Starting phenix.real_space_refine on Fri Mar 6 13:50:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u5d_26348/03_2026/7u5d_26348.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5d_26348/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7u5d_26348/03_2026/7u5d_26348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5d_26348/03_2026/7u5d_26348.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u5d_26348/03_2026/7u5d_26348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5d_26348/03_2026/7u5d_26348.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.25, per 1000 atoms: 0.20 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: 2.61 Conformation dependent library (CDL) restraints added in 1.3 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: 3.11 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: 6.12 Time building geometry restraints manager: 3.37 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: 42622 3.52 - 7.03: 1876 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: 18425 31.51 - 63.02: 682 63.02 - 94.53: 103 94.53 - 126.04: 3 126.04 - 157.54: 7 Dihedral angle restraints: 19220 sinusoidal: 8751 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 19217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3537 0.088 - 0.175: 1166 0.175 - 0.263: 167 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: 4.720 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.600 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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= 0.983 Angle : 1.650 17.579 44789 Z= 1.172 Chirality : 0.085 0.438 4930 Planarity : 0.009 0.093 5303 Dihedral : 15.664 157.545 12482 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 covalent geometry : bond 0.01320 (32561) covalent geometry : angle 1.64958 (44789) hydrogen bonds : bond 0.25423 ( 1112) hydrogen bonds : angle 7.48512 ( 3024) Misc. bond : bond 0.41143 ( 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 : 1.058 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: 0.2367 time to fit residues: 170.2603 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 : 1.093 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 58 ASN 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 J 393 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.114481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082248 restraints weight = 72271.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.080704 restraints weight = 57591.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.081172 restraints weight = 55566.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.081475 restraints weight = 45550.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081629 restraints weight = 41567.508| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32564 Z= 0.142 Angle : 0.665 13.833 44789 Z= 0.354 Chirality : 0.042 0.254 4930 Planarity : 0.005 0.057 5303 Dihedral : 17.311 170.986 5747 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.82 % Allowed : 5.92 % Favored : 93.26 % 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: 0.21 (0.14), residues: 3565 helix: 0.76 (0.14), residues: 1250 sheet: 0.22 (0.22), residues: 518 loop : -0.23 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 33 TYR 0.034 0.002 TYR J 232 PHE 0.039 0.002 PHE I 88 TRP 0.021 0.001 TRP J 259 HIS 0.007 0.001 HIS G 163 Details of bonding type rmsd covalent geometry : bond 0.00290 (32561) covalent geometry : angle 0.66454 (44789) hydrogen bonds : bond 0.05288 ( 1112) hydrogen bonds : angle 4.71894 ( 3024) Misc. bond : bond 0.00508 ( 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 308 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 1.118 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: F 132 SER cc_start: 0.9273 (m) cc_final: 0.8892 (t) REVERT: J 267 LEU cc_start: 0.8347 (mt) cc_final: 0.8071 (mt) outliers start: 25 outliers final: 13 residues processed: 300 average time/residue: 0.2152 time to fit residues: 100.3994 Evaluate side-chains 236 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 223 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 13 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 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 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: 5.9990 chunk 348 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 171 optimal weight: 0.0040 chunk 275 optimal weight: 3.9990 chunk 356 optimal weight: 6.9990 chunk 232 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN A 455 ASN B 163 HIS ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN E 231 HIS F 58 ASN G 342 GLN H 84 ASN I 77 GLN ** I 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 HIS J 154 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.070547 restraints weight = 72073.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.068949 restraints weight = 59415.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.069925 restraints weight = 57138.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.069902 restraints weight = 44554.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.070020 restraints weight = 41085.369| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 32564 Z= 0.219 Angle : 0.673 9.762 44789 Z= 0.356 Chirality : 0.044 0.256 4930 Planarity : 0.005 0.055 5303 Dihedral : 17.101 175.828 5737 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.18 % Allowed : 6.80 % Favored : 92.02 % 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: 0.89 (0.15), residues: 1260 sheet: 0.34 (0.24), residues: 437 loop : -0.71 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 33 TYR 0.020 0.002 TYR E 62 PHE 0.027 0.002 PHE I 88 TRP 0.019 0.002 TRP J 259 HIS 0.020 0.001 HIS G 163 Details of bonding type rmsd covalent geometry : bond 0.00511 (32561) covalent geometry : angle 0.67253 (44789) hydrogen bonds : bond 0.06109 ( 1112) hydrogen bonds : angle 4.55183 ( 3024) Misc. bond : bond 0.00377 ( 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 280 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 1.040 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 42 MET cc_start: 0.7621 (mpp) cc_final: 0.7421 (mmm) REVERT: A 393 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: A 401 PHE cc_start: 0.7294 (m-10) cc_final: 0.7063 (m-10) REVERT: C 309 GLN cc_start: 0.7415 (mm110) cc_final: 0.7171 (mm-40) REVERT: F 332 MET cc_start: 0.8863 (mmm) cc_final: 0.8345 (mmm) REVERT: G 70 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6205 (pp30) REVERT: G 151 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8182 (mtpp) REVERT: I 53 PHE cc_start: 0.8252 (t80) cc_final: 0.8037 (t80) REVERT: I 63 PHE cc_start: 0.9059 (p90) cc_final: 0.8849 (p90) REVERT: I 74 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8308 (mmm160) REVERT: J 267 LEU cc_start: 0.8405 (mt) cc_final: 0.8127 (mt) REVERT: J 384 HIS cc_start: 0.6324 (m-70) cc_final: 0.5561 (m-70) outliers start: 36 outliers final: 21 residues processed: 266 average time/residue: 0.2118 time to fit residues: 88.0439 Evaluate side-chains 235 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain E residue 30 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 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 311 ILE Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 236 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 125 optimal weight: 2.9990 chunk 320 optimal weight: 0.0980 chunk 267 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 249 optimal weight: 0.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS C 181 GLN D 216 GLN E 231 HIS F 181 GLN G 163 HIS I 154 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079680 restraints weight = 71594.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.078614 restraints weight = 56196.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.079392 restraints weight = 53275.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.079442 restraints weight = 43711.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.079542 restraints weight = 39498.212| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32564 Z= 0.113 Angle : 0.564 10.280 44789 Z= 0.298 Chirality : 0.040 0.239 4930 Planarity : 0.004 0.051 5303 Dihedral : 16.967 179.215 5737 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.24 % Allowed : 7.16 % Favored : 91.60 % 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: 0.15 (0.14), residues: 3565 helix: 1.17 (0.15), residues: 1250 sheet: 0.57 (0.24), residues: 447 loop : -0.75 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 33 TYR 0.021 0.001 TYR E 62 PHE 0.016 0.001 PHE J 383 TRP 0.022 0.001 TRP J 259 HIS 0.004 0.001 HIS G 163 Details of bonding type rmsd covalent geometry : bond 0.00235 (32561) covalent geometry : angle 0.56414 (44789) hydrogen bonds : bond 0.04218 ( 1112) hydrogen bonds : angle 4.17305 ( 3024) Misc. bond : bond 0.00285 ( 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 270 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 1.140 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: C 301 TYR cc_start: 0.8851 (m-80) cc_final: 0.8646 (m-80) REVERT: G 70 GLN cc_start: 0.7095 (mm-40) cc_final: 0.6271 (pp30) REVERT: H 65 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7097 (tptm) REVERT: I 28 PHE cc_start: 0.7441 (m-80) cc_final: 0.7006 (m-80) REVERT: J 384 HIS cc_start: 0.6095 (m-70) cc_final: 0.5365 (m-70) outliers start: 38 outliers final: 22 residues processed: 255 average time/residue: 0.2115 time to fit residues: 84.4474 Evaluate side-chains 231 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 293 HIS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 231 HIS 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 139 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 352 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 215 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 367 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS H 81 GLN I 400 HIS J 154 HIS ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.102085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.069736 restraints weight = 71873.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.069060 restraints weight = 69121.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.069308 restraints weight = 55758.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.069764 restraints weight = 48395.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.069846 restraints weight = 44116.725| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 32564 Z= 0.232 Angle : 0.645 11.478 44789 Z= 0.341 Chirality : 0.043 0.255 4930 Planarity : 0.006 0.111 5303 Dihedral : 16.990 178.922 5737 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.18 % Allowed : 7.95 % 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: -0.18 (0.14), residues: 3565 helix: 0.95 (0.15), residues: 1257 sheet: 0.30 (0.25), residues: 445 loop : -0.98 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG H 52 TYR 0.033 0.002 TYR H 172 PHE 0.022 0.002 PHE E 88 TRP 0.020 0.002 TRP J 259 HIS 0.020 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00550 (32561) covalent geometry : angle 0.64519 (44789) hydrogen bonds : bond 0.05792 ( 1112) hydrogen bonds : angle 4.38348 ( 3024) Misc. bond : bond 0.00232 ( 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 256 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.8307 (ptp-170) cc_final: 0.8086 (ptp-170) REVERT: A 381 MET cc_start: 0.7398 (pmm) cc_final: 0.7179 (pmm) REVERT: A 401 PHE cc_start: 0.7289 (m-10) cc_final: 0.7042 (m-10) REVERT: G 70 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6459 (pp30) REVERT: I 28 PHE cc_start: 0.7301 (m-80) cc_final: 0.6944 (m-80) REVERT: J 384 HIS cc_start: 0.5913 (m-70) cc_final: 0.5254 (m-70) outliers start: 36 outliers final: 25 residues processed: 242 average time/residue: 0.2137 time to fit residues: 80.5691 Evaluate side-chains 232 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 482 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 200 ILE 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 82 ASP 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 199 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 111 optimal weight: 0.0060 chunk 200 optimal weight: 3.9990 chunk 304 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 249 optimal weight: 0.2980 chunk 274 optimal weight: 1.9990 chunk 207 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS F 163 HIS G 70 GLN J 393 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.104581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.072303 restraints weight = 70909.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.070982 restraints weight = 56004.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.071853 restraints weight = 55045.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.071922 restraints weight = 43314.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.072001 restraints weight = 39524.176| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32564 Z= 0.113 Angle : 0.561 16.733 44789 Z= 0.293 Chirality : 0.039 0.240 4930 Planarity : 0.005 0.103 5303 Dihedral : 16.890 178.498 5737 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.05 % Allowed : 8.57 % Favored : 90.39 % 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: 1.12 (0.15), residues: 1255 sheet: 0.47 (0.24), residues: 460 loop : -0.97 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 33 TYR 0.026 0.001 TYR H 194 PHE 0.012 0.001 PHE E 88 TRP 0.025 0.001 TRP J 259 HIS 0.009 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00242 (32561) covalent geometry : angle 0.56111 (44789) hydrogen bonds : bond 0.03971 ( 1112) hydrogen bonds : angle 4.07041 ( 3024) Misc. bond : bond 0.00476 ( 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 249 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 1.106 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: 0.7447 (pmm) cc_final: 0.6526 (ppp) REVERT: H 6 TYR cc_start: 0.7365 (m-80) cc_final: 0.7085 (m-10) REVERT: J 291 PHE cc_start: 0.8068 (m-80) cc_final: 0.7822 (m-80) REVERT: J 384 HIS cc_start: 0.6090 (m-70) cc_final: 0.5450 (m-70) outliers start: 32 outliers final: 25 residues processed: 237 average time/residue: 0.2142 time to fit residues: 79.5227 Evaluate side-chains 230 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 491 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 200 ILE 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 E residue 231 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 199 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 16 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 331 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 185 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 204 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS E 231 HIS I 64 HIS ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.104583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.072319 restraints weight = 71754.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070743 restraints weight = 58724.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.071129 restraints weight = 56770.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.071351 restraints weight = 49533.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.071701 restraints weight = 42538.733| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32564 Z= 0.120 Angle : 0.565 15.570 44789 Z= 0.293 Chirality : 0.039 0.244 4930 Planarity : 0.005 0.118 5303 Dihedral : 16.847 178.115 5737 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.01 % Allowed : 9.03 % Favored : 89.96 % 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: 1.20 (0.15), residues: 1256 sheet: 0.49 (0.25), residues: 463 loop : -1.01 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 33 TYR 0.024 0.001 TYR H 194 PHE 0.047 0.001 PHE J 287 TRP 0.028 0.001 TRP J 259 HIS 0.033 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00266 (32561) covalent geometry : angle 0.56466 (44789) hydrogen bonds : bond 0.04010 ( 1112) hydrogen bonds : angle 4.01617 ( 3024) Misc. bond : bond 0.00311 ( 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 247 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 1.130 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 52 LEU cc_start: 0.9122 (tp) cc_final: 0.8865 (tp) REVERT: A 381 MET cc_start: 0.7595 (pmm) cc_final: 0.6736 (ppp) REVERT: H 65 LYS cc_start: 0.7660 (mmtp) cc_final: 0.7299 (mmmm) REVERT: I 28 PHE cc_start: 0.7742 (m-80) cc_final: 0.7398 (m-80) REVERT: J 291 PHE cc_start: 0.8160 (m-80) cc_final: 0.7838 (m-80) REVERT: J 384 HIS cc_start: 0.6281 (m-70) cc_final: 0.5643 (m-70) outliers start: 31 outliers final: 25 residues processed: 234 average time/residue: 0.2108 time to fit residues: 77.7820 Evaluate side-chains 225 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 179 LEU 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 199 ASP 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 69 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 357 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 102 optimal weight: 0.0020 chunk 251 optimal weight: 2.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN E 231 HIS I 64 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 = 0.3598 r_free = 0.3598 target = 0.102909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070691 restraints weight = 71064.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.069260 restraints weight = 61852.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.070276 restraints weight = 56715.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.070191 restraints weight = 43427.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.070298 restraints weight = 40108.190| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32564 Z= 0.167 Angle : 0.600 14.460 44789 Z= 0.313 Chirality : 0.041 0.248 4930 Planarity : 0.005 0.062 5303 Dihedral : 16.843 177.932 5737 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.21 % Allowed : 8.89 % Favored : 89.90 % 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: -0.17 (0.14), residues: 3565 helix: 1.14 (0.15), residues: 1256 sheet: 0.22 (0.24), residues: 476 loop : -1.12 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 33 TYR 0.020 0.001 TYR H 194 PHE 0.035 0.002 PHE I 88 TRP 0.031 0.001 TRP J 259 HIS 0.006 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00388 (32561) covalent geometry : angle 0.60002 (44789) hydrogen bonds : bond 0.04812 ( 1112) hydrogen bonds : angle 4.15222 ( 3024) Misc. bond : bond 0.00258 ( 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 245 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.871 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: 0.7644 (pmm) cc_final: 0.6809 (ppp) REVERT: A 393 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: H 42 ILE cc_start: 0.8994 (mp) cc_final: 0.8664 (mm) REVERT: I 28 PHE cc_start: 0.7491 (m-80) cc_final: 0.7261 (m-80) REVERT: J 384 HIS cc_start: 0.5916 (m-70) cc_final: 0.5343 (m-70) outliers start: 37 outliers final: 28 residues processed: 232 average time/residue: 0.2040 time to fit residues: 74.9059 Evaluate side-chains 232 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 GLN 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 200 ILE Chi-restraints excluded: chain B residue 202 TRP Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 179 LEU 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 E residue 231 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 199 ASP 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 69 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 165 optimal weight: 1.9990 chunk 303 optimal weight: 7.9990 chunk 322 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS I 64 HIS I 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.102985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.070256 restraints weight = 71423.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.068819 restraints weight = 56876.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.069384 restraints weight = 54589.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.069650 restraints weight = 42482.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.069696 restraints weight = 39748.770| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32564 Z= 0.138 Angle : 0.583 17.281 44789 Z= 0.303 Chirality : 0.040 0.243 4930 Planarity : 0.005 0.055 5303 Dihedral : 16.810 177.919 5737 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.05 % Allowed : 9.35 % Favored : 89.60 % 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: -0.17 (0.14), residues: 3565 helix: 1.18 (0.15), residues: 1258 sheet: 0.22 (0.25), residues: 477 loop : -1.15 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 33 TYR 0.026 0.001 TYR A 330 PHE 0.036 0.002 PHE I 88 TRP 0.033 0.001 TRP J 259 HIS 0.015 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00315 (32561) covalent geometry : angle 0.58309 (44789) hydrogen bonds : bond 0.04286 ( 1112) hydrogen bonds : angle 4.07356 ( 3024) Misc. bond : bond 0.00182 ( 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 242 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.957 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: 0.7738 (pmm) cc_final: 0.6974 (ppp) REVERT: H 42 ILE cc_start: 0.9018 (mp) cc_final: 0.8729 (mm) REVERT: I 88 PHE cc_start: 0.7130 (p90) cc_final: 0.6834 (t80) REVERT: J 384 HIS cc_start: 0.6103 (m-70) cc_final: 0.5508 (m-70) outliers start: 32 outliers final: 28 residues processed: 230 average time/residue: 0.2028 time to fit residues: 73.5310 Evaluate side-chains 230 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 576 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 202 TRP Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 179 LEU 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 E residue 231 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 199 ASP 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: 3.9990 chunk 118 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 317 optimal weight: 1.9990 chunk 305 optimal weight: 9.9990 chunk 335 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 307 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN ** 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 = 0.3590 r_free = 0.3590 target = 0.102595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.069713 restraints weight = 71641.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.069896 restraints weight = 67295.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.069989 restraints weight = 56536.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.070320 restraints weight = 46544.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.070474 restraints weight = 42316.064| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32564 Z= 0.152 Angle : 0.590 16.686 44789 Z= 0.308 Chirality : 0.041 0.245 4930 Planarity : 0.005 0.061 5303 Dihedral : 16.803 177.795 5737 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.95 % Allowed : 9.45 % Favored : 89.60 % 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: -0.21 (0.14), residues: 3565 helix: 1.17 (0.15), residues: 1257 sheet: 0.19 (0.25), residues: 476 loop : -1.20 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 33 TYR 0.020 0.001 TYR E 62 PHE 0.035 0.002 PHE I 88 TRP 0.031 0.001 TRP J 259 HIS 0.016 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00351 (32561) covalent geometry : angle 0.59038 (44789) hydrogen bonds : bond 0.04453 ( 1112) hydrogen bonds : angle 4.09527 ( 3024) Misc. bond : bond 0.00171 ( 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 233 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 1.202 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: 0.7628 (pmm) cc_final: 0.6877 (ppp) REVERT: G 97 MET cc_start: 0.7997 (mmm) cc_final: 0.7644 (mtt) REVERT: H 42 ILE cc_start: 0.8998 (mp) cc_final: 0.8731 (mm) REVERT: J 384 HIS cc_start: 0.5674 (m-70) cc_final: 0.5138 (m-70) outliers start: 29 outliers final: 28 residues processed: 222 average time/residue: 0.2128 time to fit residues: 74.4196 Evaluate side-chains 228 residues out of total 3058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 576 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 202 TRP Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 179 LEU 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 199 ASP 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 69 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 307 optimal weight: 0.8980 chunk 312 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 333 optimal weight: 2.9990 chunk 272 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 284 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 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 = 0.3588 r_free = 0.3588 target = 0.102417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.069743 restraints weight = 71680.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.068183 restraints weight = 58454.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.069038 restraints weight = 55657.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.069107 restraints weight = 43853.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.069208 restraints weight = 40188.716| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32564 Z= 0.156 Angle : 0.597 16.291 44789 Z= 0.312 Chirality : 0.041 0.245 4930 Planarity : 0.005 0.060 5303 Dihedral : 16.799 177.657 5737 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.05 % Allowed : 9.61 % Favored : 89.34 % 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: -0.26 (0.14), residues: 3565 helix: 1.13 (0.15), residues: 1262 sheet: 0.15 (0.25), residues: 476 loop : -1.22 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 33 TYR 0.029 0.001 TYR H 6 PHE 0.082 0.002 PHE I 88 TRP 0.032 0.001 TRP J 259 HIS 0.007 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00361 (32561) covalent geometry : angle 0.59658 (44789) hydrogen bonds : bond 0.04576 ( 1112) hydrogen bonds : angle 4.12035 ( 3024) Misc. bond : bond 0.00169 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4565.80 seconds wall clock time: 79 minutes 43.25 seconds (4783.25 seconds total)