Starting phenix.real_space_refine on Tue May 20 18:40:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n69_49053/05_2025/9n69_49053.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n69_49053/05_2025/9n69_49053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n69_49053/05_2025/9n69_49053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n69_49053/05_2025/9n69_49053.map" model { file = "/net/cci-nas-00/data/ceres_data/9n69_49053/05_2025/9n69_49053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n69_49053/05_2025/9n69_49053.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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 1 6.06 5 P 123 5.49 5 S 34 5.16 5 C 12685 2.51 5 N 3551 2.21 5 O 4019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20413 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3899 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 12, 'TRANS': 512} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 201 Chain: "B" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3741 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 12, 'TRANS': 499} Chain breaks: 2 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 23, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 247 Chain: "C" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3326 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 10, 'TRANS': 437} Chain breaks: 2 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 167 Chain: "D" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2943 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PTRANS': 9, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 657 Unresolved non-hydrogen dihedrals: 407 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 27, 'ASP:plan': 19} Unresolved non-hydrogen planarities: 301 Chain: "E" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2398 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 12, 'TRANS': 295} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "F" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1644 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 142 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1496 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain breaks: 1 Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 872 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 12, 'rna3p_pyr': 13} Link IDs: {'rna2p': 16, 'rna3p': 24} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16613 SG CYS F 47 55.139 108.183 32.437 1.00 99.07 S ATOM 16636 SG CYS F 50 55.117 108.553 36.241 1.00 93.97 S ATOM 16940 SG CYS F 92 55.063 105.097 34.717 1.00102.75 S ATOM 16986 SG CYS F 98 52.022 107.327 34.501 1.00 90.39 S Time building chain proxies: 13.28, per 1000 atoms: 0.65 Number of scatterers: 20413 At special positions: 0 Unit cell: (142.258, 157.661, 173.065, 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 1 29.99 S 34 16.00 P 123 15.00 O 4019 8.00 N 3551 7.00 C 12685 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: 4.77 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 98 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 92 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 47 " Number of angles added : 6 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4674 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 17 sheets defined 54.9% alpha, 15.0% beta 18 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'A' and resid 6 through 21 removed outlier: 3.828A pdb=" N SER A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 29 removed outlier: 3.802A pdb=" N LEU A 27 " --> pdb=" O ASN A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 42 removed outlier: 4.217A pdb=" N GLU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 100 removed outlier: 3.750A pdb=" N LEU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.563A pdb=" N GLU A 112 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 removed outlier: 3.651A pdb=" N ILE A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.566A pdb=" N ILE A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.697A pdb=" N GLU A 214 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 242 removed outlier: 4.148A pdb=" N THR A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 267 Processing helix chain 'A' and resid 273 through 298 Processing helix chain 'A' and resid 302 through 318 removed outlier: 4.080A pdb=" N PHE A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 350 through 371 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.872A pdb=" N GLY A 380 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.511A pdb=" N GLN A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 426 through 427 No H-bonds generated for 'chain 'A' and resid 426 through 427' Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 459 through 468 removed outlier: 3.541A pdb=" N MET A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.580A pdb=" N GLY A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 481 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.513A pdb=" N LYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 537 removed outlier: 3.508A pdb=" N CYS A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 21 removed outlier: 3.619A pdb=" N ASP B 13 " --> pdb=" O THR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 29 removed outlier: 3.904A pdb=" N LEU B 27 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.771A pdb=" N GLU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 100 removed outlier: 3.620A pdb=" N LEU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 154 through 171 removed outlier: 3.572A pdb=" N LYS B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 240 removed outlier: 3.515A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.849A pdb=" N SER B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.524A pdb=" N GLY B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 318 removed outlier: 3.516A pdb=" N TYR B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 371 removed outlier: 3.517A pdb=" N LEU B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.708A pdb=" N GLY B 380 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 removed outlier: 3.611A pdb=" N GLN B 399 " --> pdb=" O PRO B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 409 removed outlier: 3.642A pdb=" N PHE B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 3.872A pdb=" N LEU B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 425 " --> pdb=" O PRO B 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 420 through 425' Processing helix chain 'B' and resid 426 through 427 No H-bonds generated for 'chain 'B' and resid 426 through 427' Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 459 through 469 Processing helix chain 'B' and resid 476 through 491 removed outlier: 3.553A pdb=" N GLY B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TRP B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.695A pdb=" N GLU B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 536 removed outlier: 3.510A pdb=" N CYS B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 19 Processing helix chain 'C' and resid 23 through 29 removed outlier: 3.509A pdb=" N LEU C 27 " --> pdb=" O ASN C 23 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.558A pdb=" N GLN C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 100 removed outlier: 3.568A pdb=" N ILE C 83 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.945A pdb=" N VAL C 113 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 171 removed outlier: 3.549A pdb=" N ILE C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 188 removed outlier: 3.592A pdb=" N ARG C 186 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER C 187 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR C 188 " --> pdb=" O ALA C 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 188' Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.772A pdb=" N VAL C 211 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 213 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 241 removed outlier: 4.052A pdb=" N THR C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 265 removed outlier: 3.675A pdb=" N THR C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 294 Processing helix chain 'C' and resid 303 through 318 removed outlier: 4.007A pdb=" N PHE C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 318 " --> pdb=" O ILE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 350 through 371 removed outlier: 3.538A pdb=" N ILE C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 394 through 399 removed outlier: 3.527A pdb=" N GLN C 399 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 422 through 427 removed outlier: 3.871A pdb=" N VAL C 427 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'D' and resid 7 through 21 Processing helix chain 'D' and resid 23 through 30 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.515A pdb=" N GLN D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 100 removed outlier: 3.573A pdb=" N LEU D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP D 93 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.639A pdb=" N VAL D 113 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 171 removed outlier: 3.542A pdb=" N LEU D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.731A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR D 212 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 242 removed outlier: 3.724A pdb=" N PHE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 264 Processing helix chain 'D' and resid 276 through 296 Processing helix chain 'D' and resid 302 through 318 removed outlier: 3.965A pdb=" N PHE D 317 " --> pdb=" O THR D 313 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 318 " --> pdb=" O ILE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 349 No H-bonds generated for 'chain 'D' and resid 347 through 349' Processing helix chain 'D' and resid 350 through 371 removed outlier: 3.620A pdb=" N ILE D 356 " --> pdb=" O GLY D 352 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 400 through 409 Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.618A pdb=" N LEU D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 427 No H-bonds generated for 'chain 'D' and resid 426 through 427' Processing helix chain 'D' and resid 428 through 430 No H-bonds generated for 'chain 'D' and resid 428 through 430' Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 14 through 25 removed outlier: 3.551A pdb=" N ASN E 23 " --> pdb=" O GLN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 63 removed outlier: 3.539A pdb=" N ASN E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 58 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 80 through 86 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.563A pdb=" N LYS E 105 " --> pdb=" O PHE E 102 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 106 " --> pdb=" O PHE E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 106' Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.661A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 132 Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.659A pdb=" N ILE E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 176 removed outlier: 3.537A pdb=" N ASP E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP E 173 " --> pdb=" O SER E 169 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN E 176 " --> pdb=" O ASP E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 213 removed outlier: 3.525A pdb=" N VAL E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 264 removed outlier: 3.501A pdb=" N ALA E 257 " --> pdb=" O ARG E 253 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS E 258 " --> pdb=" O MET E 254 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 264 " --> pdb=" O HIS E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 287 removed outlier: 3.630A pdb=" N ASN E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY E 277 " --> pdb=" O ASN E 273 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.764A pdb=" N LYS E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 removed outlier: 3.688A pdb=" N ILE E 302 " --> pdb=" O GLY E 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 17 removed outlier: 3.780A pdb=" N LYS F 16 " --> pdb=" O SER F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 28 through 44 removed outlier: 3.622A pdb=" N GLU F 38 " --> pdb=" O GLU F 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 98 through 103 removed outlier: 3.993A pdb=" N ASP F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 122 Processing helix chain 'F' and resid 139 through 154 removed outlier: 3.792A pdb=" N LEU F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG F 151 " --> pdb=" O GLU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 173 removed outlier: 3.818A pdb=" N GLU F 165 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 191 removed outlier: 3.504A pdb=" N ILE F 177 " --> pdb=" O SER F 173 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN F 186 " --> pdb=" O GLY F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 210 removed outlier: 3.688A pdb=" N PHE F 205 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 210 " --> pdb=" O LYS F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 225 removed outlier: 3.501A pdb=" N ILE F 218 " --> pdb=" O PHE F 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 64 removed outlier: 6.718A pdb=" N GLU A 60 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS A 53 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLN A 62 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY A 51 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER A 64 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS A 49 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU A 47 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS A 129 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A 49 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE A 55 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 11.142A pdb=" N TYR A 121 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 182 removed outlier: 6.192A pdb=" N LEU A 178 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU A 385 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 180 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ASP A 387 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR A 182 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 417 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR A 70 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ARG A 433 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 71 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU A 435 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 73 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N GLU A 437 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 329 removed outlier: 4.263A pdb=" N TRP A 323 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 64 removed outlier: 6.861A pdb=" N ARG B 59 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU B 47 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS B 129 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 49 " --> pdb=" O ASN B 127 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 55 " --> pdb=" O TYR B 121 " (cutoff:3.500A) removed outlier: 11.449A pdb=" N TYR B 121 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 216 through 217 removed outlier: 8.173A pdb=" N PHE B 217 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR B 181 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR B 70 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.546A pdb=" N LYS B 325 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 64 removed outlier: 6.805A pdb=" N ARG C 59 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU C 47 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS C 129 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS C 49 " --> pdb=" O ASN C 127 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE C 55 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N TYR C 121 " --> pdb=" O PHE C 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 182 removed outlier: 6.241A pdb=" N LEU C 178 " --> pdb=" O ILE C 383 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU C 385 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA C 180 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ASP C 387 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR C 182 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 417 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR C 70 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N THR C 418 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE C 72 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ARG C 433 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL C 71 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU C 435 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 73 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N GLU C 437 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 434 " --> pdb=" O SER C 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 336 through 339 removed outlier: 3.566A pdb=" N LEU C 344 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 64 removed outlier: 6.587A pdb=" N ARG D 59 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU D 47 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS D 129 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS D 49 " --> pdb=" O ASN D 127 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE D 55 " --> pdb=" O TYR D 121 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N TYR D 121 " --> pdb=" O PHE D 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 178 through 182 removed outlier: 6.271A pdb=" N LEU D 178 " --> pdb=" O ILE D 383 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU D 385 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA D 180 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ASP D 387 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N TYR D 182 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 417 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR D 70 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR D 418 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE D 72 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 435 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 321 through 329 removed outlier: 4.245A pdb=" N TRP D 323 " --> pdb=" O LYS D 338 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 29 through 35 Processing sheet with id=AB5, first strand: chain 'E' and resid 180 through 184 removed outlier: 3.501A pdb=" N SER E 182 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP E 98 " --> pdb=" O LYS E 222 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS E 222 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 233 through 234 Processing sheet with id=AB7, first strand: chain 'F' and resid 68 through 71 removed outlier: 3.507A pdb=" N SER F 91 " --> pdb=" O HIS F 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 124 through 126 977 hydrogen bonds defined for protein. 2802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 6.53 Time building geometry restraints manager: 5.58 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: 4857 1.33 - 1.45: 4598 1.45 - 1.57: 11294 1.57 - 1.69: 240 1.69 - 1.81: 53 Bond restraints: 21042 Sorted by residual: bond pdb=" N VAL B 205 " pdb=" CA VAL B 205 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N VAL B 211 " pdb=" CA VAL B 211 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.24e-02 6.50e+03 8.59e+00 bond pdb=" N PHE B 209 " pdb=" CA PHE B 209 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.28e-02 6.10e+03 7.89e+00 bond pdb=" N ASP B 210 " pdb=" CA ASP B 210 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.17e+00 bond pdb=" N TYR B 212 " pdb=" CA TYR B 212 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.28e+00 ... (remaining 21037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 28468 1.31 - 2.62: 564 2.62 - 3.93: 104 3.93 - 5.24: 24 5.24 - 6.55: 5 Bond angle restraints: 29165 Sorted by residual: angle pdb=" N GLY C 329 " pdb=" CA GLY C 329 " pdb=" C GLY C 329 " ideal model delta sigma weight residual 112.14 107.04 5.10 1.29e+00 6.01e-01 1.56e+01 angle pdb=" N ASN A 492 " pdb=" CA ASN A 492 " pdb=" CB ASN A 492 " ideal model delta sigma weight residual 114.17 109.68 4.49 1.14e+00 7.69e-01 1.55e+01 angle pdb=" N TYR B 212 " pdb=" CA TYR B 212 " pdb=" C TYR B 212 " ideal model delta sigma weight residual 113.28 109.01 4.27 1.22e+00 6.72e-01 1.22e+01 angle pdb=" N TRP B 206 " pdb=" CA TRP B 206 " pdb=" C TRP B 206 " ideal model delta sigma weight residual 113.28 109.09 4.19 1.22e+00 6.72e-01 1.18e+01 angle pdb=" CA THR B 204 " pdb=" C THR B 204 " pdb=" O THR B 204 " ideal model delta sigma weight residual 121.54 117.58 3.96 1.16e+00 7.43e-01 1.17e+01 ... (remaining 29160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 11771 35.87 - 71.74: 608 71.74 - 107.61: 26 107.61 - 143.48: 2 143.48 - 179.35: 7 Dihedral angle restraints: 12414 sinusoidal: 5226 harmonic: 7188 Sorted by residual: dihedral pdb=" O4' U I 152 " pdb=" C1' U I 152 " pdb=" N1 U I 152 " pdb=" C2 U I 152 " ideal model delta sinusoidal sigma weight residual 232.00 60.10 171.90 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' U I 147 " pdb=" C1' U I 147 " pdb=" N1 U I 147 " pdb=" C2 U I 147 " ideal model delta sinusoidal sigma weight residual -160.00 -49.58 -110.42 1 1.50e+01 4.44e-03 5.76e+01 dihedral pdb=" C4' DG H 21 " pdb=" C3' DG H 21 " pdb=" O3' DG H 21 " pdb=" P DA H 22 " ideal model delta sinusoidal sigma weight residual -140.00 39.35 -179.35 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 12411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2850 0.047 - 0.094: 459 0.094 - 0.141: 169 0.141 - 0.188: 3 0.188 - 0.235: 3 Chirality restraints: 3484 Sorted by residual: chirality pdb=" CB VAL B 205 " pdb=" CA VAL B 205 " pdb=" CG1 VAL B 205 " pdb=" CG2 VAL B 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C3' C I 125 " pdb=" C4' C I 125 " pdb=" O3' C I 125 " pdb=" C2' C I 125 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" C3' C I 124 " pdb=" C4' C I 124 " pdb=" O3' C I 124 " pdb=" C2' C I 124 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 3481 not shown) Planarity restraints: 3284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 270 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C GLU E 270 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU E 270 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU E 271 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 394 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 395 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 395 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 395 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 10 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO F 11 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO F 11 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 11 " -0.024 5.00e-02 4.00e+02 ... (remaining 3281 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 9628 2.98 - 3.46: 19433 3.46 - 3.94: 31041 3.94 - 4.42: 34130 4.42 - 4.90: 55115 Nonbonded interactions: 149347 Sorted by model distance: nonbonded pdb=" O ASP F 196 " pdb=" OG SER F 199 " model vdw 2.495 3.040 nonbonded pdb=" O ASP B 172 " pdb=" OD1 ASN B 173 " model vdw 2.512 3.040 nonbonded pdb=" O5' A I 162 " pdb=" O4' A I 162 " model vdw 2.519 2.432 nonbonded pdb=" O5' DT H 38 " pdb=" O4' DT H 38 " model vdw 2.521 2.432 nonbonded pdb=" O5' DG H 80 " pdb=" O4' DG H 80 " model vdw 2.525 2.432 ... (remaining 149342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 14 or (resid 15 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 or (resid 31 through 35 and (nam \ e N or name CA or name C or name O or name CB )) or resid 36 through 37 or (resi \ d 38 and (name N or name CA or name C or name O or name CB )) or resid 39 throug \ h 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or re \ sid 43 through 98 or (resid 99 through 103 and (name N or name CA or name C or n \ ame O or name CB )) or resid 104 through 116 or (resid 117 through 118 and (name \ N or name CA or name C or name O or name CB )) or resid 119 through 131 or (res \ id 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thr \ ough 142 or (resid 143 through 144 and (name N or name CA or name C or name O or \ name CB )) or (resid 145 through 151 and (name N or name CA or name C or name O \ or name CB )) or resid 152 or (resid 153 and (name N or name CA or name C or na \ me O or name CB )) or resid 154 or (resid 155 and (name N or name CA or name C o \ r name O or name CB )) or resid 156 through 168 or (resid 169 and (name N or nam \ e CA or name C or name O or name CB )) or resid 170 through 185 or (resid 186 an \ d (name N or name CA or name C or name O or name CB )) or resid 187 or (resid 20 \ 3 through 206 and (name N or name CA or name C or name O or name CB )) or resid \ 207 through 209 or (resid 210 and (name N or name CA or name C or name O or name \ CB )) or resid 211 through 213 or (resid 214 and (name N or name CA or name C o \ r name O or name CB )) or resid 215 through 267 or resid 273 through 342 or (res \ id 343 and (name N or name CA or name C or name O or name CB )) or resid 344 thr \ ough 419 or (resid 420 and (name N or name CA or name C or name O or name CB )) \ or resid 421 through 451 or (resid 452 and (name N or name CA or name C or name \ O or name CB )) or resid 453 through 531 or (resid 532 and (name N or name CA or \ name C or name O or name CB )) or resid 533 or (resid 534 through 536 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 101 or (resid 102 through 103 and (nam \ e N or name CA or name C or name O or name CB )) or resid 104 through 171 or (re \ sid 172 and (name N or name CA or name C or name O or name CB )) or resid 173 th \ rough 204 or (resid 205 through 206 and (name N or name CA or name C or name O o \ r name CB )) or resid 207 through 237 or (resid 238 through 277 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 278 through 295 and (name N o \ r name CA or name C or name O or name CB )) or (resid 296 through 303 and (name \ N or name CA or name C or name O or name CB )) or resid 304 through 330 or (resi \ d 331 through 332 and (name N or name CA or name C or name O or name CB )) or re \ sid 333 through 437 or (resid 438 through 441 and (name N or name CA or name C o \ r name O or name CB )) or resid 442 through 474 or (resid 475 and (name N or nam \ e CA or name C or name O or name CB )) or resid 476 or (resid 477 and (name N or \ name CA or name C or name O or name CB )) or resid 478 through 482 or (resid 48 \ 3 through 484 and (name N or name CA or name C or name O or name CB )) or resid \ 485 through 486 or (resid 487 and (name N or name CA or name C or name O or name \ CB )) or resid 488 through 489 or (resid 490 through 493 and (name N or name CA \ or name C or name O or name CB )) or resid 494 or (resid 495 and (name N or nam \ e CA or name C or name O or name CB )) or resid 496 through 499 or (resid 500 th \ rough 501 and (name N or name CA or name C or name O or name CB )) or resid 502 \ through 527 or (resid 528 and (name N or name CA or name C or name O or name CB \ )) or resid 529 through 536)) } ncs_group { reference = (chain 'C' and ((resid 6 through 44 and (name N or name CA or name C or name O o \ r name CB )) or resid 45 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 65 or (resid 66 through 68 and (na \ me N or name CA or name C or name O or name CB )) or resid 69 through 98 or (res \ id 99 and (name N or name CA or name C or name O or name CB )) or resid 100 or ( \ resid 101 and (name N or name CA or name C or name O or name CB )) or resid 102 \ through 108 or (resid 109 and (name N or name CA or name C or name O or name CB \ )) or resid 110 through 116 or (resid 117 through 118 and (name N or name CA or \ name C or name O or name CB )) or resid 119 or (resid 120 and (name N or name CA \ or name C or name O or name CB )) or resid 121 through 124 or (resid 125 throug \ h 126 and (name N or name CA or name C or name O or name CB )) or resid 127 thro \ ugh 130 or (resid 131 through 132 and (name N or name CA or name C or name O or \ name CB )) or resid 133 through 140 or (resid 141 through 142 and (name N or nam \ e CA or name C or name O or name CB )) or resid 143 through 146 or (resid 147 th \ rough 150 and (name N or name CA or name C or name O or name CB )) or resid 151 \ through 152 or (resid 153 and (name N or name CA or name C or name O or name CB \ )) or resid 154 or (resid 155 and (name N or name CA or name C or name O or name \ CB )) or resid 156 through 162 or (resid 163 and (name N or name CA or name C o \ r name O or name CB )) or resid 164 through 165 or (resid 166 through 172 and (n \ ame N or name CA or name C or name O or name CB )) or resid 173 through 192 or ( \ resid 205 and (name N or name CA or name C or name O or name CB )) or resid 206 \ through 207 or (resid 208 and (name N or name CA or name C or name O or name CB \ )) or resid 209 or (resid 210 through 211 and (name N or name CA or name C or na \ me O or name CB )) or resid 212 through 214 or (resid 215 through 216 and (name \ N or name CA or name C or name O or name CB )) or resid 217 through 234 or (resi \ d 235 through 264 and (name N or name CA or name C or name O or name CB )) or (r \ esid 275 through 304 and (name N or name CA or name C or name O or name CB )) or \ resid 305 through 319 or (resid 320 and (name N or name CA or name C or name O \ or name CB )) or resid 321 through 333 or (resid 334 and (name N or name CA or n \ ame C or name O or name CB )) or resid 335 through 344 or (resid 345 and (name N \ or name CA or name C or name O or name CB )) or resid 346 through 352 or (resid \ 353 and (name N or name CA or name C or name O or name CB )) or resid 354 throu \ gh 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or \ resid 371 through 374 or (resid 375 and (name N or name CA or name C or name O \ or name CB )) or resid 376 through 387 or (resid 388 and (name N or name CA or n \ ame C or name O or name CB )) or resid 389 through 402 or (resid 403 and (name N \ or name CA or name C or name O or name CB )) or resid 404 through 428 or (resid \ 429 and (name N or name CA or name C or name O or name CB )) or resid 430 throu \ gh 436 or (resid 437 through 441 and (name N or name CA or name C or name O or n \ ame CB )) or resid 442 through 451 or resid 601)) selection = (chain 'D' and (resid 6 through 192 or resid 205 through 217 or (resid 218 throu \ gh 219 and (name N or name CA or name C or name O or name CB )) or resid 220 or \ (resid 221 and (name N or name CA or name C or name O or name CB )) or resid 222 \ through 241 or (resid 242 through 277 and (name N or name CA or name C or name \ O or name CB )) or resid 278 through 346 or (resid 347 and (name N or name CA or \ name C or name O or name CB )) or resid 348 through 451 or resid 601)) } 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: 6.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 52.160 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.003 0.040 21046 Z= 0.144 Angle : 0.468 6.546 29171 Z= 0.282 Chirality : 0.039 0.235 3484 Planarity : 0.003 0.044 3284 Dihedral : 19.190 179.355 7740 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.08 % Allowed : 13.19 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2415 helix: 1.39 (0.15), residues: 1105 sheet: 1.14 (0.27), residues: 384 loop : -0.52 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 206 HIS 0.003 0.001 HIS D 394 PHE 0.015 0.001 PHE C 222 TYR 0.025 0.001 TYR F 77 ARG 0.003 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.29188 ( 1018) hydrogen bonds : angle 7.12349 ( 2876) metal coordination : bond 0.00300 ( 4) metal coordination : angle 1.26984 ( 6) covalent geometry : bond 0.00269 (21042) covalent geometry : angle 0.46730 (29165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 2.134 Fit side-chains REVERT: A 34 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8549 (tm-30) REVERT: C 328 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7573 (t80) REVERT: D 112 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8372 (mm-30) REVERT: F 78 TYR cc_start: 0.8455 (m-80) cc_final: 0.8050 (m-10) outliers start: 35 outliers final: 20 residues processed: 118 average time/residue: 0.2780 time to fit residues: 54.5590 Evaluate side-chains 92 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 187 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.4980 chunk 191 optimal weight: 0.9980 chunk 105 optimal weight: 0.0170 chunk 65 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN D 127 ASN ** F 43 GLN ** 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 = 0.3633 r_free = 0.3633 target = 0.079929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056184 restraints weight = 71779.256| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.14 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21046 Z= 0.129 Angle : 0.488 7.508 29171 Z= 0.278 Chirality : 0.040 0.184 3484 Planarity : 0.003 0.043 3284 Dihedral : 19.669 177.638 4182 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.72 % Allowed : 13.84 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.17), residues: 2415 helix: 2.30 (0.15), residues: 1139 sheet: 1.10 (0.26), residues: 402 loop : -0.63 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 481 HIS 0.005 0.001 HIS A 394 PHE 0.019 0.001 PHE F 202 TYR 0.018 0.001 TYR F 77 ARG 0.007 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.05604 ( 1018) hydrogen bonds : angle 4.38440 ( 2876) metal coordination : bond 0.00152 ( 4) metal coordination : angle 0.93004 ( 6) covalent geometry : bond 0.00254 (21042) covalent geometry : angle 0.48822 (29165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 2.190 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8679 (tm-30) REVERT: A 47 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8709 (tt) REVERT: C 328 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7668 (t80) REVERT: D 112 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8320 (mm-30) REVERT: F 78 TYR cc_start: 0.8316 (m-80) cc_final: 0.7365 (m-10) REVERT: F 173 SER cc_start: 0.8934 (m) cc_final: 0.8383 (t) outliers start: 29 outliers final: 15 residues processed: 111 average time/residue: 0.2476 time to fit residues: 48.0943 Evaluate side-chains 93 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 210 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 HIS F 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.077197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050582 restraints weight = 70412.889| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 4.25 r_work: 0.2703 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21046 Z= 0.219 Angle : 0.542 8.320 29171 Z= 0.305 Chirality : 0.043 0.205 3484 Planarity : 0.003 0.046 3284 Dihedral : 19.840 176.988 4157 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.08 % Allowed : 14.85 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.17), residues: 2415 helix: 2.54 (0.15), residues: 1127 sheet: 0.86 (0.25), residues: 404 loop : -0.92 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 136 HIS 0.006 0.001 HIS E 233 PHE 0.019 0.001 PHE A 45 TYR 0.022 0.001 TYR F 77 ARG 0.004 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.05909 ( 1018) hydrogen bonds : angle 4.12671 ( 2876) metal coordination : bond 0.00527 ( 4) metal coordination : angle 1.56144 ( 6) covalent geometry : bond 0.00517 (21042) covalent geometry : angle 0.54193 (29165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 2.144 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8710 (tm-30) REVERT: A 189 ILE cc_start: 0.7679 (mm) cc_final: 0.7297 (mm) REVERT: C 328 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7275 (t80) REVERT: D 112 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8607 (mm-30) REVERT: F 78 TYR cc_start: 0.8556 (m-80) cc_final: 0.8264 (m-10) REVERT: F 111 ASP cc_start: 0.8145 (t0) cc_final: 0.7642 (t0) outliers start: 35 outliers final: 24 residues processed: 109 average time/residue: 0.2534 time to fit residues: 47.5589 Evaluate side-chains 101 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 486 LYS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 CYS Chi-restraints excluded: chain F residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 71 optimal weight: 0.2980 chunk 151 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 177 optimal weight: 0.4980 chunk 220 optimal weight: 0.0870 chunk 137 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.080121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056127 restraints weight = 70781.346| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.97 r_work: 0.2784 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21046 Z= 0.098 Angle : 0.448 8.399 29171 Z= 0.251 Chirality : 0.039 0.200 3484 Planarity : 0.003 0.043 3284 Dihedral : 19.754 176.273 4156 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.60 % Allowed : 15.33 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.17), residues: 2415 helix: 2.85 (0.16), residues: 1127 sheet: 0.98 (0.26), residues: 401 loop : -0.82 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 323 HIS 0.003 0.001 HIS E 212 PHE 0.011 0.001 PHE D 217 TYR 0.008 0.001 TYR B 212 ARG 0.004 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 1018) hydrogen bonds : angle 3.64453 ( 2876) metal coordination : bond 0.00111 ( 4) metal coordination : angle 0.45020 ( 6) covalent geometry : bond 0.00199 (21042) covalent geometry : angle 0.44830 (29165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 2.160 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8741 (tm-30) REVERT: A 47 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8759 (tt) REVERT: A 189 ILE cc_start: 0.7510 (mm) cc_final: 0.7163 (mm) REVERT: C 328 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7152 (t80) REVERT: F 78 TYR cc_start: 0.8584 (m-80) cc_final: 0.8270 (m-10) REVERT: F 111 ASP cc_start: 0.8302 (t0) cc_final: 0.7746 (t0) REVERT: F 171 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8743 (pt0) REVERT: F 173 SER cc_start: 0.8956 (m) cc_final: 0.8539 (t) outliers start: 27 outliers final: 12 residues processed: 104 average time/residue: 0.2597 time to fit residues: 46.5483 Evaluate side-chains 93 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 160 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN C 373 ASN D 46 HIS D 127 ASN F 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.076532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.049887 restraints weight = 70994.468| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 4.23 r_work: 0.2683 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21046 Z= 0.251 Angle : 0.564 8.449 29171 Z= 0.315 Chirality : 0.043 0.213 3484 Planarity : 0.003 0.046 3284 Dihedral : 19.878 175.966 4155 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 1.90 % Allowed : 16.64 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.17), residues: 2415 helix: 2.66 (0.16), residues: 1139 sheet: 0.72 (0.25), residues: 397 loop : -1.10 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 136 HIS 0.007 0.001 HIS E 233 PHE 0.023 0.001 PHE A 45 TYR 0.017 0.001 TYR D 212 ARG 0.004 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.05922 ( 1018) hydrogen bonds : angle 4.01004 ( 2876) metal coordination : bond 0.00614 ( 4) metal coordination : angle 1.93561 ( 6) covalent geometry : bond 0.00594 (21042) covalent geometry : angle 0.56350 (29165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 2.272 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8741 (tm-30) REVERT: A 189 ILE cc_start: 0.7722 (mm) cc_final: 0.7399 (mm) REVERT: C 328 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7030 (t80) REVERT: F 78 TYR cc_start: 0.8898 (m-80) cc_final: 0.8501 (m-10) REVERT: F 111 ASP cc_start: 0.8516 (t0) cc_final: 0.8126 (t0) REVERT: F 173 SER cc_start: 0.9151 (m) cc_final: 0.8648 (t) REVERT: F 226 MET cc_start: 0.8721 (tpt) cc_final: 0.8423 (tpp) outliers start: 32 outliers final: 24 residues processed: 104 average time/residue: 0.2640 time to fit residues: 47.7916 Evaluate side-chains 97 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 183 CYS Chi-restraints excluded: chain F residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 61 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 46 optimal weight: 0.0570 chunk 222 optimal weight: 3.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.078882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052425 restraints weight = 70239.507| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.16 r_work: 0.2762 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21046 Z= 0.112 Angle : 0.464 8.338 29171 Z= 0.259 Chirality : 0.040 0.200 3484 Planarity : 0.003 0.044 3284 Dihedral : 19.731 178.303 4155 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 1.84 % Allowed : 17.23 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.18), residues: 2415 helix: 2.93 (0.16), residues: 1124 sheet: 0.81 (0.25), residues: 401 loop : -0.98 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 323 HIS 0.003 0.001 HIS A 394 PHE 0.014 0.001 PHE D 217 TYR 0.017 0.001 TYR D 212 ARG 0.003 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 1018) hydrogen bonds : angle 3.60862 ( 2876) metal coordination : bond 0.00210 ( 4) metal coordination : angle 0.99053 ( 6) covalent geometry : bond 0.00241 (21042) covalent geometry : angle 0.46333 (29165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 2.281 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8743 (tm-30) REVERT: A 189 ILE cc_start: 0.7639 (mm) cc_final: 0.7321 (mm) REVERT: C 328 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7047 (t80) REVERT: F 78 TYR cc_start: 0.8878 (m-80) cc_final: 0.8491 (m-10) REVERT: F 111 ASP cc_start: 0.8735 (t0) cc_final: 0.8151 (t0) REVERT: F 145 MET cc_start: 0.8902 (mtt) cc_final: 0.8400 (mmm) REVERT: F 171 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8701 (pt0) REVERT: F 173 SER cc_start: 0.8953 (m) cc_final: 0.8579 (t) REVERT: F 226 MET cc_start: 0.8581 (tpt) cc_final: 0.8308 (tpp) outliers start: 31 outliers final: 21 residues processed: 105 average time/residue: 0.2547 time to fit residues: 46.6970 Evaluate side-chains 95 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 183 CYS Chi-restraints excluded: chain F residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 171 optimal weight: 50.0000 chunk 207 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.078706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.051944 restraints weight = 71319.351| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 4.20 r_work: 0.2751 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21046 Z= 0.120 Angle : 0.463 8.880 29171 Z= 0.259 Chirality : 0.040 0.206 3484 Planarity : 0.003 0.045 3284 Dihedral : 19.652 177.852 4153 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 1.78 % Allowed : 17.41 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.18), residues: 2415 helix: 2.96 (0.16), residues: 1136 sheet: 0.88 (0.26), residues: 394 loop : -1.00 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 323 HIS 0.004 0.001 HIS C 394 PHE 0.009 0.001 PHE B 226 TYR 0.016 0.001 TYR D 212 ARG 0.003 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 1018) hydrogen bonds : angle 3.52278 ( 2876) metal coordination : bond 0.00279 ( 4) metal coordination : angle 0.95629 ( 6) covalent geometry : bond 0.00265 (21042) covalent geometry : angle 0.46288 (29165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8723 (tm-30) REVERT: A 189 ILE cc_start: 0.7630 (mm) cc_final: 0.7313 (mm) REVERT: D 152 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6825 (p0) REVERT: F 111 ASP cc_start: 0.8832 (t0) cc_final: 0.8532 (t0) REVERT: F 173 SER cc_start: 0.9018 (m) cc_final: 0.8598 (t) REVERT: F 226 MET cc_start: 0.8578 (tpt) cc_final: 0.8333 (tpp) outliers start: 30 outliers final: 25 residues processed: 100 average time/residue: 0.2553 time to fit residues: 44.2670 Evaluate side-chains 97 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 183 CYS Chi-restraints excluded: chain F residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.078857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052051 restraints weight = 71948.243| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.23 r_work: 0.2755 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21046 Z= 0.118 Angle : 0.460 9.128 29171 Z= 0.257 Chirality : 0.040 0.205 3484 Planarity : 0.003 0.044 3284 Dihedral : 19.561 177.550 4151 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 1.84 % Allowed : 17.77 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.18), residues: 2415 helix: 3.01 (0.16), residues: 1136 sheet: 0.89 (0.25), residues: 394 loop : -0.98 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 323 HIS 0.003 0.001 HIS C 394 PHE 0.014 0.001 PHE D 217 TYR 0.015 0.001 TYR D 212 ARG 0.003 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 1018) hydrogen bonds : angle 3.47011 ( 2876) metal coordination : bond 0.00282 ( 4) metal coordination : angle 0.90421 ( 6) covalent geometry : bond 0.00263 (21042) covalent geometry : angle 0.46022 (29165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 2.262 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8719 (tm-30) REVERT: A 47 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8859 (tt) REVERT: A 189 ILE cc_start: 0.7618 (mm) cc_final: 0.7299 (mm) REVERT: D 152 ASN cc_start: 0.7117 (OUTLIER) cc_final: 0.6820 (p0) REVERT: D 159 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7122 (pttt) REVERT: F 78 TYR cc_start: 0.8910 (m-80) cc_final: 0.8575 (m-10) REVERT: F 111 ASP cc_start: 0.8845 (t0) cc_final: 0.8559 (t0) REVERT: F 173 SER cc_start: 0.8999 (m) cc_final: 0.8629 (t) REVERT: F 226 MET cc_start: 0.8587 (tpt) cc_final: 0.8357 (tpp) outliers start: 31 outliers final: 24 residues processed: 101 average time/residue: 0.2670 time to fit residues: 46.6978 Evaluate side-chains 98 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 183 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 26 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.076959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.050235 restraints weight = 70603.842| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.18 r_work: 0.2697 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21046 Z= 0.213 Angle : 0.535 8.971 29171 Z= 0.298 Chirality : 0.042 0.209 3484 Planarity : 0.003 0.046 3284 Dihedral : 19.668 177.777 4151 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 1.78 % Allowed : 17.94 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2415 helix: 2.82 (0.16), residues: 1135 sheet: 0.70 (0.25), residues: 396 loop : -1.13 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 323 HIS 0.006 0.001 HIS C 46 PHE 0.017 0.001 PHE A 45 TYR 0.015 0.001 TYR D 212 ARG 0.003 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.05236 ( 1018) hydrogen bonds : angle 3.76891 ( 2876) metal coordination : bond 0.00565 ( 4) metal coordination : angle 1.68561 ( 6) covalent geometry : bond 0.00499 (21042) covalent geometry : angle 0.53449 (29165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8714 (tm-30) REVERT: A 189 ILE cc_start: 0.7704 (mm) cc_final: 0.7389 (mm) REVERT: B 419 HIS cc_start: 0.8876 (OUTLIER) cc_final: 0.8615 (m170) REVERT: F 111 ASP cc_start: 0.8934 (t0) cc_final: 0.8630 (t0) REVERT: F 173 SER cc_start: 0.9165 (m) cc_final: 0.8751 (t) REVERT: F 226 MET cc_start: 0.8637 (tpt) cc_final: 0.8390 (tpp) outliers start: 30 outliers final: 24 residues processed: 98 average time/residue: 0.2489 time to fit residues: 42.5914 Evaluate side-chains 94 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 183 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 213 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.078687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.051915 restraints weight = 71631.971| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 4.30 r_work: 0.2750 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21046 Z= 0.116 Angle : 0.467 9.886 29171 Z= 0.260 Chirality : 0.040 0.204 3484 Planarity : 0.003 0.044 3284 Dihedral : 19.574 178.187 4151 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 1.60 % Allowed : 18.24 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.18), residues: 2415 helix: 3.02 (0.16), residues: 1132 sheet: 0.81 (0.25), residues: 396 loop : -1.01 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 323 HIS 0.004 0.001 HIS A 394 PHE 0.016 0.001 PHE D 217 TYR 0.016 0.001 TYR D 212 ARG 0.002 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 1018) hydrogen bonds : angle 3.49301 ( 2876) metal coordination : bond 0.00321 ( 4) metal coordination : angle 1.06899 ( 6) covalent geometry : bond 0.00256 (21042) covalent geometry : angle 0.46670 (29165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 2.119 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8740 (tm-30) REVERT: A 47 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8862 (tt) REVERT: A 189 ILE cc_start: 0.7586 (mm) cc_final: 0.7270 (mm) REVERT: D 159 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7097 (pttt) REVERT: F 111 ASP cc_start: 0.8937 (t0) cc_final: 0.8635 (t0) REVERT: F 173 SER cc_start: 0.9017 (m) cc_final: 0.8682 (t) REVERT: F 226 MET cc_start: 0.8580 (tpt) cc_final: 0.8366 (tpp) outliers start: 27 outliers final: 23 residues processed: 95 average time/residue: 0.2510 time to fit residues: 41.4331 Evaluate side-chains 95 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 183 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 71 optimal weight: 0.0050 chunk 232 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.079150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052365 restraints weight = 71963.902| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 4.27 r_work: 0.2764 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21046 Z= 0.113 Angle : 0.461 9.976 29171 Z= 0.256 Chirality : 0.039 0.210 3484 Planarity : 0.003 0.044 3284 Dihedral : 19.457 176.606 4151 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 1.37 % Allowed : 18.60 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.18), residues: 2415 helix: 3.13 (0.16), residues: 1133 sheet: 0.91 (0.26), residues: 394 loop : -0.93 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 323 HIS 0.003 0.001 HIS C 394 PHE 0.009 0.001 PHE B 226 TYR 0.016 0.001 TYR A 26 ARG 0.002 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 1018) hydrogen bonds : angle 3.37195 ( 2876) metal coordination : bond 0.00325 ( 4) metal coordination : angle 0.95510 ( 6) covalent geometry : bond 0.00249 (21042) covalent geometry : angle 0.46071 (29165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11600.22 seconds wall clock time: 201 minutes 17.75 seconds (12077.75 seconds total)