Starting phenix.real_space_refine on Tue Jun 17 20:32:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n69_49053/06_2025/9n69_49053.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n69_49053/06_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_49053/06_2025/9n69_49053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n69_49053/06_2025/9n69_49053.map" model { file = "/net/cci-nas-00/data/ceres_data/9n69_49053/06_2025/9n69_49053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n69_49053/06_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-5710/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: 14.81, per 1000 atoms: 0.73 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: 4.49 Conformation dependent library (CDL) restraints added in 2.8 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: 6.80 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: 7.33 Time building geometry restraints manager: 5.47 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: 7.630 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: 0.010 Extract box with map and model: 0.970 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 56.480 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.300 ------------------------------------------------------------------------------- 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 : 2.029 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: 0.2831 time to fit residues: 55.6965 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 : 2.029 ------------------------------------------------------------------------------- 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 = 0.079990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056127 restraints weight = 71911.036| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.20 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 2.201 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 47 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8708 (tt) REVERT: C 328 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7666 (t80) REVERT: D 112 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8314 (mm-30) REVERT: F 78 TYR cc_start: 0.8302 (m-80) cc_final: 0.7355 (m-10) REVERT: F 173 SER cc_start: 0.8927 (m) cc_final: 0.8377 (t) outliers start: 29 outliers final: 15 residues processed: 111 average time/residue: 0.2484 time to fit residues: 48.5216 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 : 2.032 ------------------------------------------------------------------------------- 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: 1.9990 chunk 224 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN D 394 HIS F 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.076709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.049847 restraints weight = 71791.882| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.10 r_work: 0.2691 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 21046 Z= 0.237 Angle : 0.562 8.360 29171 Z= 0.316 Chirality : 0.043 0.207 3484 Planarity : 0.003 0.046 3284 Dihedral : 19.872 175.796 4157 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.14 % Allowed : 14.97 % Favored : 82.89 % 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: 1.50 (0.17), residues: 2415 helix: 2.49 (0.15), residues: 1134 sheet: 0.79 (0.25), residues: 405 loop : -0.97 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 136 HIS 0.007 0.001 HIS E 233 PHE 0.022 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 0.06169 ( 1018) hydrogen bonds : angle 4.18007 ( 2876) metal coordination : bond 0.00530 ( 4) metal coordination : angle 1.69559 ( 6) covalent geometry : bond 0.00557 (21042) covalent geometry : angle 0.56195 (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: 36 poor density : 75 time to evaluate : 2.137 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8709 (tm-30) REVERT: A 189 ILE cc_start: 0.7668 (mm) cc_final: 0.7287 (mm) REVERT: C 328 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7226 (t80) REVERT: D 112 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8631 (mm-30) REVERT: F 77 TYR cc_start: 0.8866 (p90) cc_final: 0.8294 (p90) REVERT: F 78 TYR cc_start: 0.8615 (m-80) cc_final: 0.8011 (m-10) REVERT: F 111 ASP cc_start: 0.8209 (t0) cc_final: 0.7682 (t0) outliers start: 36 outliers final: 26 residues processed: 108 average time/residue: 0.2553 time to fit residues: 47.9478 Evaluate side-chains 100 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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 157 VAL 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 E residue 187 ASP 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: 0.0170 chunk 151 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 125 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 177 optimal weight: 0.2980 chunk 220 optimal weight: 0.0010 chunk 137 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 overall best weight: 0.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS D 127 ASN F 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.081484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057619 restraints weight = 70754.915| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.98 r_work: 0.2828 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2514 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 : 0.450 7.788 29171 Z= 0.250 Chirality : 0.039 0.201 3484 Planarity : 0.003 0.041 3284 Dihedral : 19.734 174.662 4156 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.54 % Allowed : 15.27 % Favored : 83.18 % 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: 1.89 (0.17), residues: 2415 helix: 2.84 (0.15), residues: 1129 sheet: 1.03 (0.26), residues: 401 loop : -0.81 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 323 HIS 0.004 0.001 HIS E 212 PHE 0.009 0.001 PHE B 317 TYR 0.017 0.001 TYR F 77 ARG 0.005 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 1018) hydrogen bonds : angle 3.59777 ( 2876) metal coordination : bond 0.00170 ( 4) metal coordination : angle 0.27682 ( 6) covalent geometry : bond 0.00189 (21042) covalent geometry : angle 0.45009 (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 111 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 2.381 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8741 (tm-30) REVERT: A 47 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8691 (tt) REVERT: A 189 ILE cc_start: 0.7506 (mm) cc_final: 0.7156 (mm) REVERT: C 328 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7190 (t80) REVERT: F 77 TYR cc_start: 0.9020 (p90) cc_final: 0.8566 (p90) REVERT: F 78 TYR cc_start: 0.8514 (m-80) cc_final: 0.8252 (m-10) REVERT: F 111 ASP cc_start: 0.8394 (t0) cc_final: 0.7858 (t0) REVERT: F 171 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8745 (pt0) REVERT: F 173 SER cc_start: 0.8908 (m) cc_final: 0.8518 (t) outliers start: 26 outliers final: 9 residues processed: 109 average time/residue: 0.2709 time to fit residues: 51.2845 Evaluate side-chains 89 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 F residue 56 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 160 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.079411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055162 restraints weight = 71874.626| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.18 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2458 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= 0.119 Angle : 0.456 8.217 29171 Z= 0.255 Chirality : 0.039 0.208 3484 Planarity : 0.003 0.042 3284 Dihedral : 19.683 177.079 4155 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.31 % Allowed : 16.16 % Favored : 82.53 % 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: 2.00 (0.18), residues: 2415 helix: 2.99 (0.16), residues: 1130 sheet: 1.05 (0.26), residues: 398 loop : -0.84 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 323 HIS 0.004 0.001 HIS C 394 PHE 0.011 0.001 PHE D 217 TYR 0.018 0.001 TYR D 212 ARG 0.004 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 1018) hydrogen bonds : angle 3.53850 ( 2876) metal coordination : bond 0.00215 ( 4) metal coordination : angle 0.94572 ( 6) covalent geometry : bond 0.00263 (21042) covalent geometry : angle 0.45616 (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 97 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 2.168 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8673 (tm-30) REVERT: A 189 ILE cc_start: 0.7450 (mm) cc_final: 0.7144 (mm) REVERT: C 328 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7108 (t80) REVERT: F 77 TYR cc_start: 0.9090 (p90) cc_final: 0.8595 (p90) REVERT: F 78 TYR cc_start: 0.8437 (m-80) cc_final: 0.8181 (m-10) REVERT: F 111 ASP cc_start: 0.8310 (t0) cc_final: 0.7922 (t0) REVERT: F 173 SER cc_start: 0.8998 (m) cc_final: 0.8490 (t) REVERT: F 226 MET cc_start: 0.8483 (tpt) cc_final: 0.8250 (tpp) outliers start: 22 outliers final: 14 residues processed: 94 average time/residue: 0.2633 time to fit residues: 43.3280 Evaluate side-chains 90 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 2.217 ------------------------------------------------------------------------------- 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 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 F residue 56 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 183 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 61 optimal weight: 0.7980 chunk 122 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 222 optimal weight: 0.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.078842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052120 restraints weight = 71518.908| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 4.22 r_work: 0.2760 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2541 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= 0.129 Angle : 0.465 8.701 29171 Z= 0.260 Chirality : 0.040 0.203 3484 Planarity : 0.003 0.043 3284 Dihedral : 19.654 178.165 4155 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 1.49 % Allowed : 16.58 % Favored : 81.94 % 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: 1.97 (0.17), residues: 2415 helix: 3.00 (0.16), residues: 1130 sheet: 0.99 (0.26), residues: 399 loop : -0.88 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 323 HIS 0.004 0.001 HIS C 394 PHE 0.010 0.001 PHE B 226 TYR 0.017 0.001 TYR D 212 ARG 0.003 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 1018) hydrogen bonds : angle 3.53607 ( 2876) metal coordination : bond 0.00273 ( 4) metal coordination : angle 0.97966 ( 6) covalent geometry : bond 0.00291 (21042) covalent geometry : angle 0.46441 (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 101 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.962 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8744 (tm-30) REVERT: A 47 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8987 (tt) REVERT: A 189 ILE cc_start: 0.7597 (mm) cc_final: 0.7269 (mm) REVERT: C 328 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7083 (t80) REVERT: F 77 TYR cc_start: 0.9051 (p90) cc_final: 0.8731 (p90) REVERT: F 111 ASP cc_start: 0.8769 (t0) cc_final: 0.8252 (t0) REVERT: F 145 MET cc_start: 0.8852 (mtt) cc_final: 0.8406 (mmm) REVERT: F 171 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8653 (pt0) REVERT: F 173 SER cc_start: 0.8998 (m) cc_final: 0.8552 (t) REVERT: F 226 MET cc_start: 0.8572 (tpt) cc_final: 0.8351 (tpp) outliers start: 25 outliers final: 17 residues processed: 98 average time/residue: 0.2665 time to fit residues: 46.0178 Evaluate side-chains 91 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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 C residue 46 HIS 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 160 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 16 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 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: 0.6980 chunk 171 optimal weight: 50.0000 chunk 207 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.077926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051112 restraints weight = 71006.103| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.13 r_work: 0.2730 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21046 Z= 0.155 Angle : 0.483 8.347 29171 Z= 0.271 Chirality : 0.040 0.205 3484 Planarity : 0.003 0.044 3284 Dihedral : 19.647 179.989 4155 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.31 % Rotamer: Outliers : 1.43 % Allowed : 17.53 % Favored : 81.05 % 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: 1.89 (0.17), residues: 2415 helix: 2.95 (0.16), residues: 1130 sheet: 0.92 (0.25), residues: 401 loop : -0.94 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 323 HIS 0.005 0.001 HIS C 394 PHE 0.015 0.001 PHE A 45 TYR 0.016 0.001 TYR D 212 ARG 0.003 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.04543 ( 1018) hydrogen bonds : angle 3.62209 ( 2876) metal coordination : bond 0.00384 ( 4) metal coordination : angle 1.33337 ( 6) covalent geometry : bond 0.00358 (21042) covalent geometry : angle 0.48218 (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 97 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 2.101 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8719 (tm-30) REVERT: A 189 ILE cc_start: 0.7657 (mm) cc_final: 0.7335 (mm) REVERT: D 112 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8291 (mp0) REVERT: E 254 MET cc_start: 0.8992 (ttm) cc_final: 0.8767 (ttm) REVERT: F 78 TYR cc_start: 0.8964 (m-80) cc_final: 0.8510 (m-10) REVERT: F 111 ASP cc_start: 0.8936 (t0) cc_final: 0.8123 (t0) REVERT: F 145 MET cc_start: 0.8873 (mtt) cc_final: 0.8329 (mmm) REVERT: F 173 SER cc_start: 0.9080 (m) cc_final: 0.8658 (t) REVERT: F 186 GLN cc_start: 0.9581 (mm-40) cc_final: 0.9200 (tm-30) REVERT: F 226 MET cc_start: 0.8591 (tpt) cc_final: 0.8378 (tpp) outliers start: 24 outliers final: 19 residues processed: 94 average time/residue: 0.2610 time to fit residues: 43.2923 Evaluate side-chains 92 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 154 LEU Chi-restraints excluded: chain B residue 419 HIS Chi-restraints excluded: chain B residue 424 LEU 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 160 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS D 152 ASN ** F 105 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 = 0.3584 r_free = 0.3584 target = 0.077930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.051293 restraints weight = 70487.029| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 4.13 r_work: 0.2729 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21046 Z= 0.158 Angle : 0.486 8.333 29171 Z= 0.273 Chirality : 0.041 0.204 3484 Planarity : 0.003 0.044 3284 Dihedral : 19.584 179.839 4151 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 1.49 % Allowed : 17.59 % 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: 1.82 (0.17), residues: 2415 helix: 2.91 (0.16), residues: 1136 sheet: 0.82 (0.25), residues: 401 loop : -0.99 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 323 HIS 0.005 0.001 HIS A 46 PHE 0.012 0.001 PHE A 45 TYR 0.020 0.001 TYR F 77 ARG 0.003 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 1018) hydrogen bonds : angle 3.61147 ( 2876) metal coordination : bond 0.00428 ( 4) metal coordination : angle 1.37421 ( 6) covalent geometry : bond 0.00366 (21042) covalent geometry : angle 0.48529 (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 99 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 2.184 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8719 (tm-30) REVERT: A 189 ILE cc_start: 0.7594 (mm) cc_final: 0.7266 (mm) REVERT: D 152 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6935 (p0) REVERT: F 78 TYR cc_start: 0.9030 (m-80) cc_final: 0.8636 (m-10) REVERT: F 111 ASP cc_start: 0.8938 (t0) cc_final: 0.8144 (t0) REVERT: F 145 MET cc_start: 0.8850 (mtt) cc_final: 0.8252 (mmm) REVERT: F 173 SER cc_start: 0.9012 (m) cc_final: 0.8616 (t) REVERT: F 186 GLN cc_start: 0.9579 (mm-40) cc_final: 0.9218 (tm-30) REVERT: F 226 MET cc_start: 0.8565 (tpt) cc_final: 0.8356 (tpp) outliers start: 25 outliers final: 21 residues processed: 95 average time/residue: 0.2515 time to fit residues: 42.2776 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 : 2.051 ------------------------------------------------------------------------------- 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 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 C residue 135 THR 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 90 VAL Chi-restraints excluded: chain D residue 152 ASN 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 16 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL 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: 2.9990 chunk 160 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN D 152 ASN F 43 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.076836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.050161 restraints weight = 70522.238| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 4.16 r_work: 0.2694 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21046 Z= 0.213 Angle : 0.533 8.313 29171 Z= 0.299 Chirality : 0.042 0.208 3484 Planarity : 0.003 0.046 3284 Dihedral : 19.634 177.243 4151 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 1.54 % Allowed : 17.65 % 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: 1.64 (0.18), residues: 2415 helix: 2.78 (0.16), residues: 1143 sheet: 0.66 (0.25), residues: 403 loop : -1.10 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 136 HIS 0.007 0.001 HIS C 46 PHE 0.019 0.001 PHE A 45 TYR 0.017 0.001 TYR D 212 ARG 0.002 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.05328 ( 1018) hydrogen bonds : angle 3.78914 ( 2876) metal coordination : bond 0.00612 ( 4) metal coordination : angle 1.86353 ( 6) covalent geometry : bond 0.00500 (21042) covalent geometry : angle 0.53240 (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 98 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 2.121 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8701 (tm-30) REVERT: A 189 ILE cc_start: 0.7676 (mm) cc_final: 0.7353 (mm) REVERT: D 112 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8294 (mp0) REVERT: F 78 TYR cc_start: 0.9063 (m-80) cc_final: 0.8761 (m-10) REVERT: F 111 ASP cc_start: 0.8980 (t0) cc_final: 0.8151 (t0) REVERT: F 145 MET cc_start: 0.8885 (mtt) cc_final: 0.8281 (mmm) REVERT: F 173 SER cc_start: 0.9114 (m) cc_final: 0.8744 (t) REVERT: F 186 GLN cc_start: 0.9559 (mm-40) cc_final: 0.9196 (tm-30) REVERT: F 226 MET cc_start: 0.8613 (tpt) cc_final: 0.8404 (tpp) outliers start: 26 outliers final: 22 residues processed: 95 average time/residue: 0.2579 time to fit residues: 43.5140 Evaluate side-chains 93 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 2.112 ------------------------------------------------------------------------------- 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 419 HIS Chi-restraints excluded: chain B residue 424 LEU 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 69 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 90 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 16 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL 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: 0.7980 chunk 1 optimal weight: 0.0270 chunk 65 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.078342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.051541 restraints weight = 71479.787| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 4.20 r_work: 0.2745 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2829 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= 0.121 Angle : 0.467 8.268 29171 Z= 0.262 Chirality : 0.040 0.205 3484 Planarity : 0.003 0.086 3284 Dihedral : 19.568 179.360 4151 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % Rotamer: Outliers : 1.31 % Allowed : 17.71 % Favored : 80.99 % 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: 1.82 (0.18), residues: 2415 helix: 2.96 (0.16), residues: 1135 sheet: 0.77 (0.25), residues: 401 loop : -1.04 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 323 HIS 0.005 0.001 HIS A 46 PHE 0.008 0.001 PHE B 226 TYR 0.023 0.001 TYR F 77 ARG 0.002 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 1018) hydrogen bonds : angle 3.52554 ( 2876) metal coordination : bond 0.00342 ( 4) metal coordination : angle 1.25046 ( 6) covalent geometry : bond 0.00269 (21042) covalent geometry : angle 0.46649 (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 96 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 2.124 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8699 (tm-30) REVERT: A 189 ILE cc_start: 0.7595 (mm) cc_final: 0.7270 (mm) REVERT: F 78 TYR cc_start: 0.8998 (m-80) cc_final: 0.8705 (m-10) REVERT: F 111 ASP cc_start: 0.8977 (t0) cc_final: 0.8389 (t0) REVERT: F 173 SER cc_start: 0.8984 (m) cc_final: 0.8664 (t) REVERT: F 186 GLN cc_start: 0.9578 (mm-40) cc_final: 0.9219 (tm-30) outliers start: 22 outliers final: 19 residues processed: 93 average time/residue: 0.2532 time to fit residues: 41.8001 Evaluate side-chains 93 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 2.165 ------------------------------------------------------------------------------- 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 419 HIS Chi-restraints excluded: chain B residue 424 LEU 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 160 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 201 VAL 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: 0.8980 chunk 232 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 25 optimal weight: 40.0000 chunk 216 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 213 optimal weight: 0.0770 chunk 214 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.079220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.052690 restraints weight = 70429.031| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.21 r_work: 0.2772 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21046 Z= 0.111 Angle : 0.455 9.289 29171 Z= 0.253 Chirality : 0.039 0.208 3484 Planarity : 0.003 0.070 3284 Dihedral : 19.485 176.863 4151 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 1.31 % Allowed : 17.77 % 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: 2.02 (0.18), residues: 2415 helix: 3.12 (0.16), residues: 1133 sheet: 0.87 (0.25), residues: 401 loop : -0.93 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 323 HIS 0.004 0.001 HIS A 46 PHE 0.008 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 0.03462 ( 1018) hydrogen bonds : angle 3.38528 ( 2876) metal coordination : bond 0.00252 ( 4) metal coordination : angle 0.93094 ( 6) covalent geometry : bond 0.00246 (21042) covalent geometry : angle 0.45465 (29165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12447.20 seconds wall clock time: 214 minutes 7.77 seconds (12847.77 seconds total)