS 3 309 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N CYS 3 314 " --> pdb=" O GLN 3 310 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU 3 315 " --> pdb=" O ALA 3 311 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 3 316 " --> pdb=" O ILE 3 312 " (cutoff:3.500A) Processing helix chain '3' and resid 393 through 397 Processing helix chain '3' and resid 414 through 423 removed outlier: 3.510A pdb=" N GLU 3 419 " --> pdb=" O THR 3 415 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL 3 420 " --> pdb=" O ALA 3 416 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU 3 422 " --> pdb=" O HIS 3 418 " (cutoff:3.500A) Processing helix chain '3' and resid 488 through 503 Processing helix chain '3' and resid 558 through 563 Processing helix chain '3' and resid 564 through 566 No H-bonds generated for 'chain '3' and resid 564 through 566' Processing helix chain '3' and resid 568 through 572 removed outlier: 4.244A pdb=" N MET 3 572 " --> pdb=" O ALA 3 569 " (cutoff:3.500A) Processing helix chain '3' and resid 579 through 595 removed outlier: 4.442A pdb=" N ALA 3 585 " --> pdb=" O CYS 3 581 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN 3 586 " --> pdb=" O GLU 3 582 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER 3 593 " --> pdb=" O SER 3 589 " (cutoff:3.500A) Processing helix chain '3' and resid 609 through 612 Processing helix chain '3' and resid 613 through 624 removed outlier: 4.788A pdb=" N SER 3 619 " --> pdb=" O LEU 3 615 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA 3 621 " --> pdb=" O ARG 3 617 " (cutoff:3.500A) Processing helix chain '3' and resid 632 through 638 removed outlier: 3.832A pdb=" N ALA 3 638 " --> pdb=" O ASP 3 634 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 174 removed outlier: 3.950A pdb=" N CYS 4 164 " --> pdb=" O VAL 4 160 " (cutoff:3.500A) Processing helix chain '4' and resid 177 through 182 Processing helix chain '4' and resid 194 through 203 Processing helix chain '4' and resid 215 through 220 removed outlier: 3.675A pdb=" N LYS 4 219 " --> pdb=" O ALA 4 216 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR 4 220 " --> pdb=" O HIS 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 222 through 232 removed outlier: 3.966A pdb=" N TYR 4 226 " --> pdb=" O ASP 4 222 " (cutoff:3.500A) Processing helix chain '4' and resid 236 through 252 removed outlier: 5.062A pdb=" N PHE 4 249 " --> pdb=" O ASN 4 245 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU 4 250 " --> pdb=" O GLU 4 246 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG 4 251 " --> pdb=" O MET 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 278 through 282 removed outlier: 3.713A pdb=" N MET 4 282 " --> pdb=" O PRO 4 279 " (cutoff:3.500A) Processing helix chain '4' and resid 447 through 456 removed outlier: 4.243A pdb=" N LEU 4 451 " --> pdb=" O ARG 4 447 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN 4 452 " --> pdb=" O VAL 4 448 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 462 removed outlier: 3.509A pdb=" N ILE 4 460 " --> pdb=" O LYS 4 457 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR 4 461 " --> pdb=" O PRO 4 458 " (cutoff:3.500A) Processing helix chain '4' and resid 464 through 469 removed outlier: 4.101A pdb=" N ALA 4 469 " --> pdb=" O ALA 4 465 " (cutoff:3.500A) Processing helix chain '4' and resid 481 through 485 removed outlier: 3.540A pdb=" N GLN 4 485 " --> pdb=" O ILE 4 482 " (cutoff:3.500A) Processing helix chain '4' and resid 519 through 529 Processing helix chain '4' and resid 591 through 595 Processing helix chain '4' and resid 631 through 635 Processing helix chain '4' and resid 661 through 669 removed outlier: 4.175A pdb=" N ALA 4 665 " --> pdb=" O ASP 4 661 " (cutoff:3.500A) Processing helix chain '4' and resid 670 through 675 removed outlier: 4.568A pdb=" N THR 4 675 " --> pdb=" O LEU 4 671 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 696 removed outlier: 3.511A pdb=" N ASP 4 691 " --> pdb=" O SER 4 687 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR 4 692 " --> pdb=" O VAL 4 688 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE 4 693 " --> pdb=" O LEU 4 689 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA 4 694 " --> pdb=" O ARG 4 690 " (cutoff:3.500A) Processing helix chain '4' and resid 709 through 721 removed outlier: 5.103A pdb=" N VAL 4 717 " --> pdb=" O ILE 4 713 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP 4 718 " --> pdb=" O GLN 4 714 " (cutoff:3.500A) Processing helix chain '4' and resid 722 through 724 No H-bonds generated for 'chain '4' and resid 722 through 724' Processing helix chain '4' and resid 734 through 743 Processing helix chain '4' and resid 758 through 768 removed outlier: 3.734A pdb=" N GLU 4 762 " --> pdb=" O LEU 4 758 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA 4 763 " --> pdb=" O ASP 4 759 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 19 Processing helix chain '7' and resid 31 through 42 Processing helix chain '7' and resid 51 through 57 removed outlier: 3.949A pdb=" N LEU 7 55 " --> pdb=" O ASP 7 51 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU 7 57 " --> pdb=" O ASP 7 53 " (cutoff:3.500A) Processing helix chain '7' and resid 71 through 83 Processing helix chain '7' and resid 97 through 108 removed outlier: 3.728A pdb=" N VAL 7 101 " --> pdb=" O ASP 7 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU 7 104 " --> pdb=" O ASP 7 100 " (cutoff:3.500A) Processing helix chain '7' and resid 223 through 227 Processing helix chain '7' and resid 260 through 262 No H-bonds generated for 'chain '7' and resid 260 through 262' Processing helix chain '7' and resid 323 through 330 Processing helix chain '7' and resid 334 through 340 removed outlier: 3.599A pdb=" N THR 7 338 " --> pdb=" O GLU 7 334 " (cutoff:3.500A) Processing helix chain '7' and resid 347 through 360 removed outlier: 3.855A pdb=" N LYS 7 351 " --> pdb=" O HIS 7 347 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU 7 357 " --> pdb=" O ALA 7 353 " (cutoff:3.500A) Processing helix chain '7' and resid 365 through 369 removed outlier: 4.046A pdb=" N GLY 7 368 " --> pdb=" O ARG 7 365 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 398 Processing helix chain '7' and resid 410 through 415 removed outlier: 3.942A pdb=" N THR 7 415 " --> pdb=" O GLY 7 411 " (cutoff:3.500A) Processing helix chain '7' and resid 432 through 437 Processing helix chain '7' and resid 446 through 451 removed outlier: 3.598A pdb=" N MET 7 450 " --> pdb=" O GLU 7 446 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA 7 451 " --> pdb=" O PHE 7 447 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 446 through 451' Processing helix chain '7' and resid 454 through 461 removed outlier: 3.934A pdb=" N ILE 7 458 " --> pdb=" O ASP 7 454 " (cutoff:3.500A) Processing helix chain '7' and resid 508 through 515 removed outlier: 3.880A pdb=" N LEU 7 512 " --> pdb=" O PRO 7 508 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG 7 514 " --> pdb=" O ALA 7 510 " (cutoff:3.500A) Processing helix chain '7' and resid 528 through 543 removed outlier: 4.209A pdb=" N ARG 7 532 " --> pdb=" O ASP 7 528 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU 7 533 " --> pdb=" O ASN 7 529 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL 7 540 " --> pdb=" O HIS 7 536 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) Processing helix chain '7' and resid 555 through 565 Processing helix chain '7' and resid 575 through 594 removed outlier: 3.925A pdb=" N ASP 7 579 " --> pdb=" O ASP 7 575 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL 7 582 " --> pdb=" O THR 7 578 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL 7 586 " --> pdb=" O VAL 7 582 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU 7 588 " --> pdb=" O ALA 7 584 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU 7 591 " --> pdb=" O GLU 7 587 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG 7 593 " --> pdb=" O ARG 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 621 removed outlier: 4.374A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER 7 613 " --> pdb=" O ILE 7 609 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR 7 614 " --> pdb=" O LEU 7 610 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA 7 615 " --> pdb=" O ARG 7 611 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU 7 616 " --> pdb=" O LEU 7 612 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA 7 617 " --> pdb=" O SER 7 613 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG 7 618 " --> pdb=" O THR 7 614 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU 7 619 " --> pdb=" O ALA 7 615 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 641 removed outlier: 4.007A pdb=" N ALA 7 633 " --> pdb=" O ASP 7 629 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS 7 641 " --> pdb=" O LEU 7 637 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA2, first strand: chain 'A' and resid 284 through 288 removed outlier: 4.694A pdb=" N THR A 284 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR A 375 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 460 removed outlier: 7.209A pdb=" N PHE A 459 " --> pdb=" O ILE A 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 14 through 17 Processing sheet with id=AA5, first strand: chain 'M' and resid 22 through 23 Processing sheet with id=AA6, first strand: chain 'N' and resid 180 through 181 removed outlier: 3.731A pdb=" N ILE N 211 " --> pdb=" O VAL N 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 215 through 218 Processing sheet with id=AA8, first strand: chain '2' and resid 296 through 297 Processing sheet with id=AA9, first strand: chain '2' and resid 303 through 305 removed outlier: 4.160A pdb=" N GLN 2 359 " --> pdb=" O LEU 2 383 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU 2 383 " --> pdb=" O GLN 2 359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '2' and resid 397 through 399 Processing sheet with id=AB2, first strand: chain '2' and resid 403 through 404 Processing sheet with id=AB3, first strand: chain '2' and resid 529 through 530 removed outlier: 7.111A pdb=" N VAL 2 529 " --> pdb=" O LEU 2 570 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS 2 569 " --> pdb=" O THR 2 610 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain '5' and resid 224 through 225 removed outlier: 3.502A pdb=" N ILE 5 146 " --> pdb=" O ILE 5 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '5' and resid 164 through 165 removed outlier: 4.316A pdb=" N SER 5 164 " --> pdb=" O MET 5 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '5' and resid 439 through 441 removed outlier: 3.869A pdb=" N VAL 5 374 " --> pdb=" O VAL 5 481 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA 5 483 " --> pdb=" O VAL 5 374 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU 5 375 " --> pdb=" O PHE 5 515 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL 5 517 " --> pdb=" O LEU 5 375 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU 5 377 " --> pdb=" O VAL 5 517 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '6' and resid 136 through 139 removed outlier: 4.783A pdb=" N ARG 6 137 " --> pdb=" O ARG 6 201 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS 6 199 " --> pdb=" O HIS 6 139 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE 6 220 " --> pdb=" O ILE 6 200 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '6' and resid 411 through 412 removed outlier: 7.021A pdb=" N THR 6 411 " --> pdb=" O ASP 6 452 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain '3' and resid 134 through 138 removed outlier: 3.613A pdb=" N LEU 3 196 " --> pdb=" O ILE 3 216 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP 3 215 " --> pdb=" O LEU 3 257 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP 3 230 " --> pdb=" O VAL 3 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN 3 199 " --> pdb=" O ILE 3 127 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR 3 129 " --> pdb=" O THR 3 197 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR 3 197 " --> pdb=" O THR 3 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '3' and resid 152 through 155 removed outlier: 4.395A pdb=" N VAL 3 142 " --> pdb=" O GLU 3 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 372 through 373 removed outlier: 3.802A pdb=" N ALA 3 390 " --> pdb=" O LEU 3 373 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '4' and resid 372 through 375 removed outlier: 3.761A pdb=" N LEU 4 375 " --> pdb=" O VAL 4 355 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL 4 355 " --> pdb=" O LEU 4 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 372 through 375 removed outlier: 3.761A pdb=" N LEU 4 375 " --> pdb=" O VAL 4 355 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL 4 355 " --> pdb=" O LEU 4 375 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR 4 392 " --> pdb=" O ARG 4 425 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR 4 394 " --> pdb=" O HIS 4 423 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS 4 423 " --> pdb=" O THR 4 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '4' and resid 301 through 302 Processing sheet with id=AC6, first strand: chain '4' and resid 304 through 306 Processing sheet with id=AC7, first strand: chain '4' and resid 411 through 412 Processing sheet with id=AC8, first strand: chain '4' and resid 532 through 536 removed outlier: 6.524A pdb=" N GLN 4 533 " --> pdb=" O CYS 4 574 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ASP 4 576 " --> pdb=" O GLN 4 533 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR 4 535 " --> pdb=" O ASP 4 576 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS 4 573 " --> pdb=" O SER 4 614 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU 4 616 " --> pdb=" O CYS 4 573 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '7' and resid 47 through 49 removed outlier: 6.032A pdb=" N ILE 7 48 " --> pdb=" O GLY 7 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '7' and resid 160 through 168 removed outlier: 3.969A pdb=" N LEU 7 298 " --> pdb=" O THR 7 254 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET 7 256 " --> pdb=" O LEU 7 298 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '7' and resid 176 through 179 removed outlier: 7.308A pdb=" N LYS 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '7' and resid 181 through 182 Processing sheet with id=AD4, first strand: chain '7' and resid 440 through 445 removed outlier: 6.020A pdb=" N GLY 7 440 " --> pdb=" O SER 7 483 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU 7 485 " --> pdb=" O GLY 7 440 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N CYS 7 442 " --> pdb=" O LEU 7 485 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ALA 7 487 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE 7 444 " --> pdb=" O ALA 7 487 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE 7 377 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU 7 517 " --> pdb=" O ASN 7 376 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '7' and resid 466 through 469 removed outlier: 3.672A pdb=" N THR 7 477 " --> pdb=" O ILE 7 467 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2631 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: 6.91 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.72 - 0.94: 1 0.94 - 1.16: 1 1.16 - 1.39: 15411 1.39 - 1.61: 23214 1.61 - 1.83: 359 Bond restraints: 38986 Sorted by residual: bond pdb=" C LYS 4 491 " pdb=" N LYS 4 492 " ideal model delta sigma weight residual 1.332 0.718 0.614 1.40e-02 5.10e+03 1.92e+03 bond pdb=" C ILE 5 507 " pdb=" N LEU 5 508 " ideal model delta sigma weight residual 1.332 1.041 0.291 1.40e-02 5.10e+03 4.32e+02 bond pdb=" C4 ATP 4 901 " pdb=" C5 ATP 4 901 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.11e+01 bond pdb=" C LEU 7 220 " pdb=" N TYR 7 221 " ideal model delta sigma weight residual 1.332 1.450 -0.117 1.40e-02 5.10e+03 7.04e+01 bond pdb=" C4 ATP 6 902 " pdb=" C5 ATP 6 902 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.39e+01 ... (remaining 38981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.74: 52638 8.74 - 17.48: 121 17.48 - 26.21: 15 26.21 - 34.95: 3 34.95 - 43.69: 1 Bond angle restraints: 52778 Sorted by residual: angle pdb=" O LYS 4 491 " pdb=" C LYS 4 491 " pdb=" N LYS 4 492 " ideal model delta sigma weight residual 123.29 94.09 29.20 1.18e+00 7.18e-01 6.12e+02 angle pdb=" CA ILE 5 507 " pdb=" C ILE 5 507 " pdb=" N LEU 5 508 " ideal model delta sigma weight residual 116.60 82.15 34.45 1.45e+00 4.76e-01 5.64e+02 angle pdb=" PB ATP 6 902 " pdb=" O3B ATP 6 902 " pdb=" PG ATP 6 902 " ideal model delta sigma weight residual 139.87 116.67 23.20 1.00e+00 1.00e+00 5.38e+02 angle pdb=" CA LYS 4 491 " pdb=" C LYS 4 491 " pdb=" N LYS 4 492 " ideal model delta sigma weight residual 116.28 145.33 -29.05 1.26e+00 6.30e-01 5.32e+02 angle pdb=" C ILE 5 507 " pdb=" N LEU 5 508 " pdb=" CA LEU 5 508 " ideal model delta sigma weight residual 121.54 77.85 43.69 1.91e+00 2.74e-01 5.23e+02 ... (remaining 52773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.59: 22148 28.59 - 57.19: 1481 57.19 - 85.78: 133 85.78 - 114.37: 14 114.37 - 142.96: 8 Dihedral angle restraints: 23784 sinusoidal: 9846 harmonic: 13938 Sorted by residual: dihedral pdb=" CD ARG 2 641 " pdb=" NE ARG 2 641 " pdb=" CZ ARG 2 641 " pdb=" NH1 ARG 2 641 " ideal model delta sinusoidal sigma weight residual 0.00 118.09 -118.09 1 1.00e+01 1.00e-02 1.41e+02 dihedral pdb=" CA THR A 490 " pdb=" C THR A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta harmonic sigma weight residual 180.00 120.94 59.06 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CD ARG 6 611 " pdb=" NE ARG 6 611 " pdb=" CZ ARG 6 611 " pdb=" NH1 ARG 6 611 " ideal model delta sinusoidal sigma weight residual 0.00 107.05 -107.05 1 1.00e+01 1.00e-02 1.24e+02 ... (remaining 23781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.583: 5960 0.583 - 1.166: 0 1.166 - 1.749: 24 1.749 - 2.332: 5 2.332 - 2.914: 1 Chirality restraints: 5990 Sorted by residual: chirality pdb=" CG LEU 4 545 " pdb=" CB LEU 4 545 " pdb=" CD1 LEU 4 545 " pdb=" CD2 LEU 4 545 " both_signs ideal model delta sigma weight residual False -2.59 0.32 -2.91 2.00e-01 2.50e+01 2.12e+02 chirality pdb=" CG LEU 4 766 " pdb=" CB LEU 4 766 " pdb=" CD1 LEU 4 766 " pdb=" CD2 LEU 4 766 " both_signs ideal model delta sigma weight residual False -2.59 -0.58 -2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CG LEU 4 450 " pdb=" CB LEU 4 450 " pdb=" CD1 LEU 4 450 " pdb=" CD2 LEU 4 450 " both_signs ideal model delta sigma weight residual False -2.59 -0.67 -1.92 2.00e-01 2.50e+01 9.18e+01 ... (remaining 5987 not shown) Planarity restraints: 6735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE 5 507 " -0.080 2.00e-02 2.50e+03 2.08e-01 4.34e+02 pdb=" C ILE 5 507 " 0.358 2.00e-02 2.50e+03 pdb=" O ILE 5 507 " -0.148 2.00e-02 2.50e+03 pdb=" N LEU 5 508 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 3 610 " -0.448 9.50e-02 1.11e+02 2.27e-01 1.63e+02 pdb=" NE ARG 3 610 " 0.101 2.00e-02 2.50e+03 pdb=" CZ ARG 3 610 " -0.198 2.00e-02 2.50e+03 pdb=" NH1 ARG 3 610 " 0.066 2.00e-02 2.50e+03 pdb=" NH2 ARG 3 610 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 611 " 0.936 9.50e-02 1.11e+02 4.24e-01 1.53e+02 pdb=" NE ARG 6 611 " -0.099 2.00e-02 2.50e+03 pdb=" CZ ARG 6 611 " 0.106 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 611 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 611 " -0.027 2.00e-02 2.50e+03 ... (remaining 6732 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 25 2.03 - 2.74: 5621 2.74 - 3.46: 59377 3.46 - 4.18: 91082 4.18 - 4.90: 147345 Nonbonded interactions: 303450 Sorted by model distance: nonbonded pdb=" O LYS 3 78 " pdb=" OG SER 3 82 " model vdw 1.308 3.040 nonbonded pdb=" NH1 ARG 2 374 " pdb=" OE1 GLN 6 231 " model vdw 1.431 3.120 nonbonded pdb=" OG1 THR 7 500 " pdb=" OE1 GLN 7 503 " model vdw 1.502 3.040 nonbonded pdb=" CZ ARG 2 374 " pdb=" OE1 GLN 6 231 " model vdw 1.610 3.270 nonbonded pdb=" NH2 ARG 2 374 " pdb=" OE1 GLN 6 231 " model vdw 1.739 3.120 ... (remaining 303445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 33.130 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 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 : 0.012 0.850 38999 Z= 0.749 Angle : 1.603 43.690 52780 Z= 0.920 Chirality : 0.144 2.914 5990 Planarity : 0.014 0.466 6735 Dihedral : 18.545 142.964 14709 Min Nonbonded Distance : 1.308 Molprobity Statistics. All-atom Clashscore : 23.25 Ramachandran Plot: Outliers : 0.97 % Allowed : 17.65 % Favored : 81.38 % Rotamer: Outliers : 6.20 % Allowed : 15.07 % Favored : 78.73 % Cbeta Deviations : 0.64 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.30 % Twisted General : 1.13 % 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: -5.70 (0.09), residues: 4657 helix: -3.84 (0.09), residues: 1381 sheet: -3.70 (0.21), residues: 417 loop : -3.99 (0.10), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.203 0.004 ARG 3 610 TYR 0.056 0.005 TYR 3 238 PHE 0.060 0.005 PHE 4 526 TRP 0.085 0.005 TRP 2 554 HIS 0.035 0.004 HIS H 199 Details of bonding type rmsd/Z covalent geometry : bond 0.01079 / 0.56 (38986) covalent geometry : angle 1.60257 / 0.92 (52778) SS BOND : bond 0.00674 / 0.34 ( 1) SS BOND : angle 1.30042 / 1.98 ( 2) hydrogen bonds : bond 0.24216 / 22.13 ( 926) hydrogen bonds : angle 10.21696 / 8.99 ( 2631) Misc. bond : bond 0.28046 / 17.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 1029 time to evaluate : 1.430 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 TARDY: cannot create tardy model for: "ILE H 201 " (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 TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (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 18 ARG cc_start: 0.7333 (ptp90) cc_final: 0.5060 (ptt-90) REVERT: A 45 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6389 (mmt) REVERT: A 66 GLN cc_start: 0.8270 (tp40) cc_final: 0.7824 (pm20) REVERT: A 188 ARG cc_start: 0.8676 (ttt90) cc_final: 0.7965 (ptp-170) REVERT: A 217 MET cc_start: 0.7795 (mmt) cc_final: 0.7584 (mpp) REVERT: A 261 ILE cc_start: 0.6118 (OUTLIER) cc_final: 0.5801 (mm) REVERT: A 300 THR cc_start: 0.6221 (OUTLIER) cc_final: 0.5933 (p) REVERT: A 326 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8059 (tp30) REVERT: A 442 GLN cc_start: 0.7692 (mp10) cc_final: 0.7170 (tp40) REVERT: A 459 PHE cc_start: 0.8285 (m-80) cc_final: 0.7836 (m-80) REVERT: A 519 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.6784 (mp) REVERT: H 10 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8042 (mp0) REVERT: H 69 PHE cc_start: 0.7760 (t80) cc_final: 0.7334 (t80) REVERT: H 86 TYR cc_start: 0.8399 (t80) cc_final: 0.8137 (t80) REVERT: H 129 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.7375 (t80) REVERT: L 47 TRP cc_start: 0.7963 (p-90) cc_final: 0.7683 (p-90) REVERT: L 51 HIS cc_start: 0.8049 (m90) cc_final: 0.7834 (m-70) REVERT: L 64 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8184 (mp0) REVERT: L 77 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8476 (mt-10) REVERT: L 89 CYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6198 (t) REVERT: L 112 GLU cc_start: 0.8753 (mp0) cc_final: 0.8499 (mp0) REVERT: L 136 ILE cc_start: 0.8030 (pt) cc_final: 0.7621 (pt) REVERT: L 141 THR cc_start: 0.6703 (p) cc_final: 0.6072 (p) REVERT: L 180 ASP cc_start: 0.5308 (m-30) cc_final: 0.4696 (t0) REVERT: M 17 PHE cc_start: 0.5922 (t80) cc_final: 0.5059 (t80) REVERT: M 53 ASN cc_start: 0.8156 (m110) cc_final: 0.7590 (p0) REVERT: M 112 ASP cc_start: 0.8703 (p0) cc_final: 0.8481 (p0) REVERT: M 167 TYR cc_start: 0.7847 (t80) cc_final: 0.7550 (t80) REVERT: N 105 LEU cc_start: 0.8931 (mt) cc_final: 0.8026 (mt) REVERT: N 109 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8312 (mt) REVERT: N 110 GLN cc_start: 0.8559 (mp10) cc_final: 0.8122 (mp10) REVERT: N 111 LYS cc_start: 0.8981 (mttm) cc_final: 0.8596 (mmmm) REVERT: N 144 PHE cc_start: 0.8078 (t80) cc_final: 0.7820 (t80) REVERT: N 182 PHE cc_start: 0.6274 (m-80) cc_final: 0.5311 (m-80) REVERT: 2 356 ARG cc_start: 0.8313 (ptt90) cc_final: 0.8032 (ptt-90) REVERT: 2 485 PHE cc_start: 0.6663 (m-80) cc_final: 0.4979 (m-80) REVERT: 2 499 ARG cc_start: 0.4033 (OUTLIER) cc_final: 0.2916 (mpt-90) REVERT: 2 534 GLN cc_start: 0.5756 (OUTLIER) cc_final: 0.5427 (tm-30) REVERT: 2 546 ARG cc_start: 0.2048 (OUTLIER) cc_final: 0.1497 (mtm180) REVERT: 2 703 TYR cc_start: 0.8000 (m-10) cc_final: 0.7585 (m-80) REVERT: 2 764 MET cc_start: 0.3780 (tpp) cc_final: 0.3478 (mmm) REVERT: 2 781 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7558 (pt0) REVERT: 2 788 MET cc_start: 0.7786 (ptm) cc_final: 0.7531 (ttt) REVERT: 2 795 PHE cc_start: 0.6394 (m-10) cc_final: 0.5937 (m-80) REVERT: 5 59 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6825 (tt) REVERT: 5 93 ILE cc_start: 0.8436 (tp) cc_final: 0.8205 (tp) REVERT: 5 96 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8562 (mm-30) REVERT: 5 115 HIS cc_start: 0.7465 (t70) cc_final: 0.7250 (t70) REVERT: 5 226 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6881 (pp20) REVERT: 5 249 CYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6545 (p) REVERT: 5 285 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7195 (t) REVERT: 5 426 MET cc_start: 0.1921 (mmt) cc_final: 0.1635 (mmp) REVERT: 5 441 ILE cc_start: 0.5452 (OUTLIER) cc_final: 0.5017 (tp) REVERT: 5 452 ARG cc_start: 0.3952 (OUTLIER) cc_final: 0.3646 (ttp-170) REVERT: 5 560 LYS cc_start: 0.5040 (mptt) cc_final: 0.3689 (ttmt) REVERT: 6 113 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7766 (m) REVERT: 6 120 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.6898 (mt) REVERT: 6 199 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8080 (ttpp) REVERT: 6 208 GLU cc_start: 0.8081 (tp30) cc_final: 0.7437 (tt0) REVERT: 6 236 TYR cc_start: 0.4164 (OUTLIER) cc_final: 0.3084 (p90) REVERT: 6 341 ASN cc_start: 0.6694 (OUTLIER) cc_final: 0.6462 (m-40) REVERT: 6 374 GLU cc_start: 0.8940 (pp20) cc_final: 0.8582 (pm20) REVERT: 6 398 LEU cc_start: 0.8477 (mp) cc_final: 0.8258 (mp) REVERT: 6 433 ASP cc_start: 0.6862 (t0) cc_final: 0.6208 (p0) REVERT: 6 454 PHE cc_start: 0.7590 (m-80) cc_final: 0.7136 (m-80) REVERT: 6 478 ARG cc_start: 0.7371 (mmt-90) cc_final: 0.7100 (mmt-90) REVERT: 6 492 LEU cc_start: 0.4017 (OUTLIER) cc_final: 0.3568 (mm) REVERT: 6 514 LEU cc_start: 0.1605 (OUTLIER) cc_final: 0.1115 (mt) REVERT: 6 613 LEU cc_start: 0.8197 (tp) cc_final: 0.7943 (mt) REVERT: 3 73 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: 3 77 LEU cc_start: 0.9514 (mp) cc_final: 0.9290 (tt) REVERT: 3 111 ARG cc_start: 0.7581 (tpt90) cc_final: 0.7191 (ptm160) REVERT: 3 116 ILE cc_start: 0.8901 (tt) cc_final: 0.8637 (mm) REVERT: 3 219 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: 3 466 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.4582 (pt) REVERT: 3 478 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7356 (m-10) REVERT: 3 480 MET cc_start: 0.7049 (ttm) cc_final: 0.6221 (tmm) REVERT: 3 572 MET cc_start: 0.7841 (mmp) cc_final: 0.7625 (mmm) REVERT: 4 221 PHE cc_start: 0.7033 (t80) cc_final: 0.6632 (t80) REVERT: 4 248 PHE cc_start: 0.9285 (m-80) cc_final: 0.8924 (m-80) REVERT: 4 291 MET cc_start: 0.7135 (mtt) cc_final: 0.6602 (ttm) REVERT: 4 302 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7804 (tpp) REVERT: 4 335 ASN cc_start: 0.9192 (m-40) cc_final: 0.8476 (t0) REVERT: 4 538 ARG cc_start: 0.5688 (tpp80) cc_final: 0.5400 (mmm-85) REVERT: 4 578 PHE cc_start: 0.7646 (t80) cc_final: 0.7394 (t80) REVERT: 4 649 ILE cc_start: 0.6608 (mp) cc_final: 0.6128 (pt) REVERT: 7 20 PHE cc_start: 0.7317 (t80) cc_final: 0.6537 (t80) REVERT: 7 173 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7364 (p) REVERT: 7 176 MET cc_start: 0.6650 (ttp) cc_final: 0.5935 (tpp) REVERT: 7 196 ASN cc_start: 0.7769 (t0) cc_final: 0.6482 (m110) REVERT: 7 264 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7012 (mtp) REVERT: 7 327 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7788 (mt) REVERT: 7 329 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8458 (mt0) REVERT: 7 345 TYR cc_start: 0.8549 (t80) cc_final: 0.8188 (t80) REVERT: 7 365 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8095 (tpp-160) REVERT: 7 435 VAL cc_start: 0.7963 (t) cc_final: 0.7730 (t) REVERT: 7 484 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8943 (mm) REVERT: 7 541 HIS cc_start: 0.7291 (m-70) cc_final: 0.6831 (m-70) REVERT: 7 550 ARG cc_start: 0.7082 (tpt170) cc_final: 0.6601 (tpp-160) REVERT: 7 556 MET cc_start: 0.8659 (ptt) cc_final: 0.8427 (ptt) REVERT: 7 590 ARG cc_start: 0.9187 (ppt170) cc_final: 0.8051 (tpt90) REVERT: 7 627 LYS cc_start: 0.8788 (mttt) cc_final: 0.8520 (tptp) outliers start: 254 outliers final: 88 residues processed: 1238 average time/residue: 0.2571 time to fit residues: 504.4571 Evaluate side-chains 821 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 701 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.0470 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 6.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS A 108 ASN A 229 ASN A 290 HIS ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 537 GLN A 548 GLN H 71 HIS H 75 GLN ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 HIS L 154 HIS L 171 GLN M 53 ASN M 98 HIS M 127 GLN N 36 GLN N 69 GLN N 162 ASN N 164 GLN N 170 GLN N 209 HIS N 214 GLN 2 286 HIS 2 289 GLN ** 2 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 534 GLN 2 591 GLN 2 659 GLN 2 672 HIS ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 176 ASN 5 233 GLN 5 239 HIS 5 241 GLN ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 334 GLN 5 373 ASN 5 423 ASN ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 476 ASN 5 486 ASN 6 142 HIS 6 198 GLN 6 466 HIS 6 496 ASN ** 6 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 550 ASN 6 584 HIS 6 645 ASN 3 26 GLN ** 3 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 199 GLN 3 348 GLN ** 3 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 490 GLN 4 182 GLN 4 193 GLN 4 204 HIS ** 4 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 310 ASN 4 333 ASN 4 338 HIS ** 4 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 378 HIS 4 379 ASN ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 485 GLN 4 523 GLN 4 596 GLN 7 45 GLN 7 196 ASN 7 238 GLN 7 266 GLN ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 402 GLN ** 7 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 503 GLN ** 7 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 557 ASN 7 564 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.191616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.172887 restraints weight = 140212.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.173792 restraints weight = 127976.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.174584 restraints weight = 108484.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.175165 restraints weight = 91791.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.175426 restraints weight = 85617.325| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 38999 Z= 0.219 Angle : 1.015 13.881 52780 Z= 0.526 Chirality : 0.054 0.295 5990 Planarity : 0.009 0.276 6735 Dihedral : 12.717 147.776 5460 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.11 % Favored : 85.78 % Rotamer: Outliers : 0.66 % Allowed : 7.40 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.46 % 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: -4.91 (0.10), residues: 4657 helix: -3.05 (0.10), residues: 1430 sheet: -3.11 (0.22), residues: 416 loop : -3.58 (0.10), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 6 611 TYR 0.049 0.003 TYR 6 559 PHE 0.048 0.003 PHE 6 570 TRP 0.022 0.002 TRP 2 554 HIS 0.011 0.002 HIS 2 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (38986) covalent geometry : angle 1.01467 / 0.53 (52778) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 1.29831 / 1.25 ( 2) hydrogen bonds : bond 0.06624 / 5.85 ( 926) hydrogen bonds : angle 7.95503 / 7.13 ( 2631) Misc. bond : bond 0.02216 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 924 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6535 (ptp90) cc_final: 0.6315 (ptt-90) REVERT: A 188 ARG cc_start: 0.9086 (ttt90) cc_final: 0.8078 (ptp-170) REVERT: A 229 ASN cc_start: 0.8370 (m110) cc_final: 0.8114 (m-40) REVERT: A 278 MET cc_start: 0.6477 (mmm) cc_final: 0.6276 (mmm) REVERT: A 326 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7376 (tp30) REVERT: A 380 TYR cc_start: 0.6977 (m-80) cc_final: 0.6598 (m-10) REVERT: A 429 ILE cc_start: 0.7794 (mm) cc_final: 0.7551 (mm) REVERT: A 442 GLN cc_start: 0.7907 (mp10) cc_final: 0.7482 (tp40) REVERT: H 69 PHE cc_start: 0.6756 (t80) cc_final: 0.6443 (t80) REVERT: H 106 ASP cc_start: 0.7474 (p0) cc_final: 0.7210 (p0) REVERT: L 47 TRP cc_start: 0.6873 (p-90) cc_final: 0.6452 (p-90) REVERT: L 69 ASP cc_start: 0.8805 (p0) cc_final: 0.8536 (p0) REVERT: L 105 ASP cc_start: 0.7882 (p0) cc_final: 0.7534 (p0) REVERT: L 123 ILE cc_start: 0.8702 (pt) cc_final: 0.8482 (pt) REVERT: L 136 ILE cc_start: 0.7573 (pt) cc_final: 0.6807 (pt) REVERT: L 141 THR cc_start: 0.6141 (p) cc_final: 0.5639 (m) REVERT: M 17 PHE cc_start: 0.5025 (t80) cc_final: 0.4577 (t80) REVERT: M 112 ASP cc_start: 0.8039 (p0) cc_final: 0.7645 (p0) REVERT: N 55 ILE cc_start: 0.4925 (tt) cc_final: 0.4670 (tt) REVERT: N 105 LEU cc_start: 0.8786 (mt) cc_final: 0.8204 (mt) REVERT: N 147 ASN cc_start: 0.7642 (p0) cc_final: 0.7416 (p0) REVERT: N 182 PHE cc_start: 0.6003 (m-80) cc_final: 0.5547 (m-80) REVERT: 2 240 MET cc_start: 0.7519 (mmm) cc_final: 0.6592 (mmm) REVERT: 2 278 GLU cc_start: 0.7384 (tp30) cc_final: 0.7041 (tp30) REVERT: 2 396 GLU cc_start: 0.6259 (pm20) cc_final: 0.5960 (pm20) REVERT: 2 703 TYR cc_start: 0.7316 (m-10) cc_final: 0.6981 (m-80) REVERT: 2 764 MET cc_start: 0.4756 (tpp) cc_final: 0.4341 (mmm) REVERT: 5 245 ASP cc_start: 0.6944 (p0) cc_final: 0.6559 (m-30) REVERT: 5 260 ILE cc_start: 0.9000 (pt) cc_final: 0.8555 (pt) REVERT: 5 261 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7309 (mm-40) REVERT: 5 291 ARG cc_start: 0.8337 (ptm-80) cc_final: 0.8085 (ptm160) REVERT: 5 292 VAL cc_start: 0.8670 (t) cc_final: 0.8461 (t) REVERT: 6 186 MET cc_start: 0.6382 (mtp) cc_final: 0.5603 (mmt) REVERT: 6 208 GLU cc_start: 0.8157 (tp30) cc_final: 0.7700 (tt0) REVERT: 6 317 MET cc_start: 0.1014 (tmm) cc_final: 0.0796 (tmm) REVERT: 6 399 LYS cc_start: 0.7873 (ptpp) cc_final: 0.7580 (ptpp) REVERT: 6 433 ASP cc_start: 0.6220 (t0) cc_final: 0.5878 (p0) REVERT: 6 506 LYS cc_start: 0.7885 (mmtp) cc_final: 0.7677 (mmtt) REVERT: 6 623 MET cc_start: 0.8471 (mtm) cc_final: 0.8250 (mtm) REVERT: 3 35 ASP cc_start: 0.6103 (m-30) cc_final: 0.5722 (m-30) REVERT: 3 201 MET cc_start: 0.7565 (tpt) cc_final: 0.7151 (mmm) REVERT: 3 572 MET cc_start: 0.7636 (mmp) cc_final: 0.7414 (mmm) REVERT: 3 573 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8135 (mtpp) REVERT: 4 380 ASP cc_start: 0.7016 (t0) cc_final: 0.6709 (t0) REVERT: 4 574 CYS cc_start: 0.7619 (m) cc_final: 0.6542 (m) REVERT: 4 578 PHE cc_start: 0.7167 (t80) cc_final: 0.6781 (t80) REVERT: 4 579 ASP cc_start: 0.8566 (t0) cc_final: 0.8259 (t0) REVERT: 7 20 PHE cc_start: 0.6551 (t80) cc_final: 0.6144 (t80) REVERT: 7 134 PHE cc_start: 0.8314 (p90) cc_final: 0.8044 (p90) REVERT: 7 232 PHE cc_start: 0.6666 (t80) cc_final: 0.6205 (t80) REVERT: 7 446 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7379 (mm-30) REVERT: 7 541 HIS cc_start: 0.7209 (m-70) cc_final: 0.6586 (m-70) REVERT: 7 550 ARG cc_start: 0.6869 (tpt170) cc_final: 0.6639 (tpp-160) REVERT: 7 605 ASN cc_start: 0.8585 (t0) cc_final: 0.8350 (t0) REVERT: 7 625 VAL cc_start: 0.8451 (t) cc_final: 0.7935 (t) outliers start: 27 outliers final: 12 residues processed: 946 average time/residue: 0.2478 time to fit residues: 373.2856 Evaluate side-chains 692 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 680 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 379 optimal weight: 6.9990 chunk 353 optimal weight: 0.0170 chunk 383 optimal weight: 4.9990 chunk 411 optimal weight: 7.9990 chunk 423 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 427 optimal weight: 4.9990 chunk 470 optimal weight: 8.9990 chunk 454 optimal weight: 0.8980 overall best weight: 1.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN L 27 HIS L 154 HIS L 171 GLN M 151 ASN N 170 GLN N 209 HIS 2 210 GLN 2 659 GLN 2 666 HIS ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 754 HIS 5 21 GLN ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 196 GLN 5 318 HIS ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 532 HIS ** 5 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN ** 6 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 584 HIS 3 7 GLN ** 3 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 260 ASN ** 3 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 605 GLN ** 3 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 228 GLN ** 4 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 746 HIS 7 196 ASN 7 266 GLN ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 543 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.190704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.172246 restraints weight = 140045.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.173100 restraints weight = 132044.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.174058 restraints weight = 107309.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.174379 restraints weight = 93178.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.174582 restraints weight = 87093.967| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 38999 Z= 0.226 Angle : 0.929 15.709 52780 Z= 0.485 Chirality : 0.051 0.283 5990 Planarity : 0.007 0.194 6735 Dihedral : 12.215 171.613 5460 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 15.40 % Favored : 84.58 % Rotamer: Outliers : 0.29 % Allowed : 6.40 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.15 % 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: -4.65 (0.10), residues: 4657 helix: -2.80 (0.11), residues: 1419 sheet: -3.12 (0.21), residues: 467 loop : -3.40 (0.11), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG 2 641 TYR 0.044 0.003 TYR 5 48 PHE 0.040 0.003 PHE 3 99 TRP 0.018 0.002 TRP 2 554 HIS 0.012 0.002 HIS 3 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (38986) covalent geometry : angle 0.92901 / 0.48 (52778) SS BOND : bond 0.00365 / 0.18 ( 1) SS BOND : angle 0.90229 / 0.93 ( 2) hydrogen bonds : bond 0.05976 / 5.45 ( 926) hydrogen bonds : angle 7.44975 / 6.70 ( 2631) Misc. bond : bond 0.01661 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 852 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.5517 (mmt) cc_final: 0.5047 (mmt) REVERT: A 188 ARG cc_start: 0.9072 (ttt90) cc_final: 0.8046 (mpt180) REVERT: A 217 MET cc_start: 0.8010 (mpp) cc_final: 0.7629 (pmm) REVERT: A 229 ASN cc_start: 0.8547 (m110) cc_final: 0.8009 (m-40) REVERT: A 231 ASP cc_start: 0.8539 (p0) cc_final: 0.8326 (p0) REVERT: A 326 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7583 (tp30) REVERT: A 380 TYR cc_start: 0.7179 (m-80) cc_final: 0.6939 (m-10) REVERT: A 430 ASP cc_start: 0.7629 (m-30) cc_final: 0.7391 (m-30) REVERT: A 442 GLN cc_start: 0.7986 (mp10) cc_final: 0.7602 (tt0) REVERT: A 483 LEU cc_start: 0.8732 (mt) cc_final: 0.8443 (mt) REVERT: H 106 ASP cc_start: 0.7428 (p0) cc_final: 0.7208 (p0) REVERT: L 46 LEU cc_start: 0.8142 (mm) cc_final: 0.7891 (mm) REVERT: L 106 ASP cc_start: 0.7913 (m-30) cc_final: 0.7683 (p0) REVERT: L 136 ILE cc_start: 0.7791 (pt) cc_final: 0.7275 (pt) REVERT: M 57 TRP cc_start: 0.7870 (p-90) cc_final: 0.7507 (p-90) REVERT: M 112 ASP cc_start: 0.8226 (p0) cc_final: 0.7935 (p0) REVERT: N 92 MET cc_start: 0.7693 (mmp) cc_final: 0.7241 (mmp) REVERT: N 202 ASP cc_start: 0.8279 (t0) cc_final: 0.7953 (t70) REVERT: 2 195 ARG cc_start: 0.8194 (mpp80) cc_final: 0.7821 (ptt-90) REVERT: 2 240 MET cc_start: 0.7762 (mmm) cc_final: 0.7238 (mmm) REVERT: 2 261 ARG cc_start: 0.5223 (ptt180) cc_final: 0.4472 (ptm-80) REVERT: 2 466 MET cc_start: 0.4318 (tmm) cc_final: 0.3749 (tmm) REVERT: 2 764 MET cc_start: 0.4683 (tpp) cc_final: 0.4000 (mmm) REVERT: 5 62 ARG cc_start: 0.8805 (mmm160) cc_final: 0.8534 (mmt90) REVERT: 5 261 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7497 (mm-40) REVERT: 5 292 VAL cc_start: 0.8833 (t) cc_final: 0.8522 (t) REVERT: 5 513 MET cc_start: 0.1441 (tpp) cc_final: 0.0727 (tpt) REVERT: 6 151 MET cc_start: -0.1576 (tmm) cc_final: -0.1781 (tmm) REVERT: 6 208 GLU cc_start: 0.7910 (tp30) cc_final: 0.7547 (pt0) REVERT: 6 220 ILE cc_start: 0.8459 (tt) cc_final: 0.8187 (tt) REVERT: 6 286 TYR cc_start: 0.7074 (m-80) cc_final: 0.6810 (m-80) REVERT: 6 317 MET cc_start: 0.0648 (tmm) cc_final: 0.0415 (tmm) REVERT: 6 383 ASN cc_start: 0.6619 (m110) cc_final: 0.6360 (m110) REVERT: 6 399 LYS cc_start: 0.7958 (ptpp) cc_final: 0.7632 (ptpp) REVERT: 6 454 PHE cc_start: 0.7373 (m-80) cc_final: 0.6681 (m-80) REVERT: 6 469 MET cc_start: 0.6904 (tpp) cc_final: 0.5782 (tpp) REVERT: 6 623 MET cc_start: 0.8596 (mtm) cc_final: 0.7730 (mtm) REVERT: 3 35 ASP cc_start: 0.6535 (m-30) cc_final: 0.5931 (m-30) REVERT: 3 421 MET cc_start: 0.8150 (mmm) cc_final: 0.7816 (mmm) REVERT: 3 572 MET cc_start: 0.7970 (mmp) cc_final: 0.7301 (mmm) REVERT: 4 574 CYS cc_start: 0.7625 (m) cc_final: 0.6467 (m) REVERT: 4 578 PHE cc_start: 0.7198 (t80) cc_final: 0.6805 (t80) REVERT: 4 649 ILE cc_start: 0.6331 (mp) cc_final: 0.5948 (pt) REVERT: 4 683 MET cc_start: 0.5704 (tpt) cc_final: 0.4994 (tpp) REVERT: 4 698 GLU cc_start: 0.7742 (mp0) cc_final: 0.7413 (mp0) REVERT: 7 20 PHE cc_start: 0.7143 (t80) cc_final: 0.6609 (t80) REVERT: 7 174 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7796 (tppt) REVERT: 7 176 MET cc_start: 0.6974 (ttp) cc_final: 0.6370 (tmm) REVERT: 7 234 GLU cc_start: 0.6335 (mp0) cc_final: 0.5983 (mp0) REVERT: 7 253 MET cc_start: 0.5054 (ptt) cc_final: 0.4509 (ptt) REVERT: 7 396 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7818 (mtp180) REVERT: 7 397 LEU cc_start: 0.7956 (tp) cc_final: 0.7660 (tp) REVERT: 7 400 ARG cc_start: 0.7328 (tpp-160) cc_final: 0.6907 (tpp-160) REVERT: 7 541 HIS cc_start: 0.7234 (m-70) cc_final: 0.6763 (m-70) REVERT: 7 550 ARG cc_start: 0.6789 (tpt170) cc_final: 0.6511 (tpp-160) REVERT: 7 590 ARG cc_start: 0.8717 (ptt90) cc_final: 0.7588 (tpt90) REVERT: 7 625 VAL cc_start: 0.8461 (t) cc_final: 0.8035 (t) outliers start: 12 outliers final: 4 residues processed: 861 average time/residue: 0.2397 time to fit residues: 331.0893 Evaluate side-chains 667 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 663 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 337 optimal weight: 0.0770 chunk 207 optimal weight: 10.0000 chunk 442 optimal weight: 0.5980 chunk 359 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 17 optimal weight: 0.0870 chunk 449 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 290 optimal weight: 0.0980 chunk 400 optimal weight: 0.8980 chunk 299 optimal weight: 0.7980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 537 GLN H 36 GLN H 71 HIS H 120 ASN H 146 ASN ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 171 GLN M 127 GLN 2 659 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 117 HIS ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 134 GLN 5 193 ASN ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 HIS 5 568 HIS ** 6 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN ** 6 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 70 GLN ** 3 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 348 GLN ** 3 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN 3 567 HIS 3 594 GLN ** 3 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 193 GLN ** 4 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 196 ASN 7 439 GLN 7 465 GLN ** 7 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 605 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.192943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.174560 restraints weight = 132410.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.175843 restraints weight = 119124.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.176375 restraints weight = 93236.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.176732 restraints weight = 84593.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.176988 restraints weight = 78681.807| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 38999 Z= 0.172 Angle : 0.882 15.831 52780 Z= 0.453 Chirality : 0.050 0.286 5990 Planarity : 0.008 0.433 6735 Dihedral : 12.049 168.365 5460 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.04 % Favored : 85.94 % Rotamer: Outliers : 0.29 % Allowed : 5.18 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.11 % 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: -4.37 (0.11), residues: 4657 helix: -2.55 (0.12), residues: 1416 sheet: -2.96 (0.20), residues: 507 loop : -3.21 (0.11), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG 6 521 TYR 0.039 0.003 TYR 6 559 PHE 0.044 0.003 PHE 5 94 TRP 0.035 0.002 TRP 4 626 HIS 0.018 0.001 HIS 4 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (38986) covalent geometry : angle 0.88234 / 0.45 (52778) SS BOND : bond 0.01294 / 0.65 ( 1) SS BOND : angle 2.12232 / 2.74 ( 2) hydrogen bonds : bond 0.05234 / 4.72 ( 926) hydrogen bonds : angle 7.06924 / 6.28 ( 2631) Misc. bond : bond 0.00922 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 871 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.9072 (ttt90) cc_final: 0.8057 (mpt180) REVERT: A 229 ASN cc_start: 0.8431 (m110) cc_final: 0.7627 (m-40) REVERT: A 230 MET cc_start: 0.6985 (pmm) cc_final: 0.6015 (ptt) REVERT: A 231 ASP cc_start: 0.8309 (p0) cc_final: 0.7972 (p0) REVERT: A 442 GLN cc_start: 0.7806 (mp10) cc_final: 0.7411 (tt0) REVERT: H 97 TRP cc_start: 0.4808 (m100) cc_final: 0.4342 (m100) REVERT: H 106 ASP cc_start: 0.7327 (p0) cc_final: 0.7092 (p0) REVERT: L 4 SER cc_start: 0.8967 (p) cc_final: 0.8736 (p) REVERT: L 64 GLU cc_start: 0.7323 (pm20) cc_final: 0.6869 (pm20) REVERT: L 136 ILE cc_start: 0.7693 (pt) cc_final: 0.7299 (pt) REVERT: L 154 HIS cc_start: 0.5423 (p-80) cc_final: 0.5197 (p-80) REVERT: M 54 LEU cc_start: 0.7095 (mt) cc_final: 0.6783 (mt) REVERT: M 112 ASP cc_start: 0.8089 (p0) cc_final: 0.7770 (p0) REVERT: N 91 SER cc_start: 0.9216 (m) cc_final: 0.8877 (p) REVERT: N 147 ASN cc_start: 0.7764 (p0) cc_final: 0.7438 (p0) REVERT: N 159 TYR cc_start: 0.5577 (t80) cc_final: 0.5301 (t80) REVERT: 2 240 MET cc_start: 0.7343 (mmm) cc_final: 0.6757 (mmm) REVERT: 2 358 TYR cc_start: 0.6471 (t80) cc_final: 0.6227 (t80) REVERT: 2 466 MET cc_start: 0.4153 (tmm) cc_final: 0.3588 (tmm) REVERT: 2 764 MET cc_start: 0.4658 (tpp) cc_final: 0.4009 (mmm) REVERT: 5 261 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7283 (mm-40) REVERT: 5 513 MET cc_start: 0.1435 (tpp) cc_final: 0.0969 (tpt) REVERT: 6 186 MET cc_start: 0.6455 (mmm) cc_final: 0.5819 (mmt) REVERT: 6 211 ARG cc_start: 0.6332 (tpp80) cc_final: 0.5873 (tpt170) REVERT: 6 286 TYR cc_start: 0.6983 (m-80) cc_final: 0.6760 (m-80) REVERT: 6 327 HIS cc_start: 0.8096 (m170) cc_final: 0.7886 (m170) REVERT: 6 332 MET cc_start: 0.6629 (mtm) cc_final: 0.6425 (mpp) REVERT: 6 454 PHE cc_start: 0.7371 (m-80) cc_final: 0.6548 (m-80) REVERT: 6 469 MET cc_start: 0.5591 (tpp) cc_final: 0.5008 (tpp) REVERT: 6 613 LEU cc_start: 0.7834 (mt) cc_final: 0.7468 (mt) REVERT: 6 623 MET cc_start: 0.8511 (mtm) cc_final: 0.7678 (mtm) REVERT: 3 35 ASP cc_start: 0.6149 (m-30) cc_final: 0.5743 (m-30) REVERT: 3 292 GLU cc_start: 0.8666 (tp30) cc_final: 0.8283 (tt0) REVERT: 3 348 GLN cc_start: 0.5212 (OUTLIER) cc_final: 0.4929 (tm-30) REVERT: 3 409 MET cc_start: 0.4535 (tpt) cc_final: 0.4242 (tpp) REVERT: 3 417 ILE cc_start: 0.8810 (mt) cc_final: 0.8544 (mt) REVERT: 3 421 MET cc_start: 0.8015 (mmm) cc_final: 0.7661 (mmp) REVERT: 3 473 ARG cc_start: 0.7328 (mmm160) cc_final: 0.6980 (mmp-170) REVERT: 4 274 MET cc_start: 0.6117 (tmm) cc_final: 0.5892 (tmm) REVERT: 4 302 MET cc_start: 0.6015 (tpp) cc_final: 0.5515 (tpp) REVERT: 4 390 ARG cc_start: 0.6558 (mtm180) cc_final: 0.5324 (mmm160) REVERT: 4 476 ASP cc_start: 0.8215 (m-30) cc_final: 0.8007 (m-30) REVERT: 4 574 CYS cc_start: 0.7710 (m) cc_final: 0.6482 (m) REVERT: 4 578 PHE cc_start: 0.7224 (t80) cc_final: 0.7012 (t80) REVERT: 4 683 MET cc_start: 0.6031 (tpt) cc_final: 0.5188 (tpp) REVERT: 7 64 GLU cc_start: 0.6982 (mp0) cc_final: 0.6599 (mm-30) REVERT: 7 176 MET cc_start: 0.6694 (ttp) cc_final: 0.6077 (tmm) REVERT: 7 234 GLU cc_start: 0.6254 (mp0) cc_final: 0.6044 (mp0) REVERT: 7 340 LEU cc_start: 0.8471 (tp) cc_final: 0.8180 (tp) REVERT: 7 369 MET cc_start: 0.6288 (ptp) cc_final: 0.6058 (ptp) REVERT: 7 380 MET cc_start: 0.8052 (tmm) cc_final: 0.7773 (tmm) REVERT: 7 393 TYR cc_start: 0.7795 (t80) cc_final: 0.7576 (t80) REVERT: 7 400 ARG cc_start: 0.7161 (tpp-160) cc_final: 0.6916 (tpp-160) REVERT: 7 541 HIS cc_start: 0.7391 (m-70) cc_final: 0.6581 (m-70) REVERT: 7 605 ASN cc_start: 0.8232 (m110) cc_final: 0.7939 (m110) REVERT: 7 625 VAL cc_start: 0.8301 (t) cc_final: 0.7863 (t) outliers start: 12 outliers final: 3 residues processed: 878 average time/residue: 0.2418 time to fit residues: 340.0402 Evaluate side-chains 686 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 682 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 277 optimal weight: 6.9990 chunk 397 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 350 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 433 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 GLN ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS N 170 GLN N 209 HIS ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 60 ASN ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS 5 386 GLN ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 HIS 6 67 GLN ** 6 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 GLN 6 198 GLN 6 353 ASN 6 472 GLN 3 70 GLN 3 107 HIS 3 120 ASN ** 3 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 594 GLN ** 3 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 156 HIS 7 196 ASN ** 7 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 543 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.188442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.169453 restraints weight = 133845.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.170780 restraints weight = 116690.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.171739 restraints weight = 91753.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.172092 restraints weight = 79784.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.172300 restraints weight = 75526.693| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 38999 Z= 0.195 Angle : 0.856 11.223 52780 Z= 0.444 Chirality : 0.050 0.298 5990 Planarity : 0.007 0.145 6735 Dihedral : 11.785 173.443 5460 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.67 % Favored : 85.31 % Rotamer: Outliers : 0.17 % Allowed : 4.05 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.23 (0.11), residues: 4657 helix: -2.39 (0.12), residues: 1410 sheet: -2.96 (0.20), residues: 515 loop : -3.13 (0.11), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 499 TYR 0.041 0.003 TYR 7 102 PHE 0.038 0.002 PHE 4 487 TRP 0.052 0.003 TRP M 57 HIS 0.012 0.002 HIS H 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (38986) covalent geometry : angle 0.85547 / 0.44 (52778) SS BOND : bond 0.00500 / 0.25 ( 1) SS BOND : angle 1.54867 / 2.08 ( 2) hydrogen bonds : bond 0.05073 / 4.68 ( 926) hydrogen bonds : angle 6.86527 / 6.12 ( 2631) Misc. bond : bond 0.00609 / 0.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 817 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.9048 (ttt90) cc_final: 0.8046 (mpt180) REVERT: A 229 ASN cc_start: 0.8277 (m110) cc_final: 0.7896 (m110) REVERT: A 231 ASP cc_start: 0.8584 (p0) cc_final: 0.8268 (p0) REVERT: A 380 TYR cc_start: 0.6517 (m-10) cc_final: 0.6257 (m-10) REVERT: A 442 GLN cc_start: 0.7793 (mp10) cc_final: 0.7549 (tt0) REVERT: A 482 PHE cc_start: 0.7531 (m-80) cc_final: 0.7287 (m-80) REVERT: A 540 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: H 69 PHE cc_start: 0.6830 (t80) cc_final: 0.5971 (t80) REVERT: H 97 TRP cc_start: 0.4952 (m100) cc_final: 0.4686 (m100) REVERT: H 106 ASP cc_start: 0.7434 (p0) cc_final: 0.7213 (p0) REVERT: H 160 MET cc_start: 0.6945 (ttp) cc_final: 0.6438 (tpp) REVERT: L 64 GLU cc_start: 0.7548 (pm20) cc_final: 0.6966 (pm20) REVERT: L 77 GLU cc_start: 0.7668 (pt0) cc_final: 0.7361 (pt0) REVERT: M 57 TRP cc_start: 0.7409 (p-90) cc_final: 0.6887 (p-90) REVERT: M 112 ASP cc_start: 0.7987 (p0) cc_final: 0.7676 (p0) REVERT: 2 240 MET cc_start: 0.7634 (mmm) cc_final: 0.7114 (mmm) REVERT: 2 358 TYR cc_start: 0.6500 (t80) cc_final: 0.6274 (t80) REVERT: 2 466 MET cc_start: 0.4606 (tmm) cc_final: 0.3629 (tmm) REVERT: 2 757 MET cc_start: 0.9079 (mpp) cc_final: 0.8828 (mpp) REVERT: 2 764 MET cc_start: 0.6038 (tpp) cc_final: 0.5401 (mmm) REVERT: 2 774 MET cc_start: 0.5494 (mmm) cc_final: 0.5035 (mmt) REVERT: 5 447 MET cc_start: 0.5214 (mmp) cc_final: 0.4488 (mmm) REVERT: 5 513 MET cc_start: 0.1973 (tpp) cc_final: 0.1665 (tpt) REVERT: 6 220 ILE cc_start: 0.8351 (tt) cc_final: 0.8118 (tt) REVERT: 6 317 MET cc_start: 0.0490 (tmm) cc_final: 0.0075 (ppp) REVERT: 6 363 GLN cc_start: 0.7566 (tt0) cc_final: 0.7304 (tt0) REVERT: 6 454 PHE cc_start: 0.7725 (m-80) cc_final: 0.7425 (m-80) REVERT: 6 469 MET cc_start: 0.6025 (tpp) cc_final: 0.4982 (tpp) REVERT: 6 613 LEU cc_start: 0.7825 (mt) cc_final: 0.7533 (mt) REVERT: 6 623 MET cc_start: 0.8582 (mtm) cc_final: 0.7710 (mtm) REVERT: 3 35 ASP cc_start: 0.6264 (m-30) cc_final: 0.5736 (m-30) REVERT: 3 292 GLU cc_start: 0.8713 (tp30) cc_final: 0.8317 (mm-30) REVERT: 3 627 MET cc_start: 0.6633 (mmp) cc_final: 0.5699 (mmt) REVERT: 4 228 GLN cc_start: 0.8264 (mm110) cc_final: 0.7604 (tp40) REVERT: 4 274 MET cc_start: 0.5986 (tmm) cc_final: 0.5568 (tmm) REVERT: 4 302 MET cc_start: 0.6098 (tpp) cc_final: 0.5667 (tpp) REVERT: 4 374 LEU cc_start: 0.7867 (pt) cc_final: 0.7581 (pt) REVERT: 4 390 ARG cc_start: 0.6474 (mtm180) cc_final: 0.5392 (mmm160) REVERT: 4 526 PHE cc_start: 0.8695 (p90) cc_final: 0.8222 (p90) REVERT: 4 574 CYS cc_start: 0.7532 (m) cc_final: 0.6470 (m) REVERT: 4 683 MET cc_start: 0.5939 (tpt) cc_final: 0.5158 (tpp) REVERT: 4 698 GLU cc_start: 0.7689 (mp0) cc_final: 0.7386 (mp0) REVERT: 4 736 LEU cc_start: 0.8072 (pp) cc_final: 0.7613 (pp) REVERT: 7 20 PHE cc_start: 0.6683 (t80) cc_final: 0.4765 (t80) REVERT: 7 64 GLU cc_start: 0.7002 (mp0) cc_final: 0.6528 (mp0) REVERT: 7 134 PHE cc_start: 0.8293 (p90) cc_final: 0.7919 (p90) REVERT: 7 176 MET cc_start: 0.6646 (ttp) cc_final: 0.6312 (tmm) REVERT: 7 397 LEU cc_start: 0.7750 (tp) cc_final: 0.7525 (tp) REVERT: 7 400 ARG cc_start: 0.7120 (tpp-160) cc_final: 0.6914 (tpp-160) REVERT: 7 541 HIS cc_start: 0.7290 (m-70) cc_final: 0.6697 (m-70) REVERT: 7 590 ARG cc_start: 0.8688 (ptt90) cc_final: 0.7542 (tpt90) REVERT: 7 605 ASN cc_start: 0.8224 (m110) cc_final: 0.7891 (m110) outliers start: 7 outliers final: 2 residues processed: 822 average time/residue: 0.2402 time to fit residues: 317.8113 Evaluate side-chains 647 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 644 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 161 optimal weight: 7.9990 chunk 256 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 269 optimal weight: 0.2980 chunk 376 optimal weight: 0.9990 chunk 360 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 199 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 241 GLN ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 HIS 5 635 HIS ** 6 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN 6 472 GLN 3 70 GLN 3 107 HIS 3 120 ASN ** 3 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 594 GLN ** 3 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 465 GLN ** 7 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 543 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.188688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.170019 restraints weight = 133140.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.171538 restraints weight = 114401.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.172219 restraints weight = 90063.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.172712 restraints weight = 80406.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.172769 restraints weight = 74685.528| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 38999 Z= 0.174 Angle : 0.850 23.488 52780 Z= 0.438 Chirality : 0.049 0.373 5990 Planarity : 0.007 0.239 6735 Dihedral : 11.743 175.882 5460 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.26 % Favored : 85.70 % Rotamer: Outliers : 0.15 % Allowed : 3.83 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.10 (0.11), residues: 4657 helix: -2.24 (0.12), residues: 1423 sheet: -2.80 (0.21), residues: 505 loop : -3.09 (0.11), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 2 756 TYR 0.027 0.002 TYR 6 559 PHE 0.035 0.002 PHE 4 487 TRP 0.026 0.002 TRP M 57 HIS 0.014 0.001 HIS 5 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (38986) covalent geometry : angle 0.85004 / 0.44 (52778) SS BOND : bond 0.01078 / 0.54 ( 1) SS BOND : angle 1.33115 / 2.52 ( 2) hydrogen bonds : bond 0.04880 / 4.48 ( 926) hydrogen bonds : angle 6.71535 / 5.94 ( 2631) Misc. bond : bond 0.00322 / 0.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 789 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.9040 (ttt90) cc_final: 0.8093 (mpt180) REVERT: A 229 ASN cc_start: 0.8114 (m110) cc_final: 0.7731 (m110) REVERT: A 231 ASP cc_start: 0.8486 (p0) cc_final: 0.8099 (p0) REVERT: A 442 GLN cc_start: 0.7737 (mp10) cc_final: 0.7493 (tt0) REVERT: H 69 PHE cc_start: 0.6660 (t80) cc_final: 0.6006 (t80) REVERT: H 160 MET cc_start: 0.6798 (ttp) cc_final: 0.6285 (tpp) REVERT: L 64 GLU cc_start: 0.7359 (pm20) cc_final: 0.6793 (pm20) REVERT: L 77 GLU cc_start: 0.7726 (pt0) cc_final: 0.7402 (pt0) REVERT: L 129 ARG cc_start: 0.6497 (ptp90) cc_final: 0.6281 (ptp90) REVERT: L 136 ILE cc_start: 0.7765 (pt) cc_final: 0.7546 (pt) REVERT: M 57 TRP cc_start: 0.7379 (p-90) cc_final: 0.6744 (p-90) REVERT: M 112 ASP cc_start: 0.7792 (p0) cc_final: 0.7538 (p0) REVERT: 2 240 MET cc_start: 0.7514 (mmm) cc_final: 0.6997 (mmm) REVERT: 2 358 TYR cc_start: 0.6418 (t80) cc_final: 0.6118 (t80) REVERT: 2 466 MET cc_start: 0.4634 (tmm) cc_final: 0.3652 (tmm) REVERT: 2 660 LEU cc_start: 0.6762 (pt) cc_final: 0.6443 (pp) REVERT: 2 669 MET cc_start: 0.7853 (tpp) cc_final: 0.7630 (tpp) REVERT: 2 764 MET cc_start: 0.6110 (tpp) cc_final: 0.5495 (mmm) REVERT: 5 261 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7627 (mm110) REVERT: 5 300 GLU cc_start: 0.7687 (tp30) cc_final: 0.7329 (pm20) REVERT: 5 447 MET cc_start: 0.5587 (mmp) cc_final: 0.4732 (mmm) REVERT: 5 513 MET cc_start: 0.2029 (tpp) cc_final: 0.1713 (tpt) REVERT: 6 220 ILE cc_start: 0.8238 (tt) cc_final: 0.7963 (tt) REVERT: 6 222 LEU cc_start: 0.8055 (pt) cc_final: 0.7837 (pp) REVERT: 6 454 PHE cc_start: 0.7632 (m-80) cc_final: 0.7392 (m-80) REVERT: 6 467 GLU cc_start: 0.6906 (pm20) cc_final: 0.6702 (pm20) REVERT: 6 519 MET cc_start: 0.8224 (mpp) cc_final: 0.7983 (mpp) REVERT: 6 613 LEU cc_start: 0.7825 (mt) cc_final: 0.7487 (mt) REVERT: 6 623 MET cc_start: 0.8586 (mtm) cc_final: 0.7831 (mtm) REVERT: 3 35 ASP cc_start: 0.6281 (m-30) cc_final: 0.5885 (m-30) REVERT: 3 292 GLU cc_start: 0.8754 (tp30) cc_final: 0.8402 (mm-30) REVERT: 3 409 MET cc_start: 0.2463 (tpp) cc_final: 0.0762 (ptt) REVERT: 3 417 ILE cc_start: 0.8814 (mt) cc_final: 0.8572 (mt) REVERT: 3 421 MET cc_start: 0.7965 (mmm) cc_final: 0.7506 (mmm) REVERT: 3 423 GLN cc_start: 0.8561 (tt0) cc_final: 0.8342 (tt0) REVERT: 3 572 MET cc_start: 0.7700 (mmm) cc_final: 0.6125 (mtt) REVERT: 3 627 MET cc_start: 0.6065 (mmp) cc_final: 0.4412 (mmt) REVERT: 4 228 GLN cc_start: 0.8197 (mm110) cc_final: 0.7611 (tp40) REVERT: 4 302 MET cc_start: 0.5976 (tpp) cc_final: 0.5363 (tpp) REVERT: 4 374 LEU cc_start: 0.7733 (pt) cc_final: 0.7499 (pt) REVERT: 4 390 ARG cc_start: 0.6448 (mtm180) cc_final: 0.5424 (mmp-170) REVERT: 4 476 ASP cc_start: 0.8053 (m-30) cc_final: 0.7848 (m-30) REVERT: 4 526 PHE cc_start: 0.8459 (p90) cc_final: 0.8205 (p90) REVERT: 4 574 CYS cc_start: 0.7476 (m) cc_final: 0.6555 (m) REVERT: 4 683 MET cc_start: 0.6023 (tpt) cc_final: 0.5191 (tpp) REVERT: 7 64 GLU cc_start: 0.6954 (mp0) cc_final: 0.6523 (mp0) REVERT: 7 134 PHE cc_start: 0.8109 (p90) cc_final: 0.7732 (p90) REVERT: 7 176 MET cc_start: 0.6337 (ttp) cc_final: 0.6127 (tmm) REVERT: 7 380 MET cc_start: 0.8346 (tmm) cc_final: 0.8027 (tmm) REVERT: 7 541 HIS cc_start: 0.7260 (m-70) cc_final: 0.6666 (m-70) REVERT: 7 590 ARG cc_start: 0.8482 (ptt90) cc_final: 0.7485 (tpt90) outliers start: 6 outliers final: 3 residues processed: 793 average time/residue: 0.2406 time to fit residues: 309.4006 Evaluate side-chains 643 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 640 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 165 optimal weight: 10.0000 chunk 346 optimal weight: 4.9990 chunk 187 optimal weight: 0.0770 chunk 116 optimal weight: 1.9990 chunk 430 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 285 optimal weight: 0.3980 chunk 401 optimal weight: 7.9990 chunk 286 optimal weight: 0.3980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 HIS L 97 GLN M 127 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 783 GLN ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 HIS 6 26 GLN 6 139 HIS 6 198 GLN 3 70 GLN 3 120 ASN ** 3 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 223 GLN ** 4 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 374 ASN 7 464 GLN ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 503 GLN 7 543 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.190796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.172047 restraints weight = 132112.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.173331 restraints weight = 110751.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.173539 restraints weight = 91503.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.174021 restraints weight = 83845.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.174217 restraints weight = 79682.185| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 38999 Z= 0.157 Angle : 0.834 19.348 52780 Z= 0.426 Chirality : 0.049 0.388 5990 Planarity : 0.007 0.300 6735 Dihedral : 11.694 178.195 5460 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.79 % Favored : 86.19 % Rotamer: Outliers : 0.12 % Allowed : 2.78 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.96 (0.11), residues: 4657 helix: -2.13 (0.12), residues: 1423 sheet: -2.64 (0.21), residues: 492 loop : -3.03 (0.11), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 2 742 TYR 0.038 0.002 TYR N 159 PHE 0.030 0.002 PHE 4 487 TRP 0.023 0.002 TRP L 47 HIS 0.008 0.001 HIS 5 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (38986) covalent geometry : angle 0.83389 / 0.43 (52778) SS BOND : bond 0.00364 / 0.18 ( 1) SS BOND : angle 1.28429 / 2.56 ( 2) hydrogen bonds : bond 0.04568 / 4.22 ( 926) hydrogen bonds : angle 6.56280 / 5.77 ( 2631) Misc. bond : bond 0.00849 / 0.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 793 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.5317 (mmt) cc_final: 0.4871 (mmm) REVERT: A 73 VAL cc_start: 0.8548 (t) cc_final: 0.7749 (t) REVERT: A 229 ASN cc_start: 0.8197 (m110) cc_final: 0.7882 (m110) REVERT: A 231 ASP cc_start: 0.8430 (p0) cc_final: 0.7985 (p0) REVERT: A 351 LYS cc_start: 0.8260 (mtmm) cc_final: 0.8053 (mttm) REVERT: A 442 GLN cc_start: 0.7679 (mp10) cc_final: 0.7461 (tt0) REVERT: H 69 PHE cc_start: 0.6700 (t80) cc_final: 0.6292 (t80) REVERT: H 97 TRP cc_start: 0.4694 (m100) cc_final: 0.4262 (m100) REVERT: H 160 MET cc_start: 0.6836 (ttp) cc_final: 0.6184 (tpp) REVERT: L 51 HIS cc_start: 0.7051 (m90) cc_final: 0.6448 (m90) REVERT: L 64 GLU cc_start: 0.7545 (pm20) cc_final: 0.6921 (pm20) REVERT: L 77 GLU cc_start: 0.7811 (pt0) cc_final: 0.7467 (pt0) REVERT: M 57 TRP cc_start: 0.7338 (p-90) cc_final: 0.6767 (p-90) REVERT: M 112 ASP cc_start: 0.7855 (p0) cc_final: 0.7614 (p0) REVERT: N 88 VAL cc_start: 0.9057 (t) cc_final: 0.8789 (t) REVERT: N 92 MET cc_start: 0.7972 (ptm) cc_final: 0.6981 (ttm) REVERT: N 98 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7541 (tpp80) REVERT: 2 240 MET cc_start: 0.7571 (mmm) cc_final: 0.7128 (mmm) REVERT: 2 358 TYR cc_start: 0.6419 (t80) cc_final: 0.6066 (t80) REVERT: 2 466 MET cc_start: 0.4032 (tmm) cc_final: 0.3678 (tmm) REVERT: 2 764 MET cc_start: 0.5995 (tpp) cc_final: 0.5488 (mmm) REVERT: 5 69 MET cc_start: 0.4409 (ptt) cc_final: 0.3938 (tmm) REVERT: 5 261 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7291 (mp10) REVERT: 5 447 MET cc_start: 0.5334 (mmp) cc_final: 0.4909 (mmm) REVERT: 5 513 MET cc_start: 0.1890 (tpp) cc_final: 0.1626 (tpt) REVERT: 6 222 LEU cc_start: 0.8061 (pt) cc_final: 0.7814 (pp) REVERT: 6 317 MET cc_start: 0.0362 (tmm) cc_final: 0.0080 (tmm) REVERT: 6 454 PHE cc_start: 0.7629 (m-80) cc_final: 0.7344 (m-80) REVERT: 6 469 MET cc_start: 0.5758 (tpp) cc_final: 0.5447 (tpp) REVERT: 6 519 MET cc_start: 0.8399 (mpp) cc_final: 0.8178 (mpp) REVERT: 6 613 LEU cc_start: 0.7667 (mt) cc_final: 0.7403 (mt) REVERT: 6 623 MET cc_start: 0.8661 (mtm) cc_final: 0.7844 (mtm) REVERT: 3 16 TYR cc_start: 0.6938 (m-80) cc_final: 0.6670 (m-80) REVERT: 3 35 ASP cc_start: 0.6339 (m-30) cc_final: 0.5931 (m-30) REVERT: 3 409 MET cc_start: 0.2174 (tpp) cc_final: 0.0796 (ptt) REVERT: 3 417 ILE cc_start: 0.8899 (mt) cc_final: 0.8662 (mt) REVERT: 3 423 GLN cc_start: 0.8647 (tt0) cc_final: 0.8420 (tt0) REVERT: 3 572 MET cc_start: 0.7804 (mmm) cc_final: 0.6396 (mtt) REVERT: 3 627 MET cc_start: 0.6300 (mmp) cc_final: 0.5024 (mmt) REVERT: 4 274 MET cc_start: 0.5940 (tmm) cc_final: 0.5533 (tmm) REVERT: 4 286 ILE cc_start: 0.9246 (mp) cc_final: 0.9024 (mm) REVERT: 4 302 MET cc_start: 0.5849 (tpp) cc_final: 0.5167 (tpp) REVERT: 4 374 LEU cc_start: 0.7917 (pt) cc_final: 0.7644 (pt) REVERT: 4 476 ASP cc_start: 0.8098 (m-30) cc_final: 0.7803 (m-30) REVERT: 4 526 PHE cc_start: 0.8508 (p90) cc_final: 0.8044 (p90) REVERT: 4 574 CYS cc_start: 0.7713 (m) cc_final: 0.6470 (m) REVERT: 4 683 MET cc_start: 0.5951 (tpt) cc_final: 0.5168 (tpp) REVERT: 7 64 GLU cc_start: 0.7259 (mp0) cc_final: 0.6748 (mp0) REVERT: 7 134 PHE cc_start: 0.8211 (p90) cc_final: 0.7824 (p90) REVERT: 7 174 LYS cc_start: 0.8088 (tptm) cc_final: 0.7854 (mmmm) REVERT: 7 176 MET cc_start: 0.6514 (ttp) cc_final: 0.6115 (tmm) REVERT: 7 380 MET cc_start: 0.8358 (tmm) cc_final: 0.8122 (tmm) REVERT: 7 391 LEU cc_start: 0.8998 (mm) cc_final: 0.8483 (mm) REVERT: 7 541 HIS cc_start: 0.7177 (m-70) cc_final: 0.6584 (m-70) REVERT: 7 590 ARG cc_start: 0.8610 (ptt90) cc_final: 0.7744 (tpt90) REVERT: 7 625 VAL cc_start: 0.8340 (t) cc_final: 0.7982 (t) outliers start: 5 outliers final: 2 residues processed: 796 average time/residue: 0.2426 time to fit residues: 313.8251 Evaluate side-chains 628 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 626 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 248 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 303 optimal weight: 0.9980 chunk 413 optimal weight: 2.9990 chunk 262 optimal weight: 0.0060 chunk 204 optimal weight: 0.8980 chunk 419 optimal weight: 0.0170 chunk 352 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 437 optimal weight: 4.9990 chunk 299 optimal weight: 1.9990 overall best weight: 0.5634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 GLN N 170 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS 5 461 GLN 5 537 HIS 5 568 HIS ** 5 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN 6 472 GLN 3 70 GLN 3 120 ASN ** 3 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 434 HIS 3 467 GLN ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 193 GLN 4 259 HIS ** 4 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 523 GLN ** 7 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 439 GLN 7 464 GLN ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 503 GLN 7 543 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.191738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.172419 restraints weight = 129338.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.173487 restraints weight = 110776.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.174645 restraints weight = 88806.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.174940 restraints weight = 76108.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.175365 restraints weight = 73084.697| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 38999 Z= 0.151 Angle : 0.821 12.677 52780 Z= 0.420 Chirality : 0.049 0.470 5990 Planarity : 0.006 0.107 6735 Dihedral : 11.637 179.455 5460 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.29 % Favored : 86.67 % Rotamer: Outliers : 0.12 % Allowed : 2.03 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.87 (0.11), residues: 4657 helix: -2.02 (0.12), residues: 1412 sheet: -2.54 (0.21), residues: 498 loop : -3.01 (0.11), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG 2 641 TYR 0.032 0.002 TYR 6 559 PHE 0.045 0.002 PHE 4 248 TRP 0.028 0.002 TRP A 193 HIS 0.008 0.001 HIS 5 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (38986) covalent geometry : angle 0.82101 / 0.42 (52778) SS BOND : bond 0.00381 / 0.19 ( 1) SS BOND : angle 3.79173 / 7.00 ( 2) hydrogen bonds : bond 0.04498 / 4.15 ( 926) hydrogen bonds : angle 6.46183 / 5.67 ( 2631) Misc. bond : bond 0.00356 / 0.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 774 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (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: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TRP cc_start: 0.4388 (t-100) cc_final: 0.3854 (t-100) REVERT: A 229 ASN cc_start: 0.8311 (m110) cc_final: 0.7967 (m110) REVERT: A 231 ASP cc_start: 0.8431 (p0) cc_final: 0.7990 (p0) REVERT: H 69 PHE cc_start: 0.6806 (t80) cc_final: 0.6389 (t80) REVERT: H 97 TRP cc_start: 0.4844 (m100) cc_final: 0.4257 (m100) REVERT: H 160 MET cc_start: 0.6876 (ttp) cc_final: 0.6363 (tpp) REVERT: L 64 GLU cc_start: 0.7479 (pm20) cc_final: 0.6886 (pm20) REVERT: L 77 GLU cc_start: 0.7807 (pt0) cc_final: 0.7474 (pt0) REVERT: L 129 ARG cc_start: 0.6983 (ptp90) cc_final: 0.6512 (ptp90) REVERT: L 170 TYR cc_start: 0.4104 (t80) cc_final: 0.3524 (t80) REVERT: M 57 TRP cc_start: 0.7356 (p-90) cc_final: 0.6740 (p-90) REVERT: M 112 ASP cc_start: 0.7853 (p0) cc_final: 0.7633 (p0) REVERT: N 39 LEU cc_start: 0.8829 (tt) cc_final: 0.8489 (tt) REVERT: N 88 VAL cc_start: 0.9122 (t) cc_final: 0.8794 (t) REVERT: N 91 SER cc_start: 0.8917 (p) cc_final: 0.8638 (p) REVERT: N 92 MET cc_start: 0.7476 (ptm) cc_final: 0.6719 (ttp) REVERT: N 110 GLN cc_start: 0.7934 (mp10) cc_final: 0.7721 (mp10) REVERT: 2 240 MET cc_start: 0.7597 (mmm) cc_final: 0.7199 (mmm) REVERT: 2 350 MET cc_start: 0.4629 (ttt) cc_final: 0.4196 (tpt) REVERT: 2 466 MET cc_start: 0.3735 (tmm) cc_final: 0.3370 (tmm) REVERT: 2 623 ASP cc_start: 0.8945 (m-30) cc_final: 0.8733 (m-30) REVERT: 2 764 MET cc_start: 0.5875 (tpp) cc_final: 0.5401 (mmm) REVERT: 5 69 MET cc_start: 0.4700 (ptt) cc_final: 0.4282 (tmm) REVERT: 5 71 ASP cc_start: 0.7883 (m-30) cc_final: 0.6871 (m-30) REVERT: 5 92 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7280 (tm-30) REVERT: 5 96 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6757 (mm-30) REVERT: 5 261 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7321 (mp10) REVERT: 5 447 MET cc_start: 0.5302 (mmp) cc_final: 0.4867 (mmm) REVERT: 5 513 MET cc_start: 0.2207 (tpp) cc_final: 0.1996 (tpt) REVERT: 6 222 LEU cc_start: 0.8124 (pt) cc_final: 0.7842 (pp) REVERT: 6 317 MET cc_start: -0.0140 (tmm) cc_final: -0.1097 (ppp) REVERT: 6 332 MET cc_start: 0.7630 (mtm) cc_final: 0.6772 (pmm) REVERT: 6 454 PHE cc_start: 0.7712 (m-80) cc_final: 0.7390 (m-80) REVERT: 6 469 MET cc_start: 0.5672 (tpp) cc_final: 0.5460 (tpp) REVERT: 6 519 MET cc_start: 0.8483 (mpp) cc_final: 0.8243 (mpp) REVERT: 6 590 TYR cc_start: 0.8238 (t80) cc_final: 0.7984 (t80) REVERT: 6 613 LEU cc_start: 0.7708 (mt) cc_final: 0.7319 (mt) REVERT: 6 623 MET cc_start: 0.8674 (mtm) cc_final: 0.7840 (mtm) REVERT: 3 35 ASP cc_start: 0.6273 (m-30) cc_final: 0.5868 (m-30) REVERT: 3 417 ILE cc_start: 0.8808 (mt) cc_final: 0.8486 (mt) REVERT: 3 421 MET cc_start: 0.7845 (mmp) cc_final: 0.6896 (mmm) REVERT: 3 440 ARG cc_start: 0.6114 (mmm160) cc_final: 0.5714 (mmm-85) REVERT: 3 480 MET cc_start: 0.7105 (ttm) cc_final: 0.6789 (ttm) REVERT: 3 572 MET cc_start: 0.7878 (mmm) cc_final: 0.6541 (mtt) REVERT: 3 627 MET cc_start: 0.6309 (mmp) cc_final: 0.4951 (mmt) REVERT: 4 302 MET cc_start: 0.5734 (tpp) cc_final: 0.5296 (tpp) REVERT: 4 374 LEU cc_start: 0.7966 (pt) cc_final: 0.7700 (pt) REVERT: 4 526 PHE cc_start: 0.8489 (p90) cc_final: 0.8065 (p90) REVERT: 4 574 CYS cc_start: 0.7684 (m) cc_final: 0.6335 (m) REVERT: 4 683 MET cc_start: 0.5877 (tpt) cc_final: 0.5155 (tpp) REVERT: 4 737 GLU cc_start: 0.8814 (tt0) cc_final: 0.8515 (tt0) REVERT: 7 20 PHE cc_start: 0.6811 (t80) cc_final: 0.6070 (t80) REVERT: 7 33 TYR cc_start: 0.7753 (m-10) cc_final: 0.7326 (m-10) REVERT: 7 64 GLU cc_start: 0.7109 (mp0) cc_final: 0.6545 (mp0) REVERT: 7 174 LYS cc_start: 0.8064 (tptm) cc_final: 0.7586 (tptm) REVERT: 7 369 MET cc_start: 0.6758 (ptp) cc_final: 0.6453 (ptp) REVERT: 7 541 HIS cc_start: 0.7218 (m-70) cc_final: 0.6620 (m-70) REVERT: 7 590 ARG cc_start: 0.8698 (ptt90) cc_final: 0.7838 (tpt90) outliers start: 5 outliers final: 2 residues processed: 778 average time/residue: 0.2432 time to fit residues: 308.2221 Evaluate side-chains 632 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 630 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 374 optimal weight: 6.9990 chunk 160 optimal weight: 0.0060 chunk 74 optimal weight: 0.5980 chunk 370 optimal weight: 8.9990 chunk 45 optimal weight: 0.0470 chunk 186 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 378 optimal weight: 6.9990 chunk 373 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 overall best weight: 0.4694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN A 442 GLN A 529 ASN H 71 HIS ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 ASN M 127 GLN 2 714 ASN ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS 5 537 HIS 5 568 HIS ** 5 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN 3 70 GLN 3 120 ASN ** 3 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN ** 3 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 228 GLN ** 4 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 223 GLN 7 248 HIS ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 503 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.192252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.173304 restraints weight = 135870.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.173904 restraints weight = 121968.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.174515 restraints weight = 104327.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.174902 restraints weight = 88789.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.175221 restraints weight = 83951.431| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 38999 Z= 0.149 Angle : 0.815 14.264 52780 Z= 0.414 Chirality : 0.048 0.531 5990 Planarity : 0.006 0.186 6735 Dihedral : 11.298 179.372 5460 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.01 % Favored : 86.94 % Rotamer: Outliers : 0.12 % Allowed : 1.12 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.77 (0.11), residues: 4657 helix: -1.93 (0.12), residues: 1438 sheet: -2.40 (0.21), residues: 512 loop : -2.96 (0.11), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG 7 494 TYR 0.037 0.002 TYR 6 236 PHE 0.051 0.002 PHE 4 248 TRP 0.022 0.002 TRP A 193 HIS 0.008 0.001 HIS 5 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (38986) covalent geometry : angle 0.81475 / 0.41 (52778) SS BOND : bond 0.00443 / 0.22 ( 1) SS BOND : angle 3.41484 / 5.72 ( 2) hydrogen bonds : bond 0.04326 / 4.03 ( 926) hydrogen bonds : angle 6.36145 / 5.57 ( 2631) Misc. bond : bond 0.00345 / 0.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 776 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASN cc_start: 0.8378 (m-40) cc_final: 0.8066 (m110) REVERT: A 231 ASP cc_start: 0.8421 (p0) cc_final: 0.8061 (p0) REVERT: H 69 PHE cc_start: 0.6752 (t80) cc_final: 0.6377 (t80) REVERT: H 75 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7787 (mt0) REVERT: H 97 TRP cc_start: 0.4716 (m100) cc_final: 0.4188 (m100) REVERT: H 160 MET cc_start: 0.6867 (ttp) cc_final: 0.6361 (tpp) REVERT: H 192 LEU cc_start: 0.4530 (mt) cc_final: 0.4059 (mp) REVERT: L 4 SER cc_start: 0.8316 (p) cc_final: 0.8060 (p) REVERT: L 64 GLU cc_start: 0.7692 (pm20) cc_final: 0.6993 (pm20) REVERT: L 77 GLU cc_start: 0.7849 (pt0) cc_final: 0.7649 (pt0) REVERT: L 154 HIS cc_start: 0.5398 (p-80) cc_final: 0.5165 (p-80) REVERT: M 57 TRP cc_start: 0.7323 (p-90) cc_final: 0.6803 (p-90) REVERT: M 112 ASP cc_start: 0.7939 (p0) cc_final: 0.7738 (p0) REVERT: N 88 VAL cc_start: 0.9154 (t) cc_final: 0.8893 (t) REVERT: N 92 MET cc_start: 0.7999 (ptm) cc_final: 0.6950 (ttt) REVERT: N 202 ASP cc_start: 0.7505 (t70) cc_final: 0.7269 (t70) REVERT: N 223 ASN cc_start: 0.8569 (t0) cc_final: 0.8293 (t0) REVERT: 2 240 MET cc_start: 0.7541 (mmm) cc_final: 0.6949 (mmm) REVERT: 2 350 MET cc_start: 0.4773 (ttt) cc_final: 0.4287 (tpt) REVERT: 2 485 PHE cc_start: 0.3663 (m-80) cc_final: 0.3328 (m-80) REVERT: 2 764 MET cc_start: 0.5864 (tpp) cc_final: 0.5375 (mmm) REVERT: 5 32 LYS cc_start: 0.7757 (mptt) cc_final: 0.7388 (mppt) REVERT: 5 69 MET cc_start: 0.4529 (ptt) cc_final: 0.4158 (tmm) REVERT: 5 71 ASP cc_start: 0.7949 (m-30) cc_final: 0.6863 (m-30) REVERT: 5 92 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7335 (tm-30) REVERT: 5 96 GLU cc_start: 0.7605 (mm-30) cc_final: 0.6867 (mm-30) REVERT: 5 261 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7330 (mp10) REVERT: 5 447 MET cc_start: 0.5366 (mmp) cc_final: 0.4922 (mmm) REVERT: 6 317 MET cc_start: 0.0250 (tmm) cc_final: -0.0126 (tmm) REVERT: 6 454 PHE cc_start: 0.7732 (m-80) cc_final: 0.7435 (m-80) REVERT: 6 519 MET cc_start: 0.8399 (mpp) cc_final: 0.8154 (mpp) REVERT: 6 557 ARG cc_start: 0.5747 (ttt-90) cc_final: 0.3425 (mmp80) REVERT: 6 613 LEU cc_start: 0.7647 (mt) cc_final: 0.7294 (mt) REVERT: 6 623 MET cc_start: 0.8659 (mtm) cc_final: 0.7862 (mtm) REVERT: 3 35 ASP cc_start: 0.6278 (m-30) cc_final: 0.5787 (m-30) REVERT: 3 219 ASP cc_start: 0.7370 (m-30) cc_final: 0.6981 (m-30) REVERT: 3 572 MET cc_start: 0.7768 (mmm) cc_final: 0.7167 (mtt) REVERT: 4 227 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7237 (mtm-85) REVERT: 4 274 MET cc_start: 0.6048 (tmm) cc_final: 0.5448 (tmm) REVERT: 4 526 PHE cc_start: 0.8544 (p90) cc_final: 0.8003 (p90) REVERT: 4 574 CYS cc_start: 0.7675 (m) cc_final: 0.6431 (m) REVERT: 4 683 MET cc_start: 0.5870 (tpt) cc_final: 0.5297 (tpp) REVERT: 7 64 GLU cc_start: 0.7144 (mp0) cc_final: 0.6554 (mp0) REVERT: 7 369 MET cc_start: 0.6719 (ptp) cc_final: 0.6517 (ptp) REVERT: 7 380 MET cc_start: 0.8226 (tmm) cc_final: 0.7913 (tmm) REVERT: 7 541 HIS cc_start: 0.6960 (m-70) cc_final: 0.6350 (m-70) REVERT: 7 590 ARG cc_start: 0.8603 (ptt90) cc_final: 0.7953 (tpt90) outliers start: 5 outliers final: 2 residues processed: 780 average time/residue: 0.2370 time to fit residues: 300.1252 Evaluate side-chains 621 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 619 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 34 optimal weight: 1.9990 chunk 160 optimal weight: 0.1980 chunk 9 optimal weight: 0.0470 chunk 85 optimal weight: 0.0030 chunk 446 optimal weight: 0.8980 chunk 78 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 262 optimal weight: 0.7980 overall best weight: 0.1688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN A 467 HIS A 529 ASN M 127 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS 5 537 HIS 5 628 GLN 6 198 GLN 6 472 GLN 3 70 GLN 3 120 ASN 3 467 GLN ** 3 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 228 GLN ** 4 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 223 GLN 7 233 GLN 7 248 HIS ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 439 GLN 7 465 GLN 7 503 GLN 7 605 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.194592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.174968 restraints weight = 133751.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.176158 restraints weight = 109605.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.176562 restraints weight = 91718.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.176895 restraints weight = 82299.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.177255 restraints weight = 79975.426| |-----------------------------------------------------------------------------| r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 38999 Z= 0.147 Angle : 0.812 11.757 52780 Z= 0.413 Chirality : 0.048 0.525 5990 Planarity : 0.006 0.086 6735 Dihedral : 11.136 177.846 5460 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.39 % Favored : 87.57 % Rotamer: Outliers : 0.12 % Allowed : 0.73 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.11), residues: 4657 helix: -1.84 (0.12), residues: 1436 sheet: -2.35 (0.22), residues: 495 loop : -2.91 (0.11), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 2 641 TYR 0.029 0.002 TYR 5 400 PHE 0.036 0.002 PHE 2 795 TRP 0.036 0.002 TRP L 65 HIS 0.010 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (38986) covalent geometry : angle 0.81206 / 0.41 (52778) SS BOND : bond 0.00319 / 0.16 ( 1) SS BOND : angle 3.09817 / 5.30 ( 2) hydrogen bonds : bond 0.04284 / 4.02 ( 926) hydrogen bonds : angle 6.29856 / 5.48 ( 2631) Misc. bond : bond 0.00203 / 0.19 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 784 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASN cc_start: 0.8237 (m-40) cc_final: 0.7938 (m-40) REVERT: A 231 ASP cc_start: 0.8371 (p0) cc_final: 0.7911 (p0) REVERT: H 69 PHE cc_start: 0.6680 (t80) cc_final: 0.6367 (t80) REVERT: H 75 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7852 (mt0) REVERT: H 97 TRP cc_start: 0.5030 (m100) cc_final: 0.4391 (m100) REVERT: H 106 ASP cc_start: 0.7609 (p0) cc_final: 0.7400 (p0) REVERT: H 129 TYR cc_start: 0.6502 (t80) cc_final: 0.6128 (t80) REVERT: H 160 MET cc_start: 0.6878 (ttp) cc_final: 0.6428 (tpp) REVERT: L 4 SER cc_start: 0.8210 (p) cc_final: 0.7944 (p) REVERT: L 64 GLU cc_start: 0.7814 (pm20) cc_final: 0.7217 (pm20) REVERT: L 77 GLU cc_start: 0.7685 (pt0) cc_final: 0.7429 (pt0) REVERT: L 97 GLN cc_start: 0.8126 (mt0) cc_final: 0.7864 (tt0) REVERT: L 100 MET cc_start: 0.6840 (ttt) cc_final: 0.6328 (tmm) REVERT: L 139 GLU cc_start: 0.7670 (pm20) cc_final: 0.7228 (pm20) REVERT: M 57 TRP cc_start: 0.7251 (p-90) cc_final: 0.6782 (p-90) REVERT: M 112 ASP cc_start: 0.7853 (p0) cc_final: 0.7635 (p0) REVERT: N 73 MET cc_start: 0.7141 (tpp) cc_final: 0.6883 (tpt) REVERT: N 111 LYS cc_start: 0.8820 (mttp) cc_final: 0.8578 (mttt) REVERT: N 115 PHE cc_start: 0.5924 (t80) cc_final: 0.5713 (t80) REVERT: N 223 ASN cc_start: 0.8381 (t0) cc_final: 0.8029 (t0) REVERT: 2 240 MET cc_start: 0.7412 (mmm) cc_final: 0.6795 (mmm) REVERT: 2 269 ARG cc_start: 0.6746 (mmp80) cc_final: 0.6472 (mmp80) REVERT: 2 350 MET cc_start: 0.4855 (ttt) cc_final: 0.4411 (tpt) REVERT: 2 757 MET cc_start: 0.9264 (mpp) cc_final: 0.8372 (mpp) REVERT: 2 764 MET cc_start: 0.5870 (tpp) cc_final: 0.5379 (mmm) REVERT: 5 32 LYS cc_start: 0.7557 (mptt) cc_final: 0.7237 (mppt) REVERT: 5 69 MET cc_start: 0.4480 (ptt) cc_final: 0.4238 (tmm) REVERT: 5 92 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7040 (tm-30) REVERT: 5 96 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6457 (mm-30) REVERT: 5 248 LEU cc_start: 0.6479 (mt) cc_final: 0.5822 (mt) REVERT: 5 261 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7281 (mp10) REVERT: 5 353 MET cc_start: 0.0850 (tpt) cc_final: 0.0556 (tpt) REVERT: 5 447 MET cc_start: 0.5153 (mmp) cc_final: 0.4871 (mmm) REVERT: 6 317 MET cc_start: 0.0069 (tmm) cc_final: -0.0220 (tmm) REVERT: 6 454 PHE cc_start: 0.7707 (m-80) cc_final: 0.7415 (m-80) REVERT: 6 519 MET cc_start: 0.8454 (mpp) cc_final: 0.8176 (mpp) REVERT: 6 596 ARG cc_start: 0.7420 (mmp-170) cc_final: 0.6973 (mmm160) REVERT: 6 613 LEU cc_start: 0.7638 (mt) cc_final: 0.7295 (mt) REVERT: 6 623 MET cc_start: 0.8698 (mtm) cc_final: 0.7965 (mtm) REVERT: 3 219 ASP cc_start: 0.7062 (m-30) cc_final: 0.6759 (m-30) REVERT: 3 409 MET cc_start: 0.2678 (tpp) cc_final: 0.1426 (ptt) REVERT: 3 572 MET cc_start: 0.7728 (mmm) cc_final: 0.6543 (mtt) REVERT: 3 627 MET cc_start: 0.5890 (mmp) cc_final: 0.4472 (mmt) REVERT: 4 213 LEU cc_start: 0.7184 (pt) cc_final: 0.6889 (pp) REVERT: 4 241 ASP cc_start: 0.7586 (p0) cc_final: 0.7320 (p0) REVERT: 4 274 MET cc_start: 0.5830 (tmm) cc_final: 0.5306 (tmm) REVERT: 4 390 ARG cc_start: 0.5939 (mtm180) cc_final: 0.5476 (tpt170) REVERT: 4 447 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8501 (ttp80) REVERT: 4 526 PHE cc_start: 0.8523 (p90) cc_final: 0.8163 (p90) REVERT: 4 574 CYS cc_start: 0.7616 (m) cc_final: 0.6306 (m) REVERT: 4 668 LEU cc_start: 0.8357 (mt) cc_final: 0.8031 (mp) REVERT: 4 683 MET cc_start: 0.5810 (tpt) cc_final: 0.5260 (tpp) REVERT: 7 64 GLU cc_start: 0.6998 (mp0) cc_final: 0.6429 (mp0) REVERT: 7 79 ASP cc_start: 0.8310 (p0) cc_final: 0.7973 (p0) REVERT: 7 380 MET cc_start: 0.8147 (tmm) cc_final: 0.7796 (tmm) REVERT: 7 541 HIS cc_start: 0.6881 (m-70) cc_final: 0.6314 (m-70) REVERT: 7 590 ARG cc_start: 0.8553 (ptt90) cc_final: 0.7839 (tpt90) outliers start: 5 outliers final: 2 residues processed: 788 average time/residue: 0.2362 time to fit residues: 302.2350 Evaluate side-chains 638 residues out of total 4193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 636 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 338 optimal weight: 0.0970 chunk 156 optimal weight: 9.9990 chunk 300 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 413 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 142 optimal weight: 0.0970 chunk 409 optimal weight: 5.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 529 ASN H 71 HIS M 127 GLN ** 2 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS 5 537 HIS 5 568 HIS 6 198 GLN 3 70 GLN 3 120 ASN 3 467 GLN ** 3 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 228 GLN 4 245 ASN ** 4 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 238 GLN 7 248 HIS ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 503 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.193551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.173969 restraints weight = 135110.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.174792 restraints weight = 114544.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.175528 restraints weight = 93857.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.176122 restraints weight = 82849.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.176384 restraints weight = 77573.651| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.6802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 38999 Z= 0.144 Angle : 0.800 14.345 52780 Z= 0.407 Chirality : 0.048 0.532 5990 Planarity : 0.006 0.086 6735 Dihedral : 11.024 177.002 5460 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.45 % Favored : 87.48 % Rotamer: Outliers : 0.12 % Allowed : 0.76 % Favored : 99.12 % 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: -3.59 (0.11), residues: 4657 helix: -1.80 (0.12), residues: 1431 sheet: -2.33 (0.22), residues: 481 loop : -2.84 (0.11), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 2 756 TYR 0.031 0.002 TYR 3 16 PHE 0.044 0.002 PHE 4 248 TRP 0.043 0.003 TRP 6 326 HIS 0.009 0.001 HIS H 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (38986) covalent geometry : angle 0.80008 / 0.41 (52778) SS BOND : bond 0.00355 / 0.18 ( 1) SS BOND : angle 2.07264 / 4.27 ( 2) hydrogen bonds : bond 0.04284 / 4.05 ( 926) hydrogen bonds : angle 6.19350 / 5.36 ( 2631) Misc. bond : bond 0.00377 / 0.24 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7683.05 seconds wall clock time: 133 minutes 30.85 seconds (8010.85 seconds total)