Starting phenix.real_space_refine on Mon Jul 6 00:27:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u5d_26348/07_2026/7u5d_26348.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5d_26348/07_2026/7u5d_26348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u5d_26348/07_2026/7u5d_26348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5d_26348/07_2026/7u5d_26348.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7u5d_26348/07_2026/7u5d_26348.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u5d_26348/07_2026/7u5d_26348.cif" model { file = "/net/cci-nas-00/data/ceres_data/7u5d_26348/07_2026/7u5d_26348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5d_26348/07_2026/7u5d_26348.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 140 5.49 5 S 130 5.16 5 C 19529 2.51 5 N 5570 2.21 5 O 6146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 157 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31515 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1285 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 13, 'rna2p_pyr': 13, 'rna3p_pur': 23, 'rna3p_pyr': 11} Link IDs: {'rna2p': 26, 'rna3p': 33} Chain: "2" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1127 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1, ' DG:plan': 1, ' DG:plan2': 1, ' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 35 Chain: "3" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "A" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4970 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 35, 'TRANS': 594} Chain breaks: 3 Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2711 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2711 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2711 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain: "E" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2711 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain: "F" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2711 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain: "G" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2390 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 15, 'TRANS': 284} Chain breaks: 3 Chain: "H" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1631 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "I" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3084 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain breaks: 1 Chain: "J" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2980 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 16, 'TRANS': 357} Chain breaks: 2 Time building chain proxies: 6.92, per 1000 atoms: 0.22 Number of scatterers: 31515 At special positions: 0 Unit cell: (147.537, 196.425, 174.6, 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 130 16.00 P 140 15.00 O 6146 8.00 N 5570 7.00 C 19529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 "ATOM 133 O4' A 1 7 .*. O " rejected from bonding due to valence issues. Atom "ATOM 85 O5' G 1 5 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6738 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 47 sheets defined 39.7% alpha, 14.3% beta 31 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 removed outlier: 4.225A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 Processing helix chain 'A' and resid 51 through 52 No H-bonds generated for 'chain 'A' and resid 51 through 52' Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.627A pdb=" N VAL A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 71 removed outlier: 3.604A pdb=" N SER A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.852A pdb=" N THR A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.976A pdb=" N GLY A 119 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.704A pdb=" N THR A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 173 through 187 removed outlier: 4.005A pdb=" N GLN A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.780A pdb=" N ASN A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'A' and resid 316 through 339 Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.765A pdb=" N ILE A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 380 through 394 Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 407 through 423 Processing helix chain 'A' and resid 463 through 480 removed outlier: 3.897A pdb=" N LEU A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 563 removed outlier: 3.732A pdb=" N LEU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'A' and resid 616 through 627 Processing helix chain 'A' and resid 668 through 676 removed outlier: 3.775A pdb=" N MET A 672 " --> pdb=" O ASN A 668 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 674 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 684 Processing helix chain 'B' and resid 60 through 65 removed outlier: 3.858A pdb=" N LEU B 64 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.790A pdb=" N VAL B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.530A pdb=" N LEU B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.502A pdb=" N TRP B 142 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG B 143 " --> pdb=" O TRP B 140 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 145 " --> pdb=" O TRP B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 4.385A pdb=" N ARG B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.529A pdb=" N GLU B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.761A pdb=" N ALA B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 removed outlier: 4.140A pdb=" N ASN B 270 " --> pdb=" O TRP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'C' and resid 60 through 65 removed outlier: 3.952A pdb=" N LEU C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 120 removed outlier: 3.796A pdb=" N VAL C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.710A pdb=" N ASN C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 removed outlier: 3.510A pdb=" N TRP C 142 " --> pdb=" O ILE C 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 139 through 142' Processing helix chain 'C' and resid 180 through 195 removed outlier: 3.510A pdb=" N GLU C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.834A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.839A pdb=" N THR C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'D' and resid 60 through 65 removed outlier: 3.835A pdb=" N LEU D 64 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.812A pdb=" N VAL D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY D 122 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.592A pdb=" N ASN D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY D 138 " --> pdb=" O ASN D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.591A pdb=" N TRP D 142 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG D 143 " --> pdb=" O TRP D 140 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN D 145 " --> pdb=" O TRP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 195 removed outlier: 3.543A pdb=" N GLU D 190 " --> pdb=" O GLN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.838A pdb=" N ALA D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.744A pdb=" N THR D 305 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 325 through 337 Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.846A pdb=" N LEU E 64 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.770A pdb=" N VAL E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 138 removed outlier: 3.504A pdb=" N ASN E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 145 removed outlier: 3.512A pdb=" N TRP E 142 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG E 143 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN E 145 " --> pdb=" O TRP E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 195 Processing helix chain 'E' and resid 253 through 262 removed outlier: 3.764A pdb=" N ALA E 260 " --> pdb=" O LYS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 299 through 305 removed outlier: 3.538A pdb=" N LEU E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR E 305 " --> pdb=" O TYR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'F' and resid 60 through 65 Processing helix chain 'F' and resid 104 through 120 Processing helix chain 'F' and resid 123 through 138 removed outlier: 3.797A pdb=" N GLY F 138 " --> pdb=" O ASN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.521A pdb=" N TRP F 142 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG F 143 " --> pdb=" O TRP F 140 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN F 145 " --> pdb=" O TRP F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 195 Processing helix chain 'F' and resid 253 through 262 removed outlier: 3.718A pdb=" N ALA F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 297 Processing helix chain 'F' and resid 299 through 305 removed outlier: 3.528A pdb=" N LEU F 303 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR F 305 " --> pdb=" O TYR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 325 through 337 Processing helix chain 'G' and resid 104 through 120 Processing helix chain 'G' and resid 123 through 138 removed outlier: 3.542A pdb=" N ASN G 134 " --> pdb=" O ARG G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 145 removed outlier: 6.504A pdb=" N ARG G 143 " --> pdb=" O TRP G 140 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN G 145 " --> pdb=" O TRP G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 170 removed outlier: 4.202A pdb=" N ARG G 169 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU G 170 " --> pdb=" O ALA G 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 166 through 170' Processing helix chain 'G' and resid 180 through 195 Processing helix chain 'G' and resid 253 through 262 removed outlier: 3.754A pdb=" N ALA G 260 " --> pdb=" O LYS G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 297 Processing helix chain 'G' and resid 299 through 305 removed outlier: 3.527A pdb=" N LEU G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR G 305 " --> pdb=" O TYR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'H' and resid 18 through 37 removed outlier: 3.912A pdb=" N GLY H 24 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG H 25 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 74 through 83 removed outlier: 3.528A pdb=" N GLN H 78 " --> pdb=" O ARG H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 112 removed outlier: 3.774A pdb=" N LEU H 109 " --> pdb=" O ASN H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 132 removed outlier: 3.558A pdb=" N ARG H 117 " --> pdb=" O PHE H 113 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS H 129 " --> pdb=" O LYS H 125 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 30 through 46 removed outlier: 3.537A pdb=" N VAL I 38 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TRP I 41 " --> pdb=" O SER I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 52 removed outlier: 4.138A pdb=" N ALA I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 65 removed outlier: 3.918A pdb=" N ASN I 61 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE I 62 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE I 63 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 83 removed outlier: 3.561A pdb=" N ARG I 72 " --> pdb=" O SER I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 121 No H-bonds generated for 'chain 'I' and resid 119 through 121' Processing helix chain 'I' and resid 129 through 134 Processing helix chain 'I' and resid 198 through 203 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.834A pdb=" N LEU I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 251 removed outlier: 4.039A pdb=" N LYS I 251 " --> pdb=" O ARG I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 257 through 261 Proline residue: I 260 - end of helix No H-bonds generated for 'chain 'I' and resid 257 through 261' Processing helix chain 'I' and resid 262 through 276 removed outlier: 3.770A pdb=" N MET I 270 " --> pdb=" O GLU I 266 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL I 271 " --> pdb=" O LEU I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 285 Processing helix chain 'I' and resid 286 through 292 removed outlier: 4.099A pdb=" N VAL I 290 " --> pdb=" O ASP I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 300 Processing helix chain 'I' and resid 309 through 325 Processing helix chain 'I' and resid 341 through 348 Processing helix chain 'I' and resid 351 through 361 removed outlier: 3.710A pdb=" N VAL I 355 " --> pdb=" O SER I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 396 Processing helix chain 'J' and resid 14 through 25 Processing helix chain 'J' and resid 30 through 43 removed outlier: 3.728A pdb=" N HIS J 43 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 51 Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'J' and resid 61 through 65 Processing helix chain 'J' and resid 68 through 83 Processing helix chain 'J' and resid 89 through 94 removed outlier: 3.831A pdb=" N GLN J 92 " --> pdb=" O ARG J 89 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA J 94 " --> pdb=" O LEU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 102 Processing helix chain 'J' and resid 119 through 121 No H-bonds generated for 'chain 'J' and resid 119 through 121' Processing helix chain 'J' and resid 129 through 134 Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'J' and resid 199 through 204 Processing helix chain 'J' and resid 205 through 207 No H-bonds generated for 'chain 'J' and resid 205 through 207' Processing helix chain 'J' and resid 221 through 236 Processing helix chain 'J' and resid 247 through 256 removed outlier: 4.686A pdb=" N ILE J 253 " --> pdb=" O LEU J 249 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY J 254 " --> pdb=" O THR J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 277 removed outlier: 4.440A pdb=" N TRP J 264 " --> pdb=" O PRO J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 285 Processing helix chain 'J' and resid 286 through 292 removed outlier: 3.585A pdb=" N VAL J 290 " --> pdb=" O ASP J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 300 Processing helix chain 'J' and resid 309 through 325 Processing helix chain 'J' and resid 340 through 348 Processing helix chain 'J' and resid 351 through 361 Processing helix chain 'J' and resid 385 through 396 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90 removed outlier: 4.391A pdb=" N VAL A 219 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.517A pdb=" N ILE A 607 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TRP A 493 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N LEU A 491 " --> pdb=" O PRO A 609 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG A 489 " --> pdb=" O HIS A 543 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N HIS A 543 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 491 " --> pdb=" O GLU A 541 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU A 541 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TRP A 493 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE A 539 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU A 495 " --> pdb=" O ASP A 537 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASP A 537 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 531 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N CYS A 532 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR A 448 " --> pdb=" O CYS A 532 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 534 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR A 446 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N MET A 536 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 444 " --> pdb=" O MET A 536 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 208 removed outlier: 4.021A pdb=" N GLY A 636 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY A 662 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA A 634 " --> pdb=" O GLY A 662 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA A 664 " --> pdb=" O PRO A 632 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS A 666 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU A 630 " --> pdb=" O CYS A 666 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 removed outlier: 8.681A pdb=" N CYS A 459 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 263 " --> pdb=" O CYS A 459 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 455 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 512 removed outlier: 3.869A pdb=" N LYS A 511 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AA9, first strand: chain 'B' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 22 current: chain 'B' and resid 150 through 156 Processing sheet with id=AB1, first strand: chain 'B' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 92 current: chain 'B' and resid 240 through 242 Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 41 Processing sheet with id=AB3, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AB4, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB5, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB6, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AB7, first strand: chain 'C' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 22 current: chain 'C' and resid 150 through 156 Processing sheet with id=AB8, first strand: chain 'C' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 92 current: chain 'C' and resid 240 through 242 Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AC1, first strand: chain 'C' and resid 283 through 284 Processing sheet with id=AC2, first strand: chain 'D' and resid 7 through 8 Processing sheet with id=AC3, first strand: chain 'D' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 150 through 156 Processing sheet with id=AC4, first strand: chain 'D' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 83 through 92 current: chain 'D' and resid 240 through 242 Processing sheet with id=AC5, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AC6, first strand: chain 'D' and resid 283 through 284 Processing sheet with id=AC7, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AC8, first strand: chain 'E' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 150 through 155 Processing sheet with id=AC9, first strand: chain 'E' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 83 through 92 current: chain 'E' and resid 240 through 242 Processing sheet with id=AD1, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AD2, first strand: chain 'E' and resid 283 through 284 Processing sheet with id=AD3, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AD4, first strand: chain 'F' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 150 through 156 Processing sheet with id=AD5, first strand: chain 'F' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 84 through 92 current: chain 'F' and resid 240 through 242 Processing sheet with id=AD6, first strand: chain 'F' and resid 35 through 41 Processing sheet with id=AD7, first strand: chain 'F' and resid 283 through 284 Processing sheet with id=AD8, first strand: chain 'G' and resid 7 through 8 Processing sheet with id=AD9, first strand: chain 'G' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 22 current: chain 'G' and resid 150 through 156 Processing sheet with id=AE1, first strand: chain 'G' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 83 through 92 current: chain 'G' and resid 240 through 242 Processing sheet with id=AE2, first strand: chain 'G' and resid 72 through 74 removed outlier: 7.400A pdb=" N VAL G 36 " --> pdb=" O LYS H 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 283 through 284 Processing sheet with id=AE4, first strand: chain 'H' and resid 43 through 45 Processing sheet with id=AE5, first strand: chain 'H' and resid 43 through 45 Processing sheet with id=AE6, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AE7, first strand: chain 'H' and resid 150 through 155 Processing sheet with id=AE8, first strand: chain 'I' and resid 96 through 97 Processing sheet with id=AE9, first strand: chain 'I' and resid 338 through 340 Processing sheet with id=AF1, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AF2, first strand: chain 'J' and resid 338 through 339 1077 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 6.88 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4888 1.30 - 1.43: 9637 1.43 - 1.56: 17577 1.56 - 1.68: 287 1.68 - 1.81: 172 Bond restraints: 32561 Sorted by residual: bond pdb=" O3' A 1 4 " pdb=" P G 1 5 " ideal model delta sigma weight residual 1.607 1.718 -0.111 1.50e-02 4.44e+03 5.49e+01 bond pdb=" CA ILE J 316 " pdb=" C ILE J 316 " ideal model delta sigma weight residual 1.523 1.446 0.078 1.27e-02 6.20e+03 3.74e+01 bond pdb=" CA ILE I 316 " pdb=" C ILE I 316 " ideal model delta sigma weight residual 1.524 1.445 0.078 1.30e-02 5.92e+03 3.62e+01 bond pdb=" CA LEU J 315 " pdb=" C LEU J 315 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.53e+01 bond pdb=" CA LEU I 315 " pdb=" C LEU I 315 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.50e+01 ... (remaining 32556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 42620 3.52 - 7.03: 1878 7.03 - 10.55: 247 10.55 - 14.06: 41 14.06 - 17.58: 3 Bond angle restraints: 44789 Sorted by residual: angle pdb=" C ARG J 6 " pdb=" N PRO J 7 " pdb=" CA PRO J 7 " ideal model delta sigma weight residual 120.52 133.51 -12.99 9.90e-01 1.02e+00 1.72e+02 angle pdb=" C CYS J 129 " pdb=" N PRO J 130 " pdb=" CA PRO J 130 " ideal model delta sigma weight residual 119.47 133.51 -14.04 1.16e+00 7.43e-01 1.46e+02 angle pdb=" C TRP B 176 " pdb=" N PRO B 177 " pdb=" CA PRO B 177 " ideal model delta sigma weight residual 119.89 131.22 -11.33 1.02e+00 9.61e-01 1.23e+02 angle pdb=" C TRP F 176 " pdb=" N PRO F 177 " pdb=" CA PRO F 177 " ideal model delta sigma weight residual 119.90 131.16 -11.26 1.02e+00 9.61e-01 1.22e+02 angle pdb=" C MET H 139 " pdb=" N PRO H 140 " pdb=" CA PRO H 140 " ideal model delta sigma weight residual 120.98 132.58 -11.60 1.07e+00 8.73e-01 1.18e+02 ... (remaining 44784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.51: 18327 31.51 - 63.02: 621 63.02 - 94.53: 72 94.53 - 126.04: 3 126.04 - 157.54: 7 Dihedral angle restraints: 19030 sinusoidal: 8561 harmonic: 10469 Sorted by residual: dihedral pdb=" O4' U 1 43 " pdb=" C1' U 1 43 " pdb=" N1 U 1 43 " pdb=" C2 U 1 43 " ideal model delta sinusoidal sigma weight residual 232.00 81.57 150.43 1 1.70e+01 3.46e-03 6.21e+01 dihedral pdb=" O4' U 1 45 " pdb=" C1' U 1 45 " pdb=" N1 U 1 45 " pdb=" C2 U 1 45 " ideal model delta sinusoidal sigma weight residual 200.00 88.59 111.41 1 1.50e+01 4.44e-03 5.82e+01 dihedral pdb=" N CYS I 142 " pdb=" C CYS I 142 " pdb=" CA CYS I 142 " pdb=" CB CYS I 142 " ideal model delta harmonic sigma weight residual 122.80 136.32 -13.52 0 2.50e+00 1.60e-01 2.92e+01 ... (remaining 19027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3506 0.088 - 0.175: 1195 0.175 - 0.263: 169 0.263 - 0.351: 49 0.351 - 0.438: 11 Chirality restraints: 4930 Sorted by residual: chirality pdb=" CA ASP A 132 " pdb=" N ASP A 132 " pdb=" C ASP A 132 " pdb=" CB ASP A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA TYR A 93 " pdb=" N TYR A 93 " pdb=" C TYR A 93 " pdb=" CB TYR A 93 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA CYS I 142 " pdb=" N CYS I 142 " pdb=" C CYS I 142 " pdb=" CB CYS I 142 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 ... (remaining 4927 not shown) Planarity restraints: 5303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 93 " -0.137 2.00e-02 2.50e+03 7.18e-02 1.03e+02 pdb=" CG TYR A 93 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 93 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 93 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR A 93 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR A 93 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR A 93 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 93 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 205 " 0.031 2.00e-02 2.50e+03 6.20e-02 3.85e+01 pdb=" C ASP F 205 " -0.107 2.00e-02 2.50e+03 pdb=" O ASP F 205 " 0.041 2.00e-02 2.50e+03 pdb=" N VAL F 206 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 205 " 0.031 2.00e-02 2.50e+03 6.19e-02 3.83e+01 pdb=" C ASP G 205 " -0.107 2.00e-02 2.50e+03 pdb=" O ASP G 205 " 0.041 2.00e-02 2.50e+03 pdb=" N VAL G 206 " 0.036 2.00e-02 2.50e+03 ... (remaining 5300 not shown) Histogram of nonbonded interaction distances: 0.48 - 1.37: 12 1.37 - 2.25: 79 2.25 - 3.13: 24358 3.13 - 4.02: 74955 4.02 - 4.90: 138625 Warning: very small nonbonded interaction distances. Nonbonded interactions: 238029 Sorted by model distance: nonbonded pdb=" C1' A 1 7 " pdb=" OE2 GLU A 508 " model vdw 0.483 3.470 nonbonded pdb=" P G 1 5 " pdb=" NH2 ARG A 566 " model vdw 0.704 3.480 nonbonded pdb=" CE2 PHE I 88 " pdb=" CD ARG J 395 " model vdw 0.779 3.740 nonbonded pdb=" O4' A 1 7 " pdb=" OE2 GLU A 508 " model vdw 0.947 3.040 nonbonded pdb=" OP2 DG 3 52 " pdb=" NH2 ARG I 59 " model vdw 0.950 3.120 ... (remaining 238024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 3 through 39 or resid 69 through 226 or resid 235 through \ 318 or resid 324 through 344)) selection = (chain 'C' and (resid 3 through 39 or resid 69 through 226 or resid 235 through \ 318 or resid 324 through 344)) selection = (chain 'D' and (resid 3 through 39 or resid 69 through 226 or resid 235 through \ 318 or resid 324 through 344)) selection = (chain 'E' and (resid 3 through 39 or resid 69 through 226 or resid 235 through \ 318 or resid 324 through 344)) selection = (chain 'F' and (resid 3 through 39 or resid 69 through 226 or resid 235 through \ 318 or resid 324 through 344)) selection = chain 'G' } ncs_group { reference = (chain 'I' and (resid 7 through 368 or resid 382 through 397)) selection = (chain 'J' and (resid 7 through 188 or resid 196 through 397)) } 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: 7.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.150 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.014 0.631 32564 Z= 1.014 Angle : 1.658 17.579 44789 Z= 1.194 Chirality : 0.086 0.438 4930 Planarity : 0.009 0.093 5303 Dihedral : 14.927 157.545 12292 Min Nonbonded Distance : 0.483 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 0.20 % Allowed : 0.59 % Favored : 99.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.13), residues: 3565 helix: -0.54 (0.13), residues: 1187 sheet: 0.37 (0.21), residues: 505 loop : -0.15 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.137 0.002 TYR A 93 PHE 0.049 0.002 PHE A 206 TRP 0.049 0.002 TRP A 180 HIS 0.008 0.000 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.01326 / 0.93 (32561) covalent geometry : angle 1.65806 / 1.19 (44789) hydrogen bonds : bond 0.25423 / 14.96 ( 1112) hydrogen bonds : angle 7.48512 / 7.12 ( 3024) Misc. bond : bond 0.41143 / 27.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 475 time to evaluate : 1.297 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 REVERT: A 129 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: B 197 GLN cc_start: 0.8310 (tt0) cc_final: 0.8100 (tt0) REVERT: C 153 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7099 (mt-10) REVERT: D 111 MET cc_start: 0.8758 (mmm) cc_final: 0.8556 (mmp) REVERT: I 273 ASP cc_start: 0.7642 (m-30) cc_final: 0.7436 (m-30) REVERT: J 267 LEU cc_start: 0.7592 (mt) cc_final: 0.6782 (mt) outliers start: 6 outliers final: 3 residues processed: 480 average time/residue: 0.2486 time to fit residues: 179.6893 Evaluate side-chains 259 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 255 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 59 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS B 163 HIS ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 302 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN E 231 HIS F 302 HIS F 342 GLN G 163 HIS G 342 GLN I 141 GLN ** I 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.114409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.082316 restraints weight = 72225.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.080975 restraints weight = 59147.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082011 restraints weight = 55644.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.081961 restraints weight = 43881.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082054 restraints weight = 40509.353| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 32564 Z= 0.166 Angle : 0.719 13.076 44789 Z= 0.389 Chirality : 0.044 0.259 4930 Planarity : 0.006 0.078 5303 Dihedral : 16.083 168.967 5557 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.38 % Favored : 97.59 % Rotamer: Outliers : 0.88 % Allowed : 5.98 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.13), residues: 3565 helix: 0.72 (0.14), residues: 1234 sheet: 0.21 (0.21), residues: 533 loop : -0.37 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 395 TYR 0.037 0.002 TYR J 232 PHE 0.066 0.002 PHE I 88 TRP 0.019 0.001 TRP A 686 HIS 0.009 0.001 HIS J 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (32561) covalent geometry : angle 0.71914 / 0.39 (44789) hydrogen bonds : bond 0.06114 / 3.64 ( 1112) hydrogen bonds : angle 4.89914 / 4.77 ( 3024) Misc. bond : bond 0.01283 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 289 time to evaluate : 1.161 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: A 401 PHE cc_start: 0.7475 (m-80) cc_final: 0.7102 (m-80) REVERT: B 230 ASP cc_start: 0.8040 (t0) cc_final: 0.7746 (t0) REVERT: D 111 MET cc_start: 0.8566 (mmm) cc_final: 0.8348 (mmp) REVERT: F 132 SER cc_start: 0.9289 (m) cc_final: 0.8890 (t) REVERT: H 84 ASN cc_start: 0.8782 (m110) cc_final: 0.8576 (p0) REVERT: J 267 LEU cc_start: 0.8274 (mt) cc_final: 0.8044 (mt) REVERT: J 315 LEU cc_start: 0.8985 (tt) cc_final: 0.8690 (tt) outliers start: 27 outliers final: 17 residues processed: 305 average time/residue: 0.2189 time to fit residues: 104.4229 Evaluate side-chains 246 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 229 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 163 HIS Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 352 VAL Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 352 VAL Chi-restraints excluded: chain J residue 388 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 95 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 348 optimal weight: 0.4980 chunk 66 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 275 optimal weight: 0.0170 chunk 356 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.0570 overall best weight: 1.3140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS B 293 HIS C 309 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS G 163 HIS G 342 GLN H 81 GLN I 77 GLN I 154 HIS J 393 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.111896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.079252 restraints weight = 72012.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.077917 restraints weight = 56018.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.078328 restraints weight = 57881.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.078630 restraints weight = 45817.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.078963 restraints weight = 41798.017| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32564 Z= 0.165 Angle : 0.636 11.134 44789 Z= 0.341 Chirality : 0.042 0.275 4930 Planarity : 0.005 0.058 5303 Dihedral : 15.887 169.284 5549 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.05 % Allowed : 6.34 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3565 helix: 0.97 (0.14), residues: 1250 sheet: 0.52 (0.24), residues: 444 loop : -0.62 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG G 33 TYR 0.025 0.002 TYR J 232 PHE 0.022 0.002 PHE J 102 TRP 0.021 0.001 TRP J 259 HIS 0.019 0.001 HIS G 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (32561) covalent geometry : angle 0.63602 / 0.34 (44789) hydrogen bonds : bond 0.05665 / 3.36 ( 1112) hydrogen bonds : angle 4.48215 / 4.27 ( 3024) Misc. bond : bond 0.01302 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 1.105 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: A 42 MET cc_start: 0.7489 (mpp) cc_final: 0.7289 (mmm) REVERT: A 401 PHE cc_start: 0.7410 (m-80) cc_final: 0.7056 (m-80) REVERT: B 230 ASP cc_start: 0.8101 (t0) cc_final: 0.7771 (t0) REVERT: C 309 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6989 (mm110) REVERT: H 84 ASN cc_start: 0.8838 (m110) cc_final: 0.8593 (p0) REVERT: H 172 TYR cc_start: 0.7797 (t80) cc_final: 0.7559 (t80) REVERT: I 53 PHE cc_start: 0.8140 (t80) cc_final: 0.7934 (t80) REVERT: I 88 PHE cc_start: 0.6795 (p90) cc_final: 0.6391 (p90) REVERT: J 267 LEU cc_start: 0.8450 (mt) cc_final: 0.8193 (mt) outliers start: 32 outliers final: 20 residues processed: 255 average time/residue: 0.2048 time to fit residues: 82.8690 Evaluate side-chains 236 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain J residue 352 VAL Chi-restraints excluded: chain J residue 388 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 236 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 320 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 249 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS D 216 GLN E 231 HIS J 393 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.111911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.079652 restraints weight = 71591.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.077991 restraints weight = 57321.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078925 restraints weight = 54043.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.079011 restraints weight = 42504.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079098 restraints weight = 39041.436| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32564 Z= 0.133 Angle : 0.589 11.639 44789 Z= 0.314 Chirality : 0.041 0.243 4930 Planarity : 0.005 0.054 5303 Dihedral : 15.754 174.463 5547 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.08 % Allowed : 6.70 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3565 helix: 1.04 (0.15), residues: 1259 sheet: 0.54 (0.24), residues: 437 loop : -0.69 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 395 TYR 0.023 0.001 TYR H 6 PHE 0.023 0.001 PHE I 63 TRP 0.024 0.001 TRP J 259 HIS 0.006 0.001 HIS G 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (32561) covalent geometry : angle 0.58910 / 0.31 (44789) hydrogen bonds : bond 0.04761 / 2.83 ( 1112) hydrogen bonds : angle 4.26383 / 4.04 ( 3024) Misc. bond : bond 0.01444 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 1.220 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: A 42 MET cc_start: 0.7464 (mpp) cc_final: 0.7239 (mmm) REVERT: A 401 PHE cc_start: 0.7409 (m-80) cc_final: 0.7067 (m-80) REVERT: B 230 ASP cc_start: 0.8118 (t0) cc_final: 0.7770 (t0) REVERT: F 132 SER cc_start: 0.9313 (m) cc_final: 0.8877 (t) REVERT: G 151 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8167 (mtpp) REVERT: H 172 TYR cc_start: 0.7791 (t80) cc_final: 0.7529 (t80) REVERT: I 74 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8342 (mmm160) REVERT: I 88 PHE cc_start: 0.6535 (p90) cc_final: 0.6097 (p90) REVERT: I 133 LEU cc_start: 0.8888 (tp) cc_final: 0.8670 (mt) REVERT: J 287 PHE cc_start: 0.8255 (t80) cc_final: 0.8043 (t80) REVERT: J 384 HIS cc_start: 0.6240 (m-70) cc_final: 0.5567 (m-70) outliers start: 33 outliers final: 21 residues processed: 248 average time/residue: 0.2214 time to fit residues: 85.5535 Evaluate side-chains 236 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 215 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 367 optimal weight: 0.3980 chunk 243 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 12 optimal weight: 50.0000 chunk 17 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS I 64 HIS I 284 HIS ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.104314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072114 restraints weight = 71869.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.071853 restraints weight = 68932.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.071962 restraints weight = 56918.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.074120 restraints weight = 48271.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073900 restraints weight = 37362.111| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32564 Z= 0.162 Angle : 0.601 11.144 44789 Z= 0.318 Chirality : 0.042 0.254 4930 Planarity : 0.005 0.056 5303 Dihedral : 15.698 177.617 5547 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.18 % Allowed : 7.36 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3565 helix: 1.07 (0.15), residues: 1254 sheet: 0.47 (0.24), residues: 459 loop : -0.82 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 333 TYR 0.022 0.001 TYR E 62 PHE 0.018 0.002 PHE B 20 TRP 0.030 0.001 TRP J 259 HIS 0.015 0.001 HIS J 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (32561) covalent geometry : angle 0.60133 / 0.32 (44789) hydrogen bonds : bond 0.05017 / 2.97 ( 1112) hydrogen bonds : angle 4.25147 / 3.99 ( 3024) Misc. bond : bond 0.00321 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 1.170 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: A 401 PHE cc_start: 0.7436 (m-80) cc_final: 0.7152 (m-80) REVERT: B 230 ASP cc_start: 0.7964 (t0) cc_final: 0.7721 (t0) REVERT: C 301 TYR cc_start: 0.8863 (m-80) cc_final: 0.8642 (m-80) REVERT: G 151 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8148 (mtpp) REVERT: H 172 TYR cc_start: 0.7841 (t80) cc_final: 0.7549 (t80) REVERT: I 88 PHE cc_start: 0.6411 (p90) cc_final: 0.6074 (p90) outliers start: 36 outliers final: 23 residues processed: 246 average time/residue: 0.2115 time to fit residues: 82.3279 Evaluate side-chains 222 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 304 optimal weight: 0.9990 chunk 12 optimal weight: 50.0000 chunk 229 optimal weight: 3.9990 chunk 249 optimal weight: 0.5980 chunk 274 optimal weight: 4.9990 chunk 207 optimal weight: 0.0980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN B 163 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 HIS I 379 HIS J 393 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.105453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.073475 restraints weight = 71279.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.071952 restraints weight = 61934.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.072568 restraints weight = 58685.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072809 restraints weight = 47472.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.073008 restraints weight = 42474.723| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32564 Z= 0.116 Angle : 0.576 15.772 44789 Z= 0.302 Chirality : 0.040 0.277 4930 Planarity : 0.005 0.135 5303 Dihedral : 15.642 179.340 5547 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.37 % Allowed : 7.33 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3565 helix: 1.13 (0.15), residues: 1252 sheet: 0.57 (0.25), residues: 460 loop : -0.86 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG G 33 TYR 0.021 0.001 TYR E 62 PHE 0.027 0.001 PHE I 63 TRP 0.031 0.001 TRP J 259 HIS 0.005 0.001 HIS I 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (32561) covalent geometry : angle 0.57562 / 0.30 (44789) hydrogen bonds : bond 0.04232 / 2.50 ( 1112) hydrogen bonds : angle 4.10449 / 3.85 ( 3024) Misc. bond : bond 0.00805 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 1.077 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: A 381 MET cc_start: 0.7159 (pmm) cc_final: 0.6117 (ppp) REVERT: A 401 PHE cc_start: 0.7392 (m-80) cc_final: 0.7107 (m-80) REVERT: B 230 ASP cc_start: 0.8079 (t0) cc_final: 0.7804 (t0) REVERT: C 33 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7808 (mtm110) REVERT: C 301 TYR cc_start: 0.8834 (m-80) cc_final: 0.8615 (m-80) REVERT: F 132 SER cc_start: 0.9297 (m) cc_final: 0.8840 (t) REVERT: G 151 LYS cc_start: 0.8406 (ttmt) cc_final: 0.8197 (mtpp) REVERT: H 65 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6746 (ttmt) REVERT: H 172 TYR cc_start: 0.7872 (t80) cc_final: 0.7510 (t80) REVERT: I 88 PHE cc_start: 0.6498 (p90) cc_final: 0.6151 (p90) REVERT: J 384 HIS cc_start: 0.6031 (m-70) cc_final: 0.5409 (m-70) outliers start: 42 outliers final: 26 residues processed: 244 average time/residue: 0.2069 time to fit residues: 80.5864 Evaluate side-chains 238 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 379 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 16 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 185 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 204 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 HIS I 64 HIS I 379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.105053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.072906 restraints weight = 71988.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.071273 restraints weight = 59535.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.071950 restraints weight = 54010.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.072178 restraints weight = 42490.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.072250 restraints weight = 40088.917| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32564 Z= 0.128 Angle : 0.576 15.735 44789 Z= 0.302 Chirality : 0.041 0.246 4930 Planarity : 0.005 0.099 5303 Dihedral : 15.615 179.635 5547 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.11 % Allowed : 7.88 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3565 helix: 1.13 (0.15), residues: 1255 sheet: 0.60 (0.25), residues: 460 loop : -0.90 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 52 TYR 0.021 0.001 TYR E 62 PHE 0.047 0.001 PHE J 287 TRP 0.034 0.001 TRP J 259 HIS 0.025 0.001 HIS I 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (32561) covalent geometry : angle 0.57584 / 0.30 (44789) hydrogen bonds : bond 0.04365 / 2.59 ( 1112) hydrogen bonds : angle 4.09905 / 3.83 ( 3024) Misc. bond : bond 0.00310 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 1.151 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: A 381 MET cc_start: 0.7371 (pmm) cc_final: 0.7144 (pmm) REVERT: A 401 PHE cc_start: 0.7368 (m-80) cc_final: 0.7031 (m-80) REVERT: B 230 ASP cc_start: 0.8072 (t0) cc_final: 0.7786 (t0) REVERT: C 33 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7834 (mtm110) REVERT: G 151 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8210 (mtpp) REVERT: H 172 TYR cc_start: 0.7842 (t80) cc_final: 0.7514 (t80) REVERT: I 88 PHE cc_start: 0.6663 (p90) cc_final: 0.6235 (p90) REVERT: J 291 PHE cc_start: 0.8220 (m-80) cc_final: 0.7838 (m-80) REVERT: J 384 HIS cc_start: 0.6284 (m-70) cc_final: 0.5661 (m-70) outliers start: 34 outliers final: 26 residues processed: 241 average time/residue: 0.2145 time to fit residues: 81.6823 Evaluate side-chains 232 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 119 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 357 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 64 HIS I 400 HIS J 393 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.104311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.071966 restraints weight = 71312.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.071698 restraints weight = 66469.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.071849 restraints weight = 53959.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.073039 restraints weight = 46778.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.072922 restraints weight = 40396.357| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32564 Z= 0.150 Angle : 0.603 19.034 44789 Z= 0.314 Chirality : 0.042 0.319 4930 Planarity : 0.005 0.176 5303 Dihedral : 15.616 178.792 5547 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.11 % Allowed : 8.01 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3565 helix: 1.09 (0.15), residues: 1255 sheet: 0.53 (0.25), residues: 462 loop : -0.97 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 33 TYR 0.020 0.001 TYR E 62 PHE 0.029 0.002 PHE I 63 TRP 0.039 0.001 TRP J 259 HIS 0.007 0.001 HIS I 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (32561) covalent geometry : angle 0.60282 / 0.31 (44789) hydrogen bonds : bond 0.04598 / 2.73 ( 1112) hydrogen bonds : angle 4.13063 / 3.84 ( 3024) Misc. bond : bond 0.00870 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 MET cc_start: 0.7291 (pmm) cc_final: 0.6287 (ppp) REVERT: A 401 PHE cc_start: 0.7352 (m-80) cc_final: 0.7119 (m-80) REVERT: H 172 TYR cc_start: 0.7879 (t80) cc_final: 0.7514 (t80) REVERT: I 88 PHE cc_start: 0.6411 (p90) cc_final: 0.6072 (p90) REVERT: J 384 HIS cc_start: 0.5893 (m-70) cc_final: 0.5262 (m-70) outliers start: 34 outliers final: 26 residues processed: 238 average time/residue: 0.2300 time to fit residues: 85.6999 Evaluate side-chains 229 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 165 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 chunk 322 optimal weight: 0.0970 chunk 304 optimal weight: 5.9990 chunk 336 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.104645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.072574 restraints weight = 71193.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.070972 restraints weight = 61717.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.071685 restraints weight = 54809.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.071936 restraints weight = 42634.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.072036 restraints weight = 40201.959| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32564 Z= 0.131 Angle : 0.588 17.632 44789 Z= 0.308 Chirality : 0.041 0.260 4930 Planarity : 0.005 0.100 5303 Dihedral : 15.595 178.342 5547 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.98 % Allowed : 8.50 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3565 helix: 1.16 (0.15), residues: 1252 sheet: 0.52 (0.25), residues: 462 loop : -0.98 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 33 TYR 0.020 0.001 TYR E 62 PHE 0.016 0.001 PHE A 552 TRP 0.041 0.001 TRP J 259 HIS 0.010 0.001 HIS H 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (32561) covalent geometry : angle 0.58767 / 0.31 (44789) hydrogen bonds : bond 0.04353 / 2.58 ( 1112) hydrogen bonds : angle 4.09235 / 3.80 ( 3024) Misc. bond : bond 0.00350 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 MET cc_start: 0.7419 (pmm) cc_final: 0.6466 (ppp) REVERT: A 401 PHE cc_start: 0.7334 (m-80) cc_final: 0.7077 (m-80) REVERT: H 172 TYR cc_start: 0.7866 (t80) cc_final: 0.7517 (t80) REVERT: I 88 PHE cc_start: 0.6520 (p90) cc_final: 0.6114 (p90) REVERT: J 384 HIS cc_start: 0.6077 (m-70) cc_final: 0.5453 (m-70) outliers start: 30 outliers final: 24 residues processed: 226 average time/residue: 0.2239 time to fit residues: 80.1774 Evaluate side-chains 226 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 9 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 305 optimal weight: 0.8980 chunk 335 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 307 optimal weight: 0.9990 chunk 249 optimal weight: 0.0770 chunk 186 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 64 HIS ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.073735 restraints weight = 71445.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.072342 restraints weight = 62030.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.073066 restraints weight = 54830.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073360 restraints weight = 42293.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.073411 restraints weight = 39637.820| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32564 Z= 0.112 Angle : 0.581 15.786 44789 Z= 0.304 Chirality : 0.040 0.250 4930 Planarity : 0.005 0.185 5303 Dihedral : 15.574 177.923 5547 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.78 % Allowed : 8.67 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3565 helix: 1.25 (0.15), residues: 1255 sheet: 0.63 (0.25), residues: 452 loop : -0.96 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 333 TYR 0.020 0.001 TYR E 62 PHE 0.030 0.001 PHE I 63 TRP 0.052 0.001 TRP J 259 HIS 0.015 0.001 HIS H 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (32561) covalent geometry : angle 0.58131 / 0.30 (44789) hydrogen bonds : bond 0.03978 / 2.36 ( 1112) hydrogen bonds : angle 4.04098 / 3.73 ( 3024) Misc. bond : bond 0.00280 / 0.19 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 MET cc_start: 0.7391 (pmm) cc_final: 0.6447 (ppp) REVERT: F 132 SER cc_start: 0.9296 (m) cc_final: 0.8817 (t) REVERT: H 172 TYR cc_start: 0.7866 (t80) cc_final: 0.7518 (t80) REVERT: J 384 HIS cc_start: 0.5945 (m-70) cc_final: 0.5364 (m-70) outliers start: 24 outliers final: 21 residues processed: 240 average time/residue: 0.2245 time to fit residues: 84.9271 Evaluate side-chains 224 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 307 optimal weight: 5.9990 chunk 312 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 chunk 333 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 284 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 360 HIS ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.071663 restraints weight = 71591.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.070323 restraints weight = 60635.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.070966 restraints weight = 55239.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.071225 restraints weight = 42319.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.071279 restraints weight = 39551.585| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 32564 Z= 0.169 Angle : 0.623 18.594 44789 Z= 0.325 Chirality : 0.042 0.275 4930 Planarity : 0.005 0.088 5303 Dihedral : 15.582 177.778 5547 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.85 % Allowed : 9.06 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3565 helix: 1.19 (0.15), residues: 1254 sheet: 0.58 (0.25), residues: 450 loop : -1.05 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 33 TYR 0.019 0.001 TYR E 62 PHE 0.025 0.002 PHE I 88 TRP 0.057 0.002 TRP J 259 HIS 0.014 0.001 HIS H 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (32561) covalent geometry : angle 0.62339 / 0.32 (44789) hydrogen bonds : bond 0.04660 / 2.76 ( 1112) hydrogen bonds : angle 4.13226 / 3.81 ( 3024) Misc. bond : bond 0.00376 / 0.25 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4853.30 seconds wall clock time: 84 minutes 52.08 seconds (5092.08 seconds total)