Starting phenix.real_space_refine on Sat Sep 12 15:26:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v4x_21050/09_2026/6v4x_21050.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v4x_21050/09_2026/6v4x_21050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v4x_21050/09_2026/6v4x_21050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v4x_21050/09_2026/6v4x_21050.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6v4x_21050/09_2026/6v4x_21050.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v4x_21050/09_2026/6v4x_21050.cif" model { file = "/net/cci-nas-00/data/ceres_data/6v4x_21050/09_2026/6v4x_21050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v4x_21050/09_2026/6v4x_21050.cif" } resolution = 3.2 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= 0.003 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 52 5.49 5 S 101 5.16 5 C 10276 2.51 5 N 2881 2.21 5 O 3187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16499 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain breaks: 1 Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "E" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 670 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 911 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "D" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 2 Chain: "H" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3980 Classifications: {'peptide': 499} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 479} Chain breaks: 1 Chain: "I" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4055 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 22, 'TRANS': 487} Chain breaks: 2 Chain: "J" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2461 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain: "Z" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 564 Classifications: {'RNAv2': 27} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 20} Chain: "Y" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 537 Classifications: {'RNAv2': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.59, per 1000 atoms: 0.22 Number of scatterers: 16499 At special positions: 0 Unit cell: (117.7, 149.8, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 101 16.00 P 52 15.00 O 3187 8.00 N 2881 7.00 C 10276 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 781.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 71 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 158 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 73 " pdb=" ZN H 702 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 418 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 76 " 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 22 sheets defined 34.4% alpha, 23.5% beta 10 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.713A pdb=" N ASN A 79 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 removed outlier: 3.669A pdb=" N HIS B 12 " --> pdb=" O MET B 9 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.530A pdb=" N LEU E 20 " --> pdb=" O GLN E 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'C' and resid 6 through 15 removed outlier: 3.907A pdb=" N ILE C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.976A pdb=" N LEU C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 106 removed outlier: 3.589A pdb=" N GLU C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 106 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.714A pdb=" N GLU D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 Processing helix chain 'H' and resid 48 through 53 removed outlier: 3.600A pdb=" N LEU H 53 " --> pdb=" O MET H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.542A pdb=" N GLU H 63 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 60 through 64' Processing helix chain 'H' and resid 73 through 78 Processing helix chain 'H' and resid 79 through 85 Processing helix chain 'H' and resid 96 through 107 removed outlier: 3.708A pdb=" N ALA H 101 " --> pdb=" O HIS H 97 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TRP H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 124 through 130 removed outlier: 3.816A pdb=" N GLU H 130 " --> pdb=" O THR H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 232 removed outlier: 3.578A pdb=" N ALA H 220 " --> pdb=" O GLU H 216 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 259 removed outlier: 3.532A pdb=" N LEU H 251 " --> pdb=" O GLN H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 265 removed outlier: 3.561A pdb=" N LEU H 263 " --> pdb=" O HIS H 260 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS H 264 " --> pdb=" O PRO H 261 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP H 265 " --> pdb=" O GLU H 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 260 through 265' Processing helix chain 'H' and resid 273 through 278 removed outlier: 3.668A pdb=" N LYS H 277 " --> pdb=" O SER H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 285 removed outlier: 3.731A pdb=" N TYR H 282 " --> pdb=" O CYS H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 295 Processing helix chain 'H' and resid 335 through 343 removed outlier: 3.777A pdb=" N PHE H 341 " --> pdb=" O SER H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 367 Processing helix chain 'H' and resid 368 through 370 No H-bonds generated for 'chain 'H' and resid 368 through 370' Processing helix chain 'H' and resid 398 through 410 removed outlier: 3.840A pdb=" N GLU H 404 " --> pdb=" O GLN H 400 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU H 409 " --> pdb=" O PHE H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 433 removed outlier: 3.543A pdb=" N LEU H 427 " --> pdb=" O GLU H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 472 removed outlier: 3.863A pdb=" N ASP H 472 " --> pdb=" O PHE H 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 70 through 77 Processing helix chain 'I' and resid 88 through 107 removed outlier: 3.722A pdb=" N MET I 96 " --> pdb=" O LYS I 92 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET I 98 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN I 103 " --> pdb=" O TYR I 99 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER I 104 " --> pdb=" O ASP I 100 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG I 105 " --> pdb=" O LEU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 123 Processing helix chain 'I' and resid 211 through 229 removed outlier: 3.704A pdb=" N GLU I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN I 218 " --> pdb=" O GLN I 214 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 219 " --> pdb=" O ARG I 215 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR I 226 " --> pdb=" O ASN I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 256 removed outlier: 3.504A pdb=" N ILE I 253 " --> pdb=" O LEU I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 264 removed outlier: 3.917A pdb=" N VAL I 263 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 281 removed outlier: 3.506A pdb=" N VAL I 277 " --> pdb=" O SER I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 297 removed outlier: 4.144A pdb=" N PHE I 295 " --> pdb=" O LEU I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 318 Processing helix chain 'I' and resid 336 through 345 Processing helix chain 'I' and resid 363 through 370 Processing helix chain 'I' and resid 548 through 556 removed outlier: 4.116A pdb=" N ILE I 553 " --> pdb=" O ILE I 549 " (cutoff:3.500A) Processing helix chain 'I' and resid 567 through 579 removed outlier: 3.594A pdb=" N GLN I 572 " --> pdb=" O PRO I 568 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP I 573 " --> pdb=" O GLU I 569 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS I 577 " --> pdb=" O ASP I 573 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 44 removed outlier: 4.489A pdb=" N VAL J 37 " --> pdb=" O SER J 33 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP J 38 " --> pdb=" O GLU J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 4.364A pdb=" N VAL J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN J 57 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE J 62 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 70 Processing helix chain 'J' and resid 73 through 78 removed outlier: 3.521A pdb=" N ILE J 77 " --> pdb=" O PHE J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.759A pdb=" N ALA J 82 " --> pdb=" O ALA J 79 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP J 83 " --> pdb=" O PHE J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'J' and resid 85 through 101 removed outlier: 4.113A pdb=" N ARG J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE J 93 " --> pdb=" O ARG J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 105 No H-bonds generated for 'chain 'J' and resid 103 through 105' Processing helix chain 'J' and resid 106 through 111 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 147 removed outlier: 3.816A pdb=" N VAL J 126 " --> pdb=" O ASN J 122 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS J 138 " --> pdb=" O THR J 134 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA J 140 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER J 147 " --> pdb=" O TRP J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 removed outlier: 3.584A pdb=" N CYS J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET J 160 " --> pdb=" O ALA J 156 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE J 168 " --> pdb=" O MET J 164 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE J 169 " --> pdb=" O ALA J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 176 through 192 removed outlier: 3.827A pdb=" N GLY J 189 " --> pdb=" O LYS J 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL J 192 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 244 removed outlier: 3.874A pdb=" N LYS J 233 " --> pdb=" O TRP J 229 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET J 243 " --> pdb=" O LEU J 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 244 " --> pdb=" O LEU J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 266 removed outlier: 3.688A pdb=" N GLY J 258 " --> pdb=" O THR J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 269 No H-bonds generated for 'chain 'J' and resid 267 through 269' Processing helix chain 'J' and resid 270 through 284 removed outlier: 3.667A pdb=" N ILE J 275 " --> pdb=" O MET J 271 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN J 276 " --> pdb=" O SER J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 310 removed outlier: 4.369A pdb=" N SER J 296 " --> pdb=" O SER J 292 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS J 302 " --> pdb=" O ARG J 298 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS J 310 " --> pdb=" O LEU J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 316 removed outlier: 3.806A pdb=" N LEU J 315 " --> pdb=" O PRO J 312 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU J 316 " --> pdb=" O ALA J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 328 removed outlier: 3.534A pdb=" N THR J 322 " --> pdb=" O GLN J 318 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR J 323 " --> pdb=" O ALA J 319 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL J 326 " --> pdb=" O THR J 322 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP J 327 " --> pdb=" O THR J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 337 removed outlier: 3.601A pdb=" N ILE J 335 " --> pdb=" O PRO J 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 removed outlier: 3.795A pdb=" N ALA A 56 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER A 44 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU A 32 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A 46 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY A 30 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 48 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR A 28 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A 16 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE A 17 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 73 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 19 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 71 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A 21 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU B 69 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 41 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 28 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.212A pdb=" N SER A 44 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU A 32 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A 46 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY A 30 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 48 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR A 28 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A 16 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE A 17 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 73 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 19 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 71 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A 21 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU B 69 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 41 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG B 16 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 53 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 56 through 57 removed outlier: 3.522A pdb=" N ILE F 72 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS F 22 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE F 72 " --> pdb=" O MET F 20 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET F 20 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR F 32 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN F 46 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 34 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU F 44 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL F 36 " --> pdb=" O MET F 42 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N MET F 42 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLN F 43 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE F 64 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA F 45 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL F 62 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU F 49 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N HIS F 58 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE F 51 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER F 56 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU F 61 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS D 172 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL D 356 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN D 170 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU D 358 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LYS D 168 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 56 through 57 removed outlier: 3.522A pdb=" N ILE F 72 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS F 22 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE F 72 " --> pdb=" O MET F 20 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET F 20 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR F 32 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN F 46 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 34 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU F 44 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL F 36 " --> pdb=" O MET F 42 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N MET F 42 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLN F 43 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE F 64 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA F 45 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL F 62 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU F 49 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N HIS F 58 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE F 51 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER F 56 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU F 61 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS D 172 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL D 356 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN D 170 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU D 358 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LYS D 168 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL D 171 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL D 182 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 173 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG D 180 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR D 205 " --> pdb=" O PHE D 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 71 through 75 removed outlier: 6.083A pdb=" N ALA E 61 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET E 41 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU E 35 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU E 86 " --> pdb=" O TRP E 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 54 through 56 Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 56 removed outlier: 6.498A pdb=" N VAL G 41 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS G 45 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN G 28 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU G 47 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N HIS G 26 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU G 71 " --> pdb=" O SER G 18 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET G 69 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.637A pdb=" N THR C 30 " --> pdb=" O HIS C 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.674A pdb=" N TYR C 59 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 135 through 137 removed outlier: 6.251A pdb=" N THR H 93 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU H 67 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU H 66 " --> pdb=" O LYS H 36 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N CYS H 27 " --> pdb=" O LEU H 17 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 144 through 145 removed outlier: 6.802A pdb=" N LYS H 173 " --> pdb=" O ILE H 200 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE H 202 " --> pdb=" O LYS H 173 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU H 175 " --> pdb=" O ILE H 202 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLU H 204 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU H 201 " --> pdb=" O ILE H 415 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL H 417 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE H 203 " --> pdb=" O VAL H 417 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL H 414 " --> pdb=" O HIS H 446 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 308 through 310 removed outlier: 6.646A pdb=" N ILE H 268 " --> pdb=" O SER H 309 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG H 235 " --> pdb=" O GLY H 351 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE H 353 " --> pdb=" O ARG H 235 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU H 237 " --> pdb=" O ILE H 353 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 373 through 375 Processing sheet with id=AB5, first strand: chain 'H' and resid 462 through 466 removed outlier: 4.376A pdb=" N LYS H 462 " --> pdb=" O LEU I 610 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL H 466 " --> pdb=" O TYR I 606 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR I 606 " --> pdb=" O VAL H 466 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 492 through 495 Processing sheet with id=AB7, first strand: chain 'I' and resid 29 through 30 removed outlier: 6.644A pdb=" N CYS I 20 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 58 through 59 removed outlier: 6.649A pdb=" N VAL I 58 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR I 87 " --> pdb=" O VAL I 58 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE I 84 " --> pdb=" O GLN I 127 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU I 129 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA I 86 " --> pdb=" O LEU I 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 135 through 136 Processing sheet with id=AC1, first strand: chain 'I' and resid 149 through 150 Processing sheet with id=AC2, first strand: chain 'I' and resid 172 through 173 removed outlier: 6.175A pdb=" N LEU I 198 " --> pdb=" O ILE I 562 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 308 through 311 removed outlier: 6.329A pdb=" N LEU I 266 " --> pdb=" O SER I 309 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N CYS I 311 " --> pdb=" O LEU I 266 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU I 268 " --> pdb=" O CYS I 311 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU I 327 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL I 233 " --> pdb=" O VAL I 326 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA I 328 " --> pdb=" O VAL I 233 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE I 235 " --> pdb=" O ALA I 328 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU I 234 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE I 353 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 377 through 384 547 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3900 1.33 - 1.45: 3441 1.45 - 1.57: 9290 1.57 - 1.69: 101 1.69 - 1.81: 170 Bond restraints: 16902 Sorted by residual: bond pdb=" O3' G Y 46 " pdb=" P U Y 47 " ideal model delta sigma weight residual 1.607 1.695 -0.088 1.20e-02 6.94e+03 5.34e+01 bond pdb=" O3' A Y 48 " pdb=" P A Y 49 " ideal model delta sigma weight residual 1.607 1.688 -0.081 1.20e-02 6.94e+03 4.56e+01 bond pdb=" O3' U Y 47 " pdb=" P A Y 48 " ideal model delta sigma weight residual 1.607 1.645 -0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" CA PRO H 267 " pdb=" C PRO H 267 " ideal model delta sigma weight residual 1.520 1.562 -0.043 1.42e-02 4.96e+03 9.13e+00 bond pdb=" C PRO F 7 " pdb=" N LYS F 8 " ideal model delta sigma weight residual 1.331 1.381 -0.050 2.07e-02 2.33e+03 5.77e+00 ... (remaining 16897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 22985 5.34 - 10.68: 80 10.68 - 16.02: 2 16.02 - 21.36: 1 21.36 - 26.70: 2 Bond angle restraints: 23070 Sorted by residual: angle pdb=" C3' A Y 48 " pdb=" O3' A Y 48 " pdb=" P A Y 49 " ideal model delta sigma weight residual 119.70 139.23 -19.53 1.20e+00 6.94e-01 2.65e+02 angle pdb=" N ALA H 507 " pdb=" CA ALA H 507 " pdb=" C ALA H 507 " ideal model delta sigma weight residual 111.14 123.25 -12.11 1.08e+00 8.57e-01 1.26e+02 angle pdb=" C3' U Y 47 " pdb=" O3' U Y 47 " pdb=" P A Y 48 " ideal model delta sigma weight residual 119.70 107.88 11.82 1.20e+00 6.94e-01 9.70e+01 angle pdb=" O3' A Y 48 " pdb=" P A Y 49 " pdb=" OP1 A Y 49 " ideal model delta sigma weight residual 108.00 81.30 26.70 3.00e+00 1.11e-01 7.92e+01 angle pdb=" O3' A Y 48 " pdb=" P A Y 49 " pdb=" OP2 A Y 49 " ideal model delta sigma weight residual 108.00 131.83 -23.83 3.00e+00 1.11e-01 6.31e+01 ... (remaining 23065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 9917 32.54 - 65.08: 238 65.08 - 97.62: 23 97.62 - 130.16: 0 130.16 - 162.70: 1 Dihedral angle restraints: 10179 sinusoidal: 4578 harmonic: 5601 Sorted by residual: dihedral pdb=" C4' U Y 28 " pdb=" C3' U Y 28 " pdb=" C2' U Y 28 " pdb=" C1' U Y 28 " ideal model delta sinusoidal sigma weight residual 36.34 -38.40 74.74 1 3.10e+00 1.04e-01 7.36e+02 dihedral pdb=" C4' U Z 23 " pdb=" C3' U Z 23 " pdb=" C2' U Z 23 " pdb=" C1' U Z 23 " ideal model delta sinusoidal sigma weight residual 36.34 -38.02 74.36 1 3.10e+00 1.04e-01 7.30e+02 dihedral pdb=" C4' A Z 30 " pdb=" C3' A Z 30 " pdb=" C2' A Z 30 " pdb=" C1' A Z 30 " ideal model delta sinusoidal sigma weight residual 36.34 -37.85 74.19 1 3.10e+00 1.04e-01 7.27e+02 ... (remaining 10176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2167 0.079 - 0.158: 393 0.158 - 0.237: 72 0.237 - 0.316: 45 0.316 - 0.395: 4 Chirality restraints: 2681 Sorted by residual: chirality pdb=" CA ALA H 507 " pdb=" N ALA H 507 " pdb=" C ALA H 507 " pdb=" CB ALA H 507 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CB VAL I 272 " pdb=" CA VAL I 272 " pdb=" CG1 VAL I 272 " pdb=" CG2 VAL I 272 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" P U Z 27 " pdb=" OP1 U Z 27 " pdb=" OP2 U Z 27 " pdb=" O5' U Z 27 " both_signs ideal model delta sigma weight residual True 2.17 -2.55 -0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 2678 not shown) Planarity restraints: 2755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 600 " -0.017 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C THR I 600 " 0.062 2.00e-02 2.50e+03 pdb=" O THR I 600 " -0.023 2.00e-02 2.50e+03 pdb=" N SER I 601 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 194 " -0.056 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO I 195 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO I 195 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO I 195 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 345 " 0.029 2.00e-02 2.50e+03 1.99e-02 9.93e+00 pdb=" CG TRP I 345 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP I 345 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP I 345 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 345 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 345 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 345 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 345 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 345 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 345 " 0.003 2.00e-02 2.50e+03 ... (remaining 2752 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 196 2.61 - 3.19: 13216 3.19 - 3.76: 25754 3.76 - 4.33: 36804 4.33 - 4.90: 60178 Nonbonded interactions: 136148 Sorted by model distance: nonbonded pdb=" OD2 ASP H 179 " pdb="ZN ZN H 702 " model vdw 2.043 2.230 nonbonded pdb=" O2' G Z 26 " pdb=" OP2 U Z 27 " model vdw 2.183 3.040 nonbonded pdb=" O LEU H 500 " pdb=" O THR H 504 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP H 75 " pdb="ZN ZN H 702 " model vdw 2.261 2.230 nonbonded pdb=" OG1 THR A 24 " pdb=" OE1 GLU A 26 " model vdw 2.293 3.040 ... (remaining 136143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.009 0.570 16907 Z= 0.342 Angle : 1.054 26.702 23070 Z= 0.558 Chirality : 0.073 0.395 2681 Planarity : 0.007 0.086 2755 Dihedral : 13.646 162.702 6545 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.69 % Favored : 94.26 % Rotamer: Outliers : 0.93 % Allowed : 5.14 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -4.73 (0.15), residues: 1899 helix: -4.40 (0.09), residues: 602 sheet: -2.62 (0.23), residues: 402 loop : -2.30 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 10 TYR 0.041 0.003 TYR E 24 PHE 0.035 0.003 PHE I 620 TRP 0.053 0.004 TRP I 345 HIS 0.013 0.002 HIS I 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.29 (16902) covalent geometry : angle 1.05444 / 0.56 (23070) hydrogen bonds : bond 0.30297 / 20.46 ( 532) hydrogen bonds : angle 11.05278 / 7.64 ( 1571) metal coordination : bond 0.32296 / 20.61 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 395 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8197 (tt0) cc_final: 0.7944 (tt0) REVERT: E 18 ILE cc_start: 0.8707 (tp) cc_final: 0.8418 (tp) REVERT: C 6 SER cc_start: 0.8592 (t) cc_final: 0.8344 (p) REVERT: D 142 ARG cc_start: 0.7773 (mmm-85) cc_final: 0.7334 (mtp85) REVERT: H 58 LEU cc_start: 0.8799 (mm) cc_final: 0.8572 (mp) REVERT: H 312 LYS cc_start: 0.7549 (ttmt) cc_final: 0.7157 (tttm) REVERT: H 313 SER cc_start: 0.8647 (t) cc_final: 0.8234 (p) REVERT: I 92 LYS cc_start: 0.8122 (mttm) cc_final: 0.7883 (mtpp) REVERT: I 98 MET cc_start: 0.9023 (mmm) cc_final: 0.8626 (mmm) REVERT: J 144 MET cc_start: 0.8680 (mmm) cc_final: 0.8246 (mmm) outliers start: 16 outliers final: 7 residues processed: 408 average time/residue: 0.1514 time to fit residues: 90.0061 Evaluate side-chains 279 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 272 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 327 LEU Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 699 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 ASN E 19 ASN E 83 ASN G 39 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN D 160 HIS D 352 ASN H 97 HIS ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 GLN H 301 ASN H 307 HIS H 502 ASN I 39 HIS I 62 HIS I 204 ASN I 232 ASN I 607 GLN I 619 GLN J 41 ASN J 64 ASN J 304 HIS ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.148666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120279 restraints weight = 20541.355| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.61 r_work: 0.3324 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16907 Z= 0.179 Angle : 0.936 20.727 23070 Z= 0.421 Chirality : 0.079 1.216 2681 Planarity : 0.005 0.050 2755 Dihedral : 12.877 159.308 2710 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.39 % Allowed : 8.70 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -3.40 (0.17), residues: 1899 helix: -2.51 (0.17), residues: 609 sheet: -2.28 (0.24), residues: 392 loop : -1.91 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.017 0.002 TYR I 21 PHE 0.017 0.002 PHE J 91 TRP 0.027 0.002 TRP I 345 HIS 0.008 0.001 HIS I 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (16902) covalent geometry : angle 0.93635 / 0.42 (23070) hydrogen bonds : bond 0.05260 / 3.52 ( 532) hydrogen bonds : angle 6.09517 / 4.24 ( 1571) metal coordination : bond 0.00275 / 0.15 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 292 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8499 (p) REVERT: A 78 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7270 (ptpt) REVERT: B 47 GLU cc_start: 0.8187 (tt0) cc_final: 0.7890 (tt0) REVERT: G 28 GLN cc_start: 0.8802 (mt0) cc_final: 0.8595 (mt0) REVERT: C 89 ASN cc_start: 0.8336 (t0) cc_final: 0.7973 (t0) REVERT: D 142 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.7595 (mtp85) REVERT: D 177 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8207 (mttm) REVERT: H 312 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7658 (tttp) REVERT: H 370 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7713 (mm-30) REVERT: H 467 MET cc_start: 0.5669 (pmt) cc_final: 0.5382 (pmt) REVERT: I 98 MET cc_start: 0.9281 (mmm) cc_final: 0.8942 (mmm) REVERT: J 225 TYR cc_start: 0.8187 (t80) cc_final: 0.7954 (t80) REVERT: J 307 SER cc_start: 0.7402 (t) cc_final: 0.6643 (m) outliers start: 41 outliers final: 17 residues processed: 320 average time/residue: 0.1389 time to fit residues: 64.8815 Evaluate side-chains 277 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 281 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 80 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN C 78 ASN H 227 HIS H 258 GLN I 248 GLN J 252 ASN J 293 GLN ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115342 restraints weight = 20728.691| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.61 r_work: 0.3250 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16907 Z= 0.208 Angle : 0.804 19.245 23070 Z= 0.373 Chirality : 0.065 0.861 2681 Planarity : 0.004 0.046 2755 Dihedral : 13.346 154.586 2698 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.69 % Allowed : 11.16 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -2.58 (0.18), residues: 1899 helix: -1.42 (0.20), residues: 612 sheet: -2.07 (0.25), residues: 386 loop : -1.62 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 65 TYR 0.017 0.002 TYR I 21 PHE 0.018 0.002 PHE I 620 TRP 0.030 0.002 TRP I 345 HIS 0.007 0.001 HIS I 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (16902) covalent geometry : angle 0.80414 / 0.37 (23070) hydrogen bonds : bond 0.04313 / 2.94 ( 532) hydrogen bonds : angle 5.46671 / 3.79 ( 1571) metal coordination : bond 0.00094 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 265 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: B 47 GLU cc_start: 0.8187 (tt0) cc_final: 0.7893 (tt0) REVERT: B 65 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7915 (mtm110) REVERT: E 62 GLU cc_start: 0.8757 (pt0) cc_final: 0.8522 (pt0) REVERT: C 89 ASN cc_start: 0.8225 (t0) cc_final: 0.7845 (t0) REVERT: D 142 ARG cc_start: 0.8420 (mmm-85) cc_final: 0.7665 (mtp85) REVERT: D 177 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8231 (mttm) REVERT: H 312 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7907 (tttp) REVERT: H 370 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7822 (mm-30) REVERT: H 467 MET cc_start: 0.5775 (pmt) cc_final: 0.5554 (pmt) REVERT: I 98 MET cc_start: 0.9221 (mmm) cc_final: 0.8980 (mmm) REVERT: I 550 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8667 (mtmt) REVERT: I 592 LYS cc_start: 0.8498 (mtmp) cc_final: 0.8159 (mtmm) REVERT: J 307 SER cc_start: 0.7320 (t) cc_final: 0.6552 (m) outliers start: 46 outliers final: 32 residues processed: 297 average time/residue: 0.1454 time to fit residues: 62.9429 Evaluate side-chains 277 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 550 LYS Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 68 optimal weight: 0.1980 chunk 93 optimal weight: 0.4980 chunk 106 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 HIS ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 HIS ** 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 = 0.3741 r_free = 0.3741 target = 0.145363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115395 restraints weight = 20959.478| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.68 r_work: 0.3219 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16907 Z= 0.201 Angle : 0.760 19.810 23070 Z= 0.354 Chirality : 0.060 0.743 2681 Planarity : 0.004 0.045 2755 Dihedral : 13.372 153.905 2698 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.74 % Allowed : 10.75 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -2.15 (0.19), residues: 1899 helix: -0.87 (0.21), residues: 607 sheet: -2.00 (0.25), residues: 394 loop : -1.43 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 265 TYR 0.015 0.002 TYR I 606 PHE 0.018 0.002 PHE I 620 TRP 0.026 0.002 TRP I 345 HIS 0.007 0.001 HIS H 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (16902) covalent geometry : angle 0.75955 / 0.35 (23070) hydrogen bonds : bond 0.03994 / 2.75 ( 532) hydrogen bonds : angle 5.23404 / 3.63 ( 1571) metal coordination : bond 0.00161 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 267 time to evaluate : 0.545 Fit side-chains REVERT: A 44 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8579 (p) REVERT: A 78 LYS cc_start: 0.7870 (ptpp) cc_final: 0.7484 (ptpt) REVERT: B 47 GLU cc_start: 0.8264 (tt0) cc_final: 0.7868 (tt0) REVERT: B 65 ARG cc_start: 0.8207 (mtm110) cc_final: 0.7890 (mtm110) REVERT: E 62 GLU cc_start: 0.8820 (pt0) cc_final: 0.8513 (pt0) REVERT: E 71 ARG cc_start: 0.8593 (mtp85) cc_final: 0.8350 (mtp85) REVERT: G 65 ASN cc_start: 0.8636 (t0) cc_final: 0.8411 (t0) REVERT: C 89 ASN cc_start: 0.8199 (t0) cc_final: 0.7696 (t0) REVERT: D 142 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.7643 (ttm110) REVERT: D 177 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8201 (mttm) REVERT: H 312 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8015 (tttm) REVERT: H 370 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7790 (mm-30) REVERT: H 381 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8529 (ttmm) REVERT: I 180 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8301 (ptm-80) REVERT: I 592 LYS cc_start: 0.8445 (mtmp) cc_final: 0.8105 (mtmm) REVERT: J 84 LYS cc_start: 0.8572 (tmmt) cc_final: 0.8076 (ttpp) REVERT: J 225 TYR cc_start: 0.8436 (t80) cc_final: 0.8086 (t80) REVERT: J 307 SER cc_start: 0.7193 (t) cc_final: 0.6500 (m) outliers start: 64 outliers final: 45 residues processed: 314 average time/residue: 0.1356 time to fit residues: 63.2767 Evaluate side-chains 299 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 381 LYS Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 47 optimal weight: 0.0980 chunk 173 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN I 300 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117981 restraints weight = 20893.969| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.68 r_work: 0.3262 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16907 Z= 0.142 Angle : 0.689 16.260 23070 Z= 0.323 Chirality : 0.055 0.563 2681 Planarity : 0.004 0.043 2755 Dihedral : 13.220 161.116 2698 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.39 % Allowed : 11.57 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.19), residues: 1899 helix: -0.46 (0.21), residues: 606 sheet: -1.78 (0.25), residues: 380 loop : -1.28 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 174 TYR 0.014 0.001 TYR I 606 PHE 0.015 0.001 PHE I 620 TRP 0.023 0.002 TRP I 345 HIS 0.007 0.001 HIS I 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (16902) covalent geometry : angle 0.68882 / 0.32 (23070) hydrogen bonds : bond 0.03732 / 2.61 ( 532) hydrogen bonds : angle 5.00602 / 3.47 ( 1571) metal coordination : bond 0.00105 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: A 78 LYS cc_start: 0.7877 (ptpp) cc_final: 0.7446 (ptpt) REVERT: E 62 GLU cc_start: 0.8801 (pt0) cc_final: 0.8585 (pt0) REVERT: E 71 ARG cc_start: 0.8541 (mtp85) cc_final: 0.8237 (mtp85) REVERT: G 65 ASN cc_start: 0.8603 (t0) cc_final: 0.8381 (t0) REVERT: C 89 ASN cc_start: 0.8156 (t0) cc_final: 0.7769 (t0) REVERT: D 142 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7585 (ttm110) REVERT: D 177 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8158 (mttm) REVERT: H 312 LYS cc_start: 0.8476 (ttmt) cc_final: 0.7955 (tttm) REVERT: H 370 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7760 (mm-30) REVERT: I 180 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8295 (ptm-80) REVERT: I 550 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8717 (mtmt) REVERT: I 592 LYS cc_start: 0.8422 (mtmp) cc_final: 0.7916 (mmtt) REVERT: J 84 LYS cc_start: 0.8650 (tmmt) cc_final: 0.8198 (ttpp) REVERT: J 133 MET cc_start: 0.9038 (mmm) cc_final: 0.8590 (mmm) REVERT: J 225 TYR cc_start: 0.8356 (t80) cc_final: 0.8069 (t80) REVERT: J 307 SER cc_start: 0.7166 (t) cc_final: 0.6485 (m) outliers start: 58 outliers final: 35 residues processed: 304 average time/residue: 0.1361 time to fit residues: 61.1105 Evaluate side-chains 287 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 550 LYS Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 109 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN E 83 ASN G 39 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116092 restraints weight = 20345.998| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.58 r_work: 0.3266 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16907 Z= 0.154 Angle : 0.693 16.198 23070 Z= 0.324 Chirality : 0.055 0.568 2681 Planarity : 0.004 0.042 2755 Dihedral : 13.184 165.310 2698 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.33 % Allowed : 12.38 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.19), residues: 1899 helix: -0.28 (0.22), residues: 608 sheet: -1.72 (0.25), residues: 391 loop : -1.15 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 65 TYR 0.012 0.001 TYR I 21 PHE 0.012 0.001 PHE I 620 TRP 0.021 0.002 TRP I 345 HIS 0.006 0.001 HIS I 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (16902) covalent geometry : angle 0.69261 / 0.32 (23070) hydrogen bonds : bond 0.03740 / 2.60 ( 532) hydrogen bonds : angle 4.89553 / 3.40 ( 1571) metal coordination : bond 0.00116 / 0.07 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 0.614 Fit side-chains REVERT: A 78 LYS cc_start: 0.7940 (ptpp) cc_final: 0.7503 (ptpt) REVERT: B 47 GLU cc_start: 0.8255 (tt0) cc_final: 0.8017 (tt0) REVERT: B 65 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7995 (mtm110) REVERT: E 71 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8200 (mtp85) REVERT: G 65 ASN cc_start: 0.8582 (t0) cc_final: 0.8367 (t0) REVERT: C 89 ASN cc_start: 0.8136 (t0) cc_final: 0.7756 (t0) REVERT: D 142 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7724 (mtp85) REVERT: D 177 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8124 (mttm) REVERT: H 312 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8009 (tttm) REVERT: H 370 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7784 (mm-30) REVERT: I 96 MET cc_start: 0.9008 (tpp) cc_final: 0.8695 (mmt) REVERT: I 180 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8388 (ptm-80) REVERT: I 550 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8756 (mtmt) REVERT: I 592 LYS cc_start: 0.8405 (mtmp) cc_final: 0.7935 (mmtt) REVERT: J 84 LYS cc_start: 0.8614 (tmmt) cc_final: 0.8175 (ttpp) REVERT: J 133 MET cc_start: 0.9035 (mmm) cc_final: 0.8608 (mmm) REVERT: J 167 ASP cc_start: 0.8468 (t0) cc_final: 0.8225 (m-30) REVERT: J 307 SER cc_start: 0.7263 (t) cc_final: 0.6480 (m) outliers start: 57 outliers final: 47 residues processed: 292 average time/residue: 0.1444 time to fit residues: 62.3649 Evaluate side-chains 297 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 550 LYS Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 56 optimal weight: 0.0010 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 HIS I 218 GLN I 300 ASN I 607 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117337 restraints weight = 20337.091| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.58 r_work: 0.3280 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16907 Z= 0.133 Angle : 0.668 15.283 23070 Z= 0.313 Chirality : 0.054 0.523 2681 Planarity : 0.003 0.041 2755 Dihedral : 13.124 168.294 2698 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.33 % Allowed : 12.91 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1899 helix: -0.10 (0.22), residues: 608 sheet: -1.78 (0.25), residues: 409 loop : -1.03 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 449 TYR 0.011 0.001 TYR I 21 PHE 0.013 0.001 PHE I 620 TRP 0.019 0.001 TRP I 345 HIS 0.006 0.001 HIS I 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (16902) covalent geometry : angle 0.66789 / 0.31 (23070) hydrogen bonds : bond 0.03663 / 2.56 ( 532) hydrogen bonds : angle 4.79630 / 3.33 ( 1571) metal coordination : bond 0.00085 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 265 time to evaluate : 0.646 Fit side-chains REVERT: A 8 LYS cc_start: 0.8285 (mtpt) cc_final: 0.8075 (mttt) REVERT: A 44 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 78 LYS cc_start: 0.8001 (ptpp) cc_final: 0.7573 (ptpt) REVERT: C 89 ASN cc_start: 0.8157 (t0) cc_final: 0.7907 (t0) REVERT: C 107 PHE cc_start: 0.7620 (t80) cc_final: 0.7314 (t80) REVERT: D 142 ARG cc_start: 0.8171 (mmm-85) cc_final: 0.7715 (mtp85) REVERT: D 177 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8198 (mttm) REVERT: H 312 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7960 (tttm) REVERT: H 370 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7711 (mm-30) REVERT: I 96 MET cc_start: 0.8976 (tpp) cc_final: 0.8651 (mmt) REVERT: I 180 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8406 (ptm-80) REVERT: I 550 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8750 (mtmt) REVERT: I 592 LYS cc_start: 0.8375 (mtmp) cc_final: 0.7918 (mmtt) REVERT: J 84 LYS cc_start: 0.8569 (tmmt) cc_final: 0.8221 (ttpp) REVERT: J 133 MET cc_start: 0.8993 (mmm) cc_final: 0.8579 (mmm) REVERT: J 167 ASP cc_start: 0.8465 (t0) cc_final: 0.8230 (m-30) REVERT: J 225 TYR cc_start: 0.8313 (t80) cc_final: 0.8106 (t80) REVERT: J 307 SER cc_start: 0.7137 (t) cc_final: 0.6370 (m) outliers start: 57 outliers final: 42 residues processed: 299 average time/residue: 0.1468 time to fit residues: 64.5357 Evaluate side-chains 298 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 550 LYS Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 281 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 160 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 88 optimal weight: 0.0170 chunk 154 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 124 optimal weight: 0.0370 chunk 46 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 HIS G 39 ASN I 218 GLN I 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.148353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119794 restraints weight = 20717.868| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.61 r_work: 0.3295 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16907 Z= 0.117 Angle : 0.651 14.547 23070 Z= 0.304 Chirality : 0.053 0.489 2681 Planarity : 0.003 0.037 2755 Dihedral : 13.055 169.965 2698 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.04 % Allowed : 13.61 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.20), residues: 1899 helix: 0.04 (0.22), residues: 608 sheet: -1.72 (0.25), residues: 409 loop : -0.95 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 65 TYR 0.011 0.001 TYR I 21 PHE 0.012 0.001 PHE I 620 TRP 0.019 0.001 TRP I 345 HIS 0.006 0.001 HIS I 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16902) covalent geometry : angle 0.65092 / 0.30 (23070) hydrogen bonds : bond 0.03603 / 2.53 ( 532) hydrogen bonds : angle 4.67703 / 3.24 ( 1571) metal coordination : bond 0.00094 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 269 time to evaluate : 0.568 Fit side-chains REVERT: A 44 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 77 LEU cc_start: 0.8695 (tp) cc_final: 0.7818 (mp) REVERT: A 78 LYS cc_start: 0.7953 (ptpp) cc_final: 0.7532 (ptpt) REVERT: B 47 GLU cc_start: 0.8170 (tt0) cc_final: 0.7762 (tt0) REVERT: B 65 ARG cc_start: 0.8288 (mtm110) cc_final: 0.7761 (mtm110) REVERT: C 89 ASN cc_start: 0.8154 (t0) cc_final: 0.7901 (t0) REVERT: C 107 PHE cc_start: 0.7613 (t80) cc_final: 0.7308 (t80) REVERT: D 142 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7719 (mtp85) REVERT: D 177 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8112 (mttm) REVERT: H 132 MET cc_start: 0.9124 (mmm) cc_final: 0.8809 (mmm) REVERT: H 312 LYS cc_start: 0.8430 (ttmt) cc_final: 0.7904 (tttm) REVERT: H 357 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7866 (p90) REVERT: H 370 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7710 (mm-30) REVERT: H 462 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8097 (ptmt) REVERT: I 96 MET cc_start: 0.8936 (tpp) cc_final: 0.8616 (mmt) REVERT: I 180 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8405 (ptm-80) REVERT: I 550 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8745 (mtmt) REVERT: I 592 LYS cc_start: 0.8327 (mtmp) cc_final: 0.7872 (mmtt) REVERT: J 84 LYS cc_start: 0.8557 (tmmt) cc_final: 0.8247 (ttpp) REVERT: J 133 MET cc_start: 0.8972 (mmm) cc_final: 0.8559 (mmm) REVERT: J 167 ASP cc_start: 0.8396 (t0) cc_final: 0.8147 (m-30) REVERT: J 225 TYR cc_start: 0.8363 (t80) cc_final: 0.8056 (t80) REVERT: J 307 SER cc_start: 0.7243 (t) cc_final: 0.6485 (m) outliers start: 52 outliers final: 41 residues processed: 302 average time/residue: 0.1447 time to fit residues: 64.2041 Evaluate side-chains 298 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 462 LYS Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 550 LYS Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 135 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 HIS I 565 HIS I 607 GLN ** J 81 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 = 0.3728 r_free = 0.3728 target = 0.143793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114860 restraints weight = 20718.128| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.62 r_work: 0.3232 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16907 Z= 0.205 Angle : 0.724 16.363 23070 Z= 0.340 Chirality : 0.057 0.620 2681 Planarity : 0.004 0.038 2755 Dihedral : 13.114 169.085 2698 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.86 % Allowed : 14.19 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.20), residues: 1899 helix: 0.01 (0.22), residues: 608 sheet: -1.69 (0.25), residues: 418 loop : -0.96 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 299 TYR 0.012 0.002 TYR E 24 PHE 0.016 0.002 PHE I 620 TRP 0.019 0.002 TRP I 345 HIS 0.007 0.001 HIS H 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (16902) covalent geometry : angle 0.72436 / 0.34 (23070) hydrogen bonds : bond 0.03823 / 2.64 ( 532) hydrogen bonds : angle 4.82757 / 3.34 ( 1571) metal coordination : bond 0.00175 / 0.10 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 0.664 Fit side-chains REVERT: A 44 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8595 (p) REVERT: A 77 LEU cc_start: 0.8747 (tp) cc_final: 0.7848 (mp) REVERT: A 78 LYS cc_start: 0.8106 (ptpp) cc_final: 0.7662 (ptpt) REVERT: B 65 ARG cc_start: 0.8330 (mtm110) cc_final: 0.8059 (mtm110) REVERT: C 89 ASN cc_start: 0.8187 (t0) cc_final: 0.7937 (t0) REVERT: C 107 PHE cc_start: 0.7725 (t80) cc_final: 0.7439 (t80) REVERT: D 142 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7778 (mtp85) REVERT: D 177 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8082 (mttm) REVERT: H 132 MET cc_start: 0.9109 (mmm) cc_final: 0.8775 (mmm) REVERT: H 312 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8056 (tttm) REVERT: H 357 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7868 (p90) REVERT: H 370 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7752 (mm-30) REVERT: H 462 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8014 (ptmt) REVERT: I 96 MET cc_start: 0.9067 (tpp) cc_final: 0.8744 (mmt) REVERT: I 180 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8445 (ptm-80) REVERT: I 592 LYS cc_start: 0.8344 (mtmp) cc_final: 0.8024 (mtmm) REVERT: J 84 LYS cc_start: 0.8691 (tmmt) cc_final: 0.8428 (ttpp) REVERT: J 133 MET cc_start: 0.9053 (mmm) cc_final: 0.8657 (mmm) REVERT: J 167 ASP cc_start: 0.8509 (t0) cc_final: 0.8268 (m-30) REVERT: J 307 SER cc_start: 0.7176 (t) cc_final: 0.6487 (m) outliers start: 49 outliers final: 38 residues processed: 295 average time/residue: 0.1396 time to fit residues: 60.9050 Evaluate side-chains 295 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 462 LYS Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 138 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 HIS G 65 ASN I 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116861 restraints weight = 20403.704| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.58 r_work: 0.3277 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16907 Z= 0.139 Angle : 0.675 15.119 23070 Z= 0.317 Chirality : 0.054 0.516 2681 Planarity : 0.003 0.037 2755 Dihedral : 13.056 169.872 2698 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.39 % Allowed : 15.30 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.20), residues: 1899 helix: 0.16 (0.22), residues: 610 sheet: -1.66 (0.25), residues: 413 loop : -0.91 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 65 TYR 0.013 0.001 TYR E 36 PHE 0.013 0.001 PHE I 620 TRP 0.019 0.001 TRP I 345 HIS 0.005 0.001 HIS I 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (16902) covalent geometry : angle 0.67500 / 0.32 (23070) hydrogen bonds : bond 0.03662 / 2.55 ( 532) hydrogen bonds : angle 4.72643 / 3.27 ( 1571) metal coordination : bond 0.00107 / 0.06 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.586 Fit side-chains REVERT: A 44 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8523 (p) REVERT: A 77 LEU cc_start: 0.8780 (tp) cc_final: 0.7948 (mp) REVERT: A 78 LYS cc_start: 0.8231 (ptpp) cc_final: 0.7783 (ptpt) REVERT: E 60 ASP cc_start: 0.8098 (m-30) cc_final: 0.7839 (t0) REVERT: C 71 ASP cc_start: 0.8312 (t0) cc_final: 0.8090 (t0) REVERT: C 89 ASN cc_start: 0.8152 (t0) cc_final: 0.7926 (t0) REVERT: C 107 PHE cc_start: 0.7710 (t80) cc_final: 0.7390 (t80) REVERT: D 142 ARG cc_start: 0.8090 (mmm-85) cc_final: 0.7746 (mtp85) REVERT: D 177 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8161 (mttm) REVERT: H 132 MET cc_start: 0.9095 (mmm) cc_final: 0.8769 (mmm) REVERT: H 312 LYS cc_start: 0.8488 (ttmt) cc_final: 0.7984 (tttm) REVERT: H 370 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7769 (mm-30) REVERT: I 36 TRP cc_start: 0.8807 (OUTLIER) cc_final: 0.8348 (t60) REVERT: I 96 MET cc_start: 0.8934 (tpp) cc_final: 0.8627 (mmt) REVERT: I 180 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8441 (ptm-80) REVERT: I 592 LYS cc_start: 0.8334 (mtmp) cc_final: 0.8022 (mtmm) REVERT: J 84 LYS cc_start: 0.8615 (tmmt) cc_final: 0.8376 (ttpp) REVERT: J 133 MET cc_start: 0.8996 (mmm) cc_final: 0.8597 (mmm) REVERT: J 167 ASP cc_start: 0.8472 (t0) cc_final: 0.8243 (m-30) REVERT: J 307 SER cc_start: 0.7173 (t) cc_final: 0.6490 (m) outliers start: 41 outliers final: 34 residues processed: 279 average time/residue: 0.1433 time to fit residues: 59.3835 Evaluate side-chains 280 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 ASN ** J 113 ASN ** 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 = 0.3725 r_free = 0.3725 target = 0.143022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114128 restraints weight = 20282.930| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.57 r_work: 0.3237 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16907 Z= 0.197 Angle : 0.721 16.269 23070 Z= 0.339 Chirality : 0.057 0.609 2681 Planarity : 0.004 0.036 2755 Dihedral : 13.074 169.026 2698 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.75 % Allowed : 15.01 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.20), residues: 1899 helix: 0.13 (0.22), residues: 609 sheet: -1.66 (0.25), residues: 425 loop : -0.90 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 65 TYR 0.012 0.002 TYR I 21 PHE 0.016 0.002 PHE I 620 TRP 0.020 0.002 TRP I 345 HIS 0.007 0.001 HIS I 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (16902) covalent geometry : angle 0.72082 / 0.34 (23070) hydrogen bonds : bond 0.03790 / 2.61 ( 532) hydrogen bonds : angle 4.81309 / 3.34 ( 1571) metal coordination : bond 0.00166 / 0.09 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4334.60 seconds wall clock time: 75 minutes 3.16 seconds (4503.16 seconds total)