Starting phenix.real_space_refine on Sat Mar 16 09:51:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3u_30567/03_2024/7d3u_30567_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3u_30567/03_2024/7d3u_30567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3u_30567/03_2024/7d3u_30567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3u_30567/03_2024/7d3u_30567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3u_30567/03_2024/7d3u_30567_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3u_30567/03_2024/7d3u_30567_updated.pdb" } resolution = 3.0 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= 1.000 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 9488 2.51 5 N 2293 2.21 5 O 2495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D GLU 444": "OE1" <-> "OE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14333 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 3897 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 507} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 6661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6661 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 40, 'TRANS': 863} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 938 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 629 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "G" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "E" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 892 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 201 Unusual residues: {'LMT': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 416 Unresolved non-hydrogen chiralities: 80 Chain: "A" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 292 Unusual residues: {'LMT': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 100 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 20 Time building chain proxies: 8.20, per 1000 atoms: 0.57 Number of scatterers: 14333 At special positions: 0 Unit cell: (86.32, 86.32, 161.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2495 8.00 N 2293 7.00 C 9488 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 - 3.50 Amino acid : False - 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: 5.88 Conformation dependent library (CDL) restraints added in 2.9 seconds 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 4 sheets defined 65.8% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'D' and resid 5 through 23 removed outlier: 3.525A pdb=" N THR D 8 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 12 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL D 13 " --> pdb=" O PHE D 10 " (cutoff:3.500A) Proline residue: D 14 - end of helix removed outlier: 4.138A pdb=" N ALA D 18 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D 22 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 50 removed outlier: 3.630A pdb=" N PHE D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.704A pdb=" N ALA D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 125 Processing helix chain 'D' and resid 129 through 146 Proline residue: D 142 - end of helix Processing helix chain 'D' and resid 157 through 187 removed outlier: 3.774A pdb=" N SER D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 221 removed outlier: 3.750A pdb=" N ALA D 209 " --> pdb=" O ALA D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 No H-bonds generated for 'chain 'D' and resid 228 through 231' Processing helix chain 'D' and resid 239 through 247 removed outlier: 3.517A pdb=" N ALA D 243 " --> pdb=" O PRO D 239 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 263 Processing helix chain 'D' and resid 272 through 292 removed outlier: 3.653A pdb=" N VAL D 287 " --> pdb=" O MET D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 316 removed outlier: 3.666A pdb=" N LEU D 300 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY D 314 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 350 removed outlier: 3.748A pdb=" N THR D 324 " --> pdb=" O PRO D 320 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.622A pdb=" N SER D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 401 Processing helix chain 'D' and resid 405 through 429 removed outlier: 4.466A pdb=" N SER D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE D 416 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 417 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 528 through 546 Proline residue: D 533 - end of helix removed outlier: 3.539A pdb=" N LEU D 537 " --> pdb=" O PRO D 533 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 538 " --> pdb=" O ALA D 534 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 545 " --> pdb=" O THR D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 561 removed outlier: 3.504A pdb=" N LEU D 554 " --> pdb=" O LEU D 550 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN D 561 " --> pdb=" O THR D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 572 removed outlier: 3.674A pdb=" N ALA D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 removed outlier: 3.655A pdb=" N ALA A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 27 through 45 Proline residue: A 31 - end of helix removed outlier: 4.178A pdb=" N LEU A 36 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY A 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 38 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TRP A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 94 removed outlier: 3.966A pdb=" N MET A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.849A pdb=" N LEU A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 142 Processing helix chain 'A' and resid 146 through 164 removed outlier: 3.798A pdb=" N GLY A 149 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN A 151 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Proline residue: A 152 - end of helix removed outlier: 3.516A pdb=" N THR A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 162 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY A 163 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 183 through 186 No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.784A pdb=" N VAL A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 243 through 255 removed outlier: 4.025A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 284 removed outlier: 3.679A pdb=" N CYS A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 308 removed outlier: 3.514A pdb=" N ALA A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 343 removed outlier: 3.759A pdb=" N VAL A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 373 removed outlier: 3.616A pdb=" N ALA A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 393 removed outlier: 4.479A pdb=" N ASP A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 423 removed outlier: 3.657A pdb=" N PHE A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 Proline residue: A 462 - end of helix removed outlier: 3.545A pdb=" N LEU A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 477 through 484 Processing helix chain 'A' and resid 504 through 530 removed outlier: 4.501A pdb=" N SER A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N HIS A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 540 through 561 removed outlier: 4.627A pdb=" N ASP A 544 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 545 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 558 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 559 " --> pdb=" O ARG A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 571 through 587 removed outlier: 3.560A pdb=" N VAL A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 617 removed outlier: 3.741A pdb=" N TRP A 603 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE A 604 " --> pdb=" O GLU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 642 Processing helix chain 'A' and resid 646 through 667 removed outlier: 3.620A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 701 removed outlier: 3.503A pdb=" N VAL A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 739 through 762 Processing helix chain 'A' and resid 784 through 787 No H-bonds generated for 'chain 'A' and resid 784 through 787' Processing helix chain 'A' and resid 789 through 812 removed outlier: 4.093A pdb=" N ARG A 796 " --> pdb=" O ARG A 792 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) Proline residue: A 800 - end of helix removed outlier: 3.667A pdb=" N VAL A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 837 removed outlier: 3.681A pdb=" N GLY A 830 " --> pdb=" O ILE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 870 removed outlier: 4.271A pdb=" N GLY A 868 " --> pdb=" O THR A 864 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N PHE A 869 " --> pdb=" O GLY A 865 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 912 removed outlier: 3.568A pdb=" N LEU A 912 " --> pdb=" O ALA A 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 19 removed outlier: 3.769A pdb=" N VAL C 7 " --> pdb=" O LEU C 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 19 " --> pdb=" O VAL C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 44 removed outlier: 3.898A pdb=" N GLY C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 91 removed outlier: 3.882A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'F' and resid 2 through 23 Processing helix chain 'F' and resid 30 through 52 removed outlier: 3.721A pdb=" N ALA F 35 " --> pdb=" O ARG F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 65 Processing helix chain 'F' and resid 71 through 80 removed outlier: 4.275A pdb=" N LEU F 76 " --> pdb=" O SER F 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 28 Processing helix chain 'G' and resid 35 through 61 removed outlier: 4.002A pdb=" N ALA G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY G 47 " --> pdb=" O GLY G 43 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 95 removed outlier: 3.875A pdb=" N ALA G 73 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA G 85 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 34 removed outlier: 3.828A pdb=" N THR E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 66 Processing helix chain 'E' and resid 96 through 111 Processing sheet with id= A, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= B, first strand: chain 'A' and resid 880 through 882 Processing sheet with id= C, first strand: chain 'A' and resid 52 through 58 removed outlier: 3.954A pdb=" N TRP A 57 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A 63 " --> pdb=" O TRP A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 43 through 48 removed outlier: 3.756A pdb=" N GLY E 74 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N HIS E 89 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR E 72 " --> pdb=" O HIS E 89 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4268 1.34 - 1.45: 1894 1.45 - 1.57: 8351 1.57 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 14622 Sorted by residual: bond pdb=" C5 LMT A1207 " pdb=" C6 LMT A1207 " ideal model delta sigma weight residual 1.527 1.263 0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C6 LMT A1207 " pdb=" C7 LMT A1207 " ideal model delta sigma weight residual 1.527 1.316 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C8 LMT A1210 " pdb=" C9 LMT A1210 " ideal model delta sigma weight residual 1.531 1.367 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" C7 LMT A1210 " pdb=" C8 LMT A1210 " ideal model delta sigma weight residual 1.529 1.374 0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C2 LMT A1207 " pdb=" C3 LMT A1207 " ideal model delta sigma weight residual 1.529 1.376 0.153 2.00e-02 2.50e+03 5.86e+01 ... (remaining 14617 not shown) Histogram of bond angle deviations from ideal: 87.75 - 97.01: 3 97.01 - 106.26: 458 106.26 - 115.52: 9387 115.52 - 124.77: 9791 124.77 - 134.03: 249 Bond angle restraints: 19888 Sorted by residual: angle pdb=" C6 LMT A1210 " pdb=" C7 LMT A1210 " pdb=" C8 LMT A1210 " ideal model delta sigma weight residual 117.26 87.75 29.51 3.00e+00 1.11e-01 9.67e+01 angle pdb=" C5 LMT A1207 " pdb=" C6 LMT A1207 " pdb=" C7 LMT A1207 " ideal model delta sigma weight residual 115.22 89.90 25.32 3.00e+00 1.11e-01 7.12e+01 angle pdb=" N PRO D 517 " pdb=" CA PRO D 517 " pdb=" CB PRO D 517 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" C4 LMT A1207 " pdb=" C5 LMT A1207 " pdb=" C6 LMT A1207 " ideal model delta sigma weight residual 115.09 94.85 20.24 3.00e+00 1.11e-01 4.55e+01 angle pdb=" C3 LMT A1207 " pdb=" C4 LMT A1207 " pdb=" C5 LMT A1207 " ideal model delta sigma weight residual 115.20 133.51 -18.31 3.00e+00 1.11e-01 3.72e+01 ... (remaining 19883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.53: 8277 25.53 - 51.05: 439 51.05 - 76.58: 73 76.58 - 102.11: 42 102.11 - 127.64: 46 Dihedral angle restraints: 8877 sinusoidal: 3569 harmonic: 5308 Sorted by residual: dihedral pdb=" N TRP E 84 " pdb=" C TRP E 84 " pdb=" CA TRP E 84 " pdb=" CB TRP E 84 " ideal model delta harmonic sigma weight residual 122.80 135.47 -12.67 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" C1' LMT A1206 " pdb=" C5' LMT A1206 " pdb=" O5' LMT A1206 " pdb=" C4' LMT A1206 " ideal model delta sinusoidal sigma weight residual -62.78 64.86 -127.64 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CA ASP A 919 " pdb=" C ASP A 919 " pdb=" N GLU A 920 " pdb=" CA GLU A 920 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 8874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2436 0.114 - 0.228: 42 0.228 - 0.342: 7 0.342 - 0.456: 0 0.456 - 0.570: 2 Chirality restraints: 2487 Sorted by residual: chirality pdb=" C5' LMT A1206 " pdb=" C4' LMT A1206 " pdb=" C6' LMT A1206 " pdb=" O5' LMT A1206 " both_signs ideal model delta sigma weight residual False -2.51 -1.94 -0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" CA TRP E 84 " pdb=" N TRP E 84 " pdb=" C TRP E 84 " pdb=" CB TRP E 84 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" C3B LMT A1214 " pdb=" C2B LMT A1214 " pdb=" C4B LMT A1214 " pdb=" O3B LMT A1214 " both_signs ideal model delta sigma weight residual False 2.50 2.22 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2484 not shown) Planarity restraints: 2395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 383 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO D 384 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 384 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 384 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 920 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 921 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 921 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 921 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 535 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C ALA A 535 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA A 535 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 536 " 0.011 2.00e-02 2.50e+03 ... (remaining 2392 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 257 2.68 - 3.23: 14741 3.23 - 3.79: 23465 3.79 - 4.34: 32068 4.34 - 4.90: 52688 Nonbonded interactions: 123219 Sorted by model distance: nonbonded pdb=" O ASP E 83 " pdb=" O TRP E 84 " model vdw 2.119 3.040 nonbonded pdb=" O LEU A 734 " pdb=" OG1 THR A 742 " model vdw 2.230 2.440 nonbonded pdb=" NE2 GLN A 284 " pdb=" CD1 LEU A 530 " model vdw 2.239 3.540 nonbonded pdb=" O ARG A 681 " pdb=" OG SER A 685 " model vdw 2.257 2.440 nonbonded pdb=" O ASP D 77 " pdb=" ND2 ASN D 561 " model vdw 2.268 2.520 ... (remaining 123214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 6.730 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 41.770 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.008 0.264 14622 Z= 0.522 Angle : 1.029 29.508 19888 Z= 0.441 Chirality : 0.049 0.570 2487 Planarity : 0.004 0.063 2395 Dihedral : 19.880 127.635 5475 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 0.50 % Allowed : 16.23 % Favored : 83.27 % Cbeta Deviations : 0.06 % 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: -3.05 (0.17), residues: 1857 helix: -1.49 (0.13), residues: 1281 sheet: -2.25 (0.86), residues: 30 loop : -2.99 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.006 0.001 HIS G 61 PHE 0.028 0.001 PHE A 328 TYR 0.023 0.001 TYR A 418 ARG 0.003 0.000 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 248 time to evaluate : 1.654 Fit side-chains REVERT: D 1 MET cc_start: 0.7004 (mmm) cc_final: 0.6736 (mmm) REVERT: D 77 ASP cc_start: 0.8151 (p0) cc_final: 0.7824 (p0) REVERT: D 332 HIS cc_start: 0.8783 (OUTLIER) cc_final: 0.8563 (t-90) REVERT: D 364 LYS cc_start: 0.8759 (tttm) cc_final: 0.8468 (tttp) REVERT: D 570 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8044 (tp-100) REVERT: A 88 MET cc_start: 0.8994 (mmt) cc_final: 0.8693 (mmp) REVERT: A 148 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8798 (tptm) REVERT: A 281 PHE cc_start: 0.8506 (m-80) cc_final: 0.8297 (m-10) REVERT: A 488 ILE cc_start: 0.7863 (pt) cc_final: 0.7619 (pt) REVERT: A 523 ARG cc_start: 0.7325 (ttp-110) cc_final: 0.6823 (ptp-170) REVERT: A 785 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8496 (tm-30) REVERT: A 814 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8723 (t-90) REVERT: C 59 ASP cc_start: 0.8301 (t70) cc_final: 0.7907 (t0) REVERT: C 121 ASP cc_start: 0.8501 (t0) cc_final: 0.7946 (p0) REVERT: F 24 ARG cc_start: 0.7763 (ttt-90) cc_final: 0.7467 (tpp80) REVERT: G 64 TRP cc_start: 0.8411 (t-100) cc_final: 0.8160 (m100) REVERT: E 112 ARG cc_start: 0.8376 (ttm170) cc_final: 0.8009 (ttm-80) outliers start: 7 outliers final: 2 residues processed: 255 average time/residue: 1.0323 time to fit residues: 294.2664 Evaluate side-chains 176 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 814 HIS Chi-restraints excluded: chain C residue 101 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 140 optimal weight: 0.0270 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 0.0000 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 227 HIS ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 450 HIS A 151 GLN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN F 27 HIS G 61 HIS ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 109 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14622 Z= 0.218 Angle : 0.671 9.093 19888 Z= 0.319 Chirality : 0.042 0.243 2487 Planarity : 0.005 0.067 2395 Dihedral : 14.465 101.506 2668 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.83 % Allowed : 20.91 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1857 helix: -0.33 (0.14), residues: 1287 sheet: -2.14 (0.77), residues: 35 loop : -2.39 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 263 HIS 0.011 0.001 HIS E 109 PHE 0.028 0.001 PHE A 328 TYR 0.025 0.002 TYR A 418 ARG 0.005 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 198 time to evaluate : 1.539 Fit side-chains REVERT: D 1 MET cc_start: 0.7011 (mmm) cc_final: 0.6764 (mmm) REVERT: D 77 ASP cc_start: 0.8017 (p0) cc_final: 0.7634 (p0) REVERT: D 332 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.8529 (t-90) REVERT: D 364 LYS cc_start: 0.8772 (tttm) cc_final: 0.8473 (tttp) REVERT: D 570 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8079 (tp-100) REVERT: A 58 MET cc_start: 0.8920 (mtm) cc_final: 0.8617 (mtt) REVERT: A 88 MET cc_start: 0.8816 (mmt) cc_final: 0.8610 (mpm) REVERT: A 148 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8772 (tptm) REVERT: A 358 MET cc_start: 0.7467 (mtp) cc_final: 0.6892 (mmm) REVERT: A 523 ARG cc_start: 0.7236 (ttp-110) cc_final: 0.6741 (ptp-170) REVERT: A 556 ARG cc_start: 0.6817 (mtp180) cc_final: 0.6586 (ttm110) REVERT: A 636 MET cc_start: 0.8601 (mmm) cc_final: 0.8371 (mmm) REVERT: A 769 ARG cc_start: 0.7558 (ttp80) cc_final: 0.7322 (ptt-90) REVERT: A 785 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8391 (tm-30) REVERT: A 814 HIS cc_start: 0.9064 (OUTLIER) cc_final: 0.8846 (t-90) REVERT: F 24 ARG cc_start: 0.7701 (ttt-90) cc_final: 0.7416 (tpp80) REVERT: G 64 TRP cc_start: 0.8385 (t-100) cc_final: 0.8148 (m100) REVERT: E 50 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.8028 (ttt-90) REVERT: E 112 ARG cc_start: 0.8388 (ttm170) cc_final: 0.8030 (ttm-80) outliers start: 54 outliers final: 30 residues processed: 237 average time/residue: 1.0565 time to fit residues: 280.6606 Evaluate side-chains 204 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 814 HIS Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 76 HIS Chi-restraints excluded: chain E residue 91 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.4980 chunk 52 optimal weight: 0.0870 chunk 139 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 0.0070 chunk 149 optimal weight: 0.4980 chunk 166 optimal weight: 0.0060 chunk 57 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 overall best weight: 0.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 121 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14622 Z= 0.165 Angle : 0.596 9.030 19888 Z= 0.288 Chirality : 0.040 0.276 2487 Planarity : 0.004 0.069 2395 Dihedral : 10.998 99.323 2666 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.61 % Allowed : 22.68 % Favored : 73.71 % 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: -0.71 (0.19), residues: 1857 helix: 0.26 (0.14), residues: 1281 sheet: -1.25 (0.80), residues: 37 loop : -2.07 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.007 0.001 HIS A 776 PHE 0.026 0.001 PHE A 328 TYR 0.023 0.001 TYR A 418 ARG 0.003 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 208 time to evaluate : 1.459 Fit side-chains REVERT: D 77 ASP cc_start: 0.7934 (p0) cc_final: 0.7518 (p0) REVERT: D 308 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8477 (mp) REVERT: D 332 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.8409 (t-90) REVERT: D 364 LYS cc_start: 0.8719 (tttm) cc_final: 0.8423 (tttp) REVERT: D 570 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8046 (tp-100) REVERT: A 58 MET cc_start: 0.8936 (mtm) cc_final: 0.8689 (mtt) REVERT: A 88 MET cc_start: 0.8785 (mmt) cc_final: 0.8573 (mpm) REVERT: A 148 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8695 (tptm) REVERT: A 358 MET cc_start: 0.7448 (mtp) cc_final: 0.7179 (mmm) REVERT: A 500 HIS cc_start: 0.6760 (OUTLIER) cc_final: 0.6460 (t70) REVERT: A 523 ARG cc_start: 0.7137 (ttp-110) cc_final: 0.6627 (ptp-170) REVERT: A 556 ARG cc_start: 0.6787 (mtp180) cc_final: 0.6578 (ttm110) REVERT: A 769 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7283 (ttp80) REVERT: A 785 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8553 (tm-30) REVERT: C 112 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8307 (tt0) REVERT: C 121 ASP cc_start: 0.8394 (t0) cc_final: 0.8003 (p0) REVERT: F 24 ARG cc_start: 0.7639 (ttt-90) cc_final: 0.7373 (tpp80) REVERT: G 48 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7151 (tp) REVERT: G 64 TRP cc_start: 0.8376 (t-100) cc_final: 0.8141 (m100) REVERT: E 28 LYS cc_start: 0.8639 (ttmm) cc_final: 0.7637 (tppt) REVERT: E 112 ARG cc_start: 0.8320 (ttm170) cc_final: 0.8015 (ttm-80) REVERT: E 115 ARG cc_start: 0.7387 (mtt90) cc_final: 0.6772 (mtt90) outliers start: 51 outliers final: 21 residues processed: 245 average time/residue: 1.0371 time to fit residues: 285.8370 Evaluate side-chains 216 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 0.0010 overall best weight: 0.8766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 249 HIS ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14622 Z= 0.225 Angle : 0.603 8.689 19888 Z= 0.294 Chirality : 0.041 0.315 2487 Planarity : 0.004 0.071 2395 Dihedral : 9.454 64.784 2664 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.61 % Allowed : 22.47 % Favored : 72.93 % 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: -0.41 (0.20), residues: 1857 helix: 0.47 (0.15), residues: 1285 sheet: -1.22 (0.84), residues: 35 loop : -1.91 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 131 HIS 0.007 0.001 HIS A 776 PHE 0.027 0.001 PHE A 328 TYR 0.019 0.001 TYR A 418 ARG 0.004 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 196 time to evaluate : 1.562 Fit side-chains REVERT: D 77 ASP cc_start: 0.8026 (p0) cc_final: 0.7662 (p0) REVERT: D 332 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.8473 (t-90) REVERT: D 364 LYS cc_start: 0.8756 (tttm) cc_final: 0.8443 (tttp) REVERT: D 570 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8043 (tp-100) REVERT: A 58 MET cc_start: 0.8904 (mtm) cc_final: 0.8659 (mtt) REVERT: A 148 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8705 (tptm) REVERT: A 283 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7951 (ttm) REVERT: A 358 MET cc_start: 0.7507 (mtp) cc_final: 0.7286 (mmm) REVERT: A 500 HIS cc_start: 0.6697 (OUTLIER) cc_final: 0.6432 (t70) REVERT: A 523 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6565 (ptp-170) REVERT: A 556 ARG cc_start: 0.6838 (mtp180) cc_final: 0.6538 (mtm110) REVERT: A 636 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8161 (mmm) REVERT: A 769 ARG cc_start: 0.7560 (ttp80) cc_final: 0.7331 (ttp80) REVERT: A 785 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8545 (tm-30) REVERT: A 814 HIS cc_start: 0.9037 (OUTLIER) cc_final: 0.8810 (t-90) REVERT: C 59 ASP cc_start: 0.8294 (t70) cc_final: 0.7927 (t0) REVERT: C 121 ASP cc_start: 0.8383 (t0) cc_final: 0.8000 (p0) REVERT: F 24 ARG cc_start: 0.7607 (ttt-90) cc_final: 0.7370 (tpp80) REVERT: G 48 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7393 (tp) REVERT: G 64 TRP cc_start: 0.8387 (t-100) cc_final: 0.8142 (m100) REVERT: E 49 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7131 (m) REVERT: E 112 ARG cc_start: 0.8340 (ttm170) cc_final: 0.8052 (ttm-80) outliers start: 65 outliers final: 29 residues processed: 239 average time/residue: 1.0530 time to fit residues: 282.3315 Evaluate side-chains 214 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 814 HIS Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 76 HIS Chi-restraints excluded: chain E residue 91 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.0870 chunk 101 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 152 optimal weight: 0.0370 chunk 123 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14622 Z= 0.173 Angle : 0.571 8.859 19888 Z= 0.281 Chirality : 0.040 0.278 2487 Planarity : 0.004 0.070 2395 Dihedral : 8.441 59.954 2664 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.83 % Allowed : 23.95 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.20), residues: 1857 helix: 0.63 (0.15), residues: 1290 sheet: -0.91 (0.82), residues: 37 loop : -1.80 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 131 HIS 0.007 0.001 HIS A 776 PHE 0.026 0.001 PHE A 328 TYR 0.021 0.001 TYR A 418 ARG 0.003 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 190 time to evaluate : 1.479 Fit side-chains REVERT: D 30 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7869 (tp) REVERT: D 77 ASP cc_start: 0.7989 (p0) cc_final: 0.7574 (p0) REVERT: D 308 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8509 (mp) REVERT: D 364 LYS cc_start: 0.8730 (tttm) cc_final: 0.8407 (tttp) REVERT: D 570 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8022 (tp-100) REVERT: A 58 MET cc_start: 0.8933 (mtm) cc_final: 0.8694 (mtt) REVERT: A 88 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7505 (mpm) REVERT: A 148 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8676 (tptm) REVERT: A 189 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8333 (t0) REVERT: A 283 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7969 (ttm) REVERT: A 358 MET cc_start: 0.7482 (mtp) cc_final: 0.7046 (mmm) REVERT: A 500 HIS cc_start: 0.6645 (OUTLIER) cc_final: 0.6416 (t70) REVERT: A 523 ARG cc_start: 0.6959 (ttp-110) cc_final: 0.6522 (ptp-170) REVERT: A 556 ARG cc_start: 0.6784 (mtp180) cc_final: 0.6399 (mtm110) REVERT: A 769 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7274 (ttp80) REVERT: A 785 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8499 (tm-30) REVERT: A 814 HIS cc_start: 0.9043 (OUTLIER) cc_final: 0.8799 (t-90) REVERT: C 121 ASP cc_start: 0.8338 (t0) cc_final: 0.7989 (p0) REVERT: F 24 ARG cc_start: 0.7585 (ttt-90) cc_final: 0.7342 (tpp80) REVERT: G 64 TRP cc_start: 0.8373 (t-100) cc_final: 0.8128 (m100) REVERT: E 28 LYS cc_start: 0.8647 (ttmm) cc_final: 0.7625 (tppt) REVERT: E 110 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8273 (ttp) REVERT: E 112 ARG cc_start: 0.8264 (ttm170) cc_final: 0.8033 (ttm-80) REVERT: E 115 ARG cc_start: 0.7436 (mtt90) cc_final: 0.7084 (mtt90) outliers start: 54 outliers final: 32 residues processed: 222 average time/residue: 1.0770 time to fit residues: 267.6476 Evaluate side-chains 230 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 190 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 814 HIS Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain E residue 76 HIS Chi-restraints excluded: chain E residue 110 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 148 optimal weight: 0.0270 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14622 Z= 0.251 Angle : 0.590 9.035 19888 Z= 0.292 Chirality : 0.040 0.246 2487 Planarity : 0.004 0.071 2395 Dihedral : 8.137 59.157 2664 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.96 % Allowed : 22.61 % Favored : 72.43 % 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: -0.08 (0.20), residues: 1857 helix: 0.69 (0.15), residues: 1288 sheet: -1.02 (0.85), residues: 35 loop : -1.75 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.005 0.001 HIS A 776 PHE 0.027 0.001 PHE A 328 TYR 0.019 0.001 TYR A 418 ARG 0.002 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 194 time to evaluate : 1.706 Fit side-chains REVERT: D 30 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7907 (tp) REVERT: D 77 ASP cc_start: 0.8081 (p0) cc_final: 0.7732 (p0) REVERT: D 364 LYS cc_start: 0.8738 (tttm) cc_final: 0.8403 (tttp) REVERT: D 570 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 58 MET cc_start: 0.8947 (mtm) cc_final: 0.8724 (mtt) REVERT: A 88 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7478 (mpm) REVERT: A 148 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8681 (tptm) REVERT: A 189 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8265 (t0) REVERT: A 283 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7955 (ttm) REVERT: A 287 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7402 (p0) REVERT: A 358 MET cc_start: 0.7477 (mtp) cc_final: 0.7053 (mmm) REVERT: A 500 HIS cc_start: 0.6670 (OUTLIER) cc_final: 0.6468 (t70) REVERT: A 523 ARG cc_start: 0.7016 (ttp-110) cc_final: 0.6572 (ptp-170) REVERT: A 556 ARG cc_start: 0.6820 (mtp180) cc_final: 0.6440 (mtm110) REVERT: A 769 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7297 (ttp80) REVERT: A 785 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 814 HIS cc_start: 0.9039 (OUTLIER) cc_final: 0.8766 (t-90) REVERT: C 59 ASP cc_start: 0.8379 (t70) cc_final: 0.7995 (t70) REVERT: C 121 ASP cc_start: 0.8334 (t0) cc_final: 0.7972 (p0) REVERT: F 24 ARG cc_start: 0.7598 (ttt-90) cc_final: 0.7375 (tpp80) REVERT: G 64 TRP cc_start: 0.8412 (t-100) cc_final: 0.8136 (m100) REVERT: E 112 ARG cc_start: 0.8253 (ttm170) cc_final: 0.8043 (ttm-80) outliers start: 70 outliers final: 40 residues processed: 241 average time/residue: 1.0082 time to fit residues: 273.0134 Evaluate side-chains 232 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 185 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 814 HIS Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 76 HIS Chi-restraints excluded: chain E residue 91 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14622 Z= 0.203 Angle : 0.579 8.971 19888 Z= 0.286 Chirality : 0.039 0.220 2487 Planarity : 0.004 0.070 2395 Dihedral : 7.895 59.430 2664 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.75 % Allowed : 23.53 % Favored : 71.72 % 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: 0.08 (0.20), residues: 1857 helix: 0.80 (0.15), residues: 1288 sheet: -0.76 (0.82), residues: 37 loop : -1.66 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.006 0.001 HIS A 776 PHE 0.026 0.001 PHE A 328 TYR 0.021 0.001 TYR A 418 ARG 0.003 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 197 time to evaluate : 1.534 Fit side-chains REVERT: D 30 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7920 (tp) REVERT: D 77 ASP cc_start: 0.8043 (p0) cc_final: 0.7678 (p0) REVERT: D 137 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7585 (mm-30) REVERT: D 364 LYS cc_start: 0.8743 (tttm) cc_final: 0.8403 (tttp) REVERT: D 570 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 58 MET cc_start: 0.8952 (mtm) cc_final: 0.8736 (mtt) REVERT: A 88 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7477 (mpm) REVERT: A 148 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8659 (tptm) REVERT: A 189 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8255 (t0) REVERT: A 283 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7971 (ttm) REVERT: A 287 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7310 (p0) REVERT: A 358 MET cc_start: 0.7463 (mtp) cc_final: 0.7053 (mmm) REVERT: A 500 HIS cc_start: 0.6649 (OUTLIER) cc_final: 0.6443 (t70) REVERT: A 523 ARG cc_start: 0.6935 (ttp-110) cc_final: 0.6511 (ptp-170) REVERT: A 556 ARG cc_start: 0.6702 (mtp180) cc_final: 0.6349 (mtm110) REVERT: A 769 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7284 (ttp80) REVERT: A 785 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 814 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8788 (t-90) REVERT: C 59 ASP cc_start: 0.8420 (t70) cc_final: 0.8060 (t0) REVERT: C 121 ASP cc_start: 0.8336 (t0) cc_final: 0.7968 (p0) REVERT: F 24 ARG cc_start: 0.7586 (ttt-90) cc_final: 0.7368 (tpp80) REVERT: G 48 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7235 (tp) REVERT: G 64 TRP cc_start: 0.8440 (t-100) cc_final: 0.8164 (m100) REVERT: E 28 LYS cc_start: 0.8654 (ttmm) cc_final: 0.7627 (tppt) REVERT: E 112 ARG cc_start: 0.8209 (ttm170) cc_final: 0.8000 (ttm-80) outliers start: 67 outliers final: 43 residues processed: 242 average time/residue: 0.9615 time to fit residues: 262.4913 Evaluate side-chains 235 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 184 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 814 HIS Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain E residue 76 HIS Chi-restraints excluded: chain E residue 91 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 88 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14622 Z= 0.184 Angle : 0.576 8.967 19888 Z= 0.285 Chirality : 0.039 0.219 2487 Planarity : 0.004 0.069 2395 Dihedral : 7.624 58.875 2664 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.18 % Allowed : 24.17 % Favored : 71.65 % 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: 0.23 (0.20), residues: 1857 helix: 0.93 (0.15), residues: 1283 sheet: -0.77 (0.80), residues: 39 loop : -1.61 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 263 HIS 0.006 0.001 HIS A 776 PHE 0.025 0.001 PHE A 328 TYR 0.021 0.001 TYR A 418 ARG 0.003 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 193 time to evaluate : 1.710 Fit side-chains REVERT: D 30 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7916 (tp) REVERT: D 77 ASP cc_start: 0.7977 (p0) cc_final: 0.7605 (p0) REVERT: D 137 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7563 (mm-30) REVERT: D 364 LYS cc_start: 0.8732 (tttm) cc_final: 0.8386 (tttp) REVERT: D 570 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8228 (tm-30) REVERT: A 58 MET cc_start: 0.8953 (mtm) cc_final: 0.8737 (mtt) REVERT: A 88 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7510 (mpm) REVERT: A 148 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8585 (tptm) REVERT: A 283 MET cc_start: 0.8377 (ttm) cc_final: 0.7974 (ttm) REVERT: A 287 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7288 (p0) REVERT: A 358 MET cc_start: 0.7434 (mtp) cc_final: 0.7034 (mmm) REVERT: A 523 ARG cc_start: 0.6918 (ttp-110) cc_final: 0.6485 (ptp-170) REVERT: A 556 ARG cc_start: 0.6658 (mtp180) cc_final: 0.6337 (mtm110) REVERT: A 769 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7297 (ttp80) REVERT: A 785 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8539 (tm-30) REVERT: A 814 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8763 (t-90) REVERT: C 59 ASP cc_start: 0.8415 (t70) cc_final: 0.8062 (t0) REVERT: C 121 ASP cc_start: 0.8312 (t0) cc_final: 0.7846 (p0) REVERT: F 24 ARG cc_start: 0.7587 (ttt-90) cc_final: 0.7369 (tpp80) REVERT: F 55 SER cc_start: 0.8497 (t) cc_final: 0.8282 (p) REVERT: G 48 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7267 (tp) REVERT: G 64 TRP cc_start: 0.8432 (t-100) cc_final: 0.8162 (m100) REVERT: E 28 LYS cc_start: 0.8665 (ttmm) cc_final: 0.7679 (tppt) REVERT: E 112 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7981 (ttm-80) outliers start: 59 outliers final: 37 residues processed: 234 average time/residue: 1.0412 time to fit residues: 274.0975 Evaluate side-chains 229 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 814 HIS Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 0.0060 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14622 Z= 0.186 Angle : 0.591 8.790 19888 Z= 0.291 Chirality : 0.039 0.219 2487 Planarity : 0.004 0.069 2395 Dihedral : 7.501 58.188 2664 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.83 % Allowed : 24.88 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.30 (0.20), residues: 1857 helix: 0.98 (0.15), residues: 1282 sheet: -0.60 (0.81), residues: 39 loop : -1.58 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 131 HIS 0.005 0.001 HIS A 776 PHE 0.025 0.001 PHE A 328 TYR 0.022 0.001 TYR A 418 ARG 0.003 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 196 time to evaluate : 1.571 Fit side-chains REVERT: D 30 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7918 (tp) REVERT: D 77 ASP cc_start: 0.7963 (p0) cc_final: 0.7570 (p0) REVERT: D 137 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7595 (mm-30) REVERT: D 190 THR cc_start: 0.8733 (p) cc_final: 0.8285 (t) REVERT: D 332 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8473 (t70) REVERT: D 364 LYS cc_start: 0.8719 (tttm) cc_final: 0.8372 (tttp) REVERT: D 570 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 58 MET cc_start: 0.8958 (mtm) cc_final: 0.8741 (mtt) REVERT: A 88 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7568 (mpm) REVERT: A 148 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8571 (tptm) REVERT: A 283 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7959 (ttm) REVERT: A 287 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7294 (p0) REVERT: A 358 MET cc_start: 0.7387 (mtp) cc_final: 0.6988 (mmm) REVERT: A 523 ARG cc_start: 0.6894 (ttp-110) cc_final: 0.6470 (ptp-170) REVERT: A 556 ARG cc_start: 0.6601 (mtp180) cc_final: 0.6295 (mtm110) REVERT: A 769 ARG cc_start: 0.7570 (ttp80) cc_final: 0.7283 (ttp80) REVERT: A 785 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8508 (tm-30) REVERT: A 814 HIS cc_start: 0.9030 (OUTLIER) cc_final: 0.8752 (t-90) REVERT: C 59 ASP cc_start: 0.8481 (t70) cc_final: 0.8115 (t70) REVERT: C 121 ASP cc_start: 0.8311 (t0) cc_final: 0.7845 (p0) REVERT: F 24 ARG cc_start: 0.7591 (ttt-90) cc_final: 0.7376 (tpp80) REVERT: G 48 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7266 (tp) REVERT: G 64 TRP cc_start: 0.8474 (t-100) cc_final: 0.8152 (m100) REVERT: E 28 LYS cc_start: 0.8675 (ttmm) cc_final: 0.7655 (tppt) REVERT: E 116 ARG cc_start: 0.6395 (mmp-170) cc_final: 0.5105 (mpt180) outliers start: 54 outliers final: 36 residues processed: 233 average time/residue: 1.0568 time to fit residues: 275.8208 Evaluate side-chains 230 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 187 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 814 HIS Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 184 optimal weight: 0.0170 chunk 169 optimal weight: 0.2980 chunk 146 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14622 Z= 0.189 Angle : 0.600 9.182 19888 Z= 0.294 Chirality : 0.039 0.220 2487 Planarity : 0.004 0.069 2395 Dihedral : 7.393 59.246 2664 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.54 % Allowed : 25.66 % Favored : 70.80 % 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: 0.31 (0.20), residues: 1857 helix: 0.97 (0.15), residues: 1281 sheet: -0.52 (0.82), residues: 39 loop : -1.56 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 52 HIS 0.005 0.001 HIS A 321 PHE 0.026 0.001 PHE A 328 TYR 0.021 0.001 TYR A 418 ARG 0.012 0.000 ARG E 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 193 time to evaluate : 1.574 Fit side-chains REVERT: D 30 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7921 (tp) REVERT: D 77 ASP cc_start: 0.7963 (p0) cc_final: 0.7565 (p0) REVERT: D 137 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7634 (mm-30) REVERT: D 190 THR cc_start: 0.8676 (p) cc_final: 0.8269 (t) REVERT: D 332 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.8507 (t70) REVERT: D 364 LYS cc_start: 0.8675 (tttm) cc_final: 0.8322 (tttp) REVERT: D 570 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 58 MET cc_start: 0.8962 (mtm) cc_final: 0.8746 (mtt) REVERT: A 88 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.7602 (mpm) REVERT: A 115 MET cc_start: 0.8098 (mmm) cc_final: 0.7795 (mmm) REVERT: A 148 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8559 (tptm) REVERT: A 283 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8048 (ttm) REVERT: A 287 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7299 (p0) REVERT: A 358 MET cc_start: 0.7416 (mtp) cc_final: 0.6991 (mmm) REVERT: A 523 ARG cc_start: 0.6904 (ttp-110) cc_final: 0.6491 (ptp-170) REVERT: A 556 ARG cc_start: 0.6587 (mtp180) cc_final: 0.6058 (mtm110) REVERT: A 769 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7272 (ttp80) REVERT: A 785 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8587 (tm-30) REVERT: A 814 HIS cc_start: 0.9029 (OUTLIER) cc_final: 0.8745 (t-90) REVERT: C 59 ASP cc_start: 0.8425 (t70) cc_final: 0.8058 (t70) REVERT: C 121 ASP cc_start: 0.8308 (t0) cc_final: 0.7844 (p0) REVERT: F 24 ARG cc_start: 0.7632 (ttt-90) cc_final: 0.7400 (tpp80) REVERT: G 48 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7243 (tp) REVERT: G 64 TRP cc_start: 0.8472 (t-100) cc_final: 0.8148 (m100) REVERT: E 28 LYS cc_start: 0.8625 (ttmm) cc_final: 0.7627 (tppt) outliers start: 50 outliers final: 36 residues processed: 229 average time/residue: 1.0702 time to fit residues: 274.1575 Evaluate side-chains 226 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 814 HIS Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 135 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 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 = 0.3346 r_free = 0.3346 target = 0.109475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.090093 restraints weight = 20459.855| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.19 r_work: 0.2954 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14622 Z= 0.195 Angle : 0.606 10.270 19888 Z= 0.297 Chirality : 0.040 0.220 2487 Planarity : 0.004 0.069 2395 Dihedral : 7.347 59.593 2664 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.33 % Allowed : 26.01 % Favored : 70.66 % 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: 0.30 (0.20), residues: 1857 helix: 0.99 (0.15), residues: 1284 sheet: -0.44 (0.83), residues: 39 loop : -1.62 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 52 HIS 0.006 0.001 HIS A 321 PHE 0.025 0.001 PHE A 328 TYR 0.021 0.001 TYR A 418 ARG 0.005 0.000 ARG E 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4986.30 seconds wall clock time: 89 minutes 5.59 seconds (5345.59 seconds total)