Starting phenix.real_space_refine on Sat Feb 17 18:48:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/02_2024/6o1p_0594.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/02_2024/6o1p_0594.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/6o1p_0594/02_2024/6o1p_0594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/02_2024/6o1p_0594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/02_2024/6o1p_0594.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1p_0594/02_2024/6o1p_0594.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= 0.008 sd= 0.106 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 140 5.16 5 C 12660 2.51 5 N 3320 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19608 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain: "B" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain: "C" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain: "D" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Time building chain proxies: 9.91, per 1000 atoms: 0.51 Number of scatterers: 19608 At special positions: 0 Unit cell: (132.375, 132.375, 124.962, 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 140 16.00 O 3488 8.00 N 3320 7.00 C 12660 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: 6.81 Conformation dependent library (CDL) restraints added in 3.6 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 59.8% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.739A pdb=" N LYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.586A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.620A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.578A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.621A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.513A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.955A pdb=" N VAL A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.711A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 443 Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.678A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.584A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 486 removed outlier: 3.632A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.512A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 567 removed outlier: 3.929A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 585 removed outlier: 3.518A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.550A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.739A pdb=" N LYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.587A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.619A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.578A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.621A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.513A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 394 removed outlier: 3.954A pdb=" N VAL B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.711A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 443 Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.678A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.584A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 486 removed outlier: 3.632A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.513A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 removed outlier: 3.928A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 585 removed outlier: 3.518A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.550A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.740A pdb=" N LYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.586A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.620A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.577A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.620A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.513A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.955A pdb=" N VAL C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.711A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 443 Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.677A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.583A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 486 removed outlier: 3.633A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.512A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 567 removed outlier: 3.929A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 585 removed outlier: 3.517A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 585 " --> pdb=" O THR C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.550A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 4.321A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.739A pdb=" N LYS D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.587A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.620A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.764A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.562A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.613A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.577A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.591A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.620A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.512A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.769A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.710A pdb=" N PHE D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.522A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 394 removed outlier: 3.955A pdb=" N VAL D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 411 removed outlier: 3.679A pdb=" N LEU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.711A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 443 Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.677A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.583A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 486 removed outlier: 3.632A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'D' and resid 504 through 512 removed outlier: 3.608A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.512A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 567 removed outlier: 3.929A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 585 removed outlier: 3.517A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 585 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.551A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP D 593 " --> pdb=" O ARG D 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AA2, first strand: chain 'B' and resid 264 through 266 Processing sheet with id=AA3, first strand: chain 'C' and resid 264 through 266 Processing sheet with id=AA4, first strand: chain 'D' and resid 264 through 266 820 hydrogen bonds defined for protein. 2352 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: 5.59 Time building geometry restraints manager: 7.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3484 1.32 - 1.45: 5405 1.45 - 1.57: 10947 1.57 - 1.70: 0 1.70 - 1.83: 228 Bond restraints: 20064 Sorted by residual: bond pdb=" CA TRP B 286 " pdb=" C TRP B 286 " ideal model delta sigma weight residual 1.526 1.422 0.103 1.31e-02 5.83e+03 6.21e+01 bond pdb=" CA TRP D 286 " pdb=" C TRP D 286 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.31e-02 5.83e+03 6.15e+01 bond pdb=" CA TRP A 286 " pdb=" C TRP A 286 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.31e-02 5.83e+03 6.15e+01 bond pdb=" CA TRP C 286 " pdb=" C TRP C 286 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.31e-02 5.83e+03 6.15e+01 bond pdb=" N TRP A 286 " pdb=" CA TRP A 286 " ideal model delta sigma weight residual 1.458 1.380 0.078 1.00e-02 1.00e+04 6.12e+01 ... (remaining 20059 not shown) Histogram of bond angle deviations from ideal: 85.18 - 95.35: 16 95.35 - 105.53: 508 105.53 - 115.70: 12276 115.70 - 125.87: 14068 125.87 - 136.05: 380 Bond angle restraints: 27248 Sorted by residual: angle pdb=" N LEU B 612 " pdb=" CA LEU B 612 " pdb=" C LEU B 612 " ideal model delta sigma weight residual 111.04 136.05 -25.01 1.55e+00 4.16e-01 2.60e+02 angle pdb=" N LEU C 612 " pdb=" CA LEU C 612 " pdb=" C LEU C 612 " ideal model delta sigma weight residual 111.04 136.03 -24.99 1.55e+00 4.16e-01 2.60e+02 angle pdb=" N LEU A 612 " pdb=" CA LEU A 612 " pdb=" C LEU A 612 " ideal model delta sigma weight residual 111.04 136.02 -24.98 1.55e+00 4.16e-01 2.60e+02 angle pdb=" N LEU D 612 " pdb=" CA LEU D 612 " pdb=" C LEU D 612 " ideal model delta sigma weight residual 111.04 136.01 -24.97 1.55e+00 4.16e-01 2.59e+02 angle pdb=" N LEU C 354 " pdb=" CA LEU C 354 " pdb=" C LEU C 354 " ideal model delta sigma weight residual 108.99 85.57 23.42 1.57e+00 4.06e-01 2.23e+02 ... (remaining 27243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 11120 15.24 - 30.47: 652 30.47 - 45.71: 144 45.71 - 60.94: 8 60.94 - 76.18: 12 Dihedral angle restraints: 11936 sinusoidal: 4780 harmonic: 7156 Sorted by residual: dihedral pdb=" N TRP C 613 " pdb=" C TRP C 613 " pdb=" CA TRP C 613 " pdb=" CB TRP C 613 " ideal model delta harmonic sigma weight residual 122.80 92.84 29.96 0 2.50e+00 1.60e-01 1.44e+02 dihedral pdb=" N TRP D 613 " pdb=" C TRP D 613 " pdb=" CA TRP D 613 " pdb=" CB TRP D 613 " ideal model delta harmonic sigma weight residual 122.80 92.84 29.96 0 2.50e+00 1.60e-01 1.44e+02 dihedral pdb=" N TRP A 613 " pdb=" C TRP A 613 " pdb=" CA TRP A 613 " pdb=" CB TRP A 613 " ideal model delta harmonic sigma weight residual 122.80 92.86 29.94 0 2.50e+00 1.60e-01 1.43e+02 ... (remaining 11933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 3036 0.199 - 0.397: 48 0.397 - 0.596: 4 0.596 - 0.795: 8 0.795 - 0.993: 4 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CA LEU C 612 " pdb=" N LEU C 612 " pdb=" C LEU C 612 " pdb=" CB LEU C 612 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA LEU B 612 " pdb=" N LEU B 612 " pdb=" C LEU B 612 " pdb=" CB LEU B 612 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CA LEU A 612 " pdb=" N LEU A 612 " pdb=" C LEU A 612 " pdb=" CB LEU A 612 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.45e+01 ... (remaining 3097 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 285 " -0.052 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C SER B 285 " 0.211 2.00e-02 2.50e+03 pdb=" O SER B 285 " -0.087 2.00e-02 2.50e+03 pdb=" N TRP B 286 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 285 " -0.053 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C SER D 285 " 0.211 2.00e-02 2.50e+03 pdb=" O SER D 285 " -0.087 2.00e-02 2.50e+03 pdb=" N TRP D 286 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 285 " -0.052 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C SER A 285 " 0.210 2.00e-02 2.50e+03 pdb=" O SER A 285 " -0.087 2.00e-02 2.50e+03 pdb=" N TRP A 286 " -0.071 2.00e-02 2.50e+03 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 79 2.50 - 3.10: 13170 3.10 - 3.70: 30008 3.70 - 4.30: 44383 4.30 - 4.90: 71847 Nonbonded interactions: 159487 Sorted by model distance: nonbonded pdb=" O SER B 285 " pdb=" CD1 TRP B 286 " model vdw 1.899 3.260 nonbonded pdb=" O SER D 285 " pdb=" CD1 TRP D 286 " model vdw 1.899 3.260 nonbonded pdb=" O SER A 285 " pdb=" CD1 TRP A 286 " model vdw 1.900 3.260 nonbonded pdb=" O SER C 285 " pdb=" CD1 TRP C 286 " model vdw 1.900 3.260 nonbonded pdb=" N GLN A 230 " pdb=" OE1 GLN A 230 " model vdw 2.096 2.520 ... (remaining 159482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.060 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: 4.540 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 49.020 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.100 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:15.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.012 0.145 20064 Z= 0.791 Angle : 1.528 25.188 27248 Z= 0.875 Chirality : 0.087 0.993 3100 Planarity : 0.009 0.122 3460 Dihedral : 10.643 76.176 7312 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.89 % Favored : 92.79 % Rotamer: Outliers : 0.57 % Allowed : 1.32 % Favored : 98.11 % Cbeta Deviations : 1.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.75 (0.12), residues: 2440 helix: -3.98 (0.07), residues: 1428 sheet: -3.16 (0.62), residues: 64 loop : -3.31 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.006 TRP B 286 HIS 0.016 0.003 HIS A 238 PHE 0.041 0.004 PHE C 508 TYR 0.045 0.004 TYR B 349 ARG 0.015 0.001 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 607 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 THR cc_start: 0.8463 (p) cc_final: 0.8107 (t) REVERT: A 301 LYS cc_start: 0.8184 (tptm) cc_final: 0.7788 (mmmt) REVERT: B 114 PRO cc_start: 0.8021 (Cg_endo) cc_final: 0.7522 (Cg_exo) REVERT: B 208 ASN cc_start: 0.5430 (t0) cc_final: 0.4744 (p0) REVERT: C 301 LYS cc_start: 0.8249 (tptm) cc_final: 0.7887 (mmmt) REVERT: C 554 MET cc_start: 0.8165 (tpt) cc_final: 0.7945 (tpt) REVERT: C 565 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8575 (mm) REVERT: D 379 THR cc_start: 0.7523 (t) cc_final: 0.6894 (m) outliers start: 12 outliers final: 4 residues processed: 616 average time/residue: 1.3404 time to fit residues: 925.1741 Evaluate side-chains 358 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 353 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 621 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 0.0970 chunk 116 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 37 ASN ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS A 206 GLN A 238 HIS A 265 HIS A 446 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 51 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 158 ASN B 206 GLN B 238 HIS B 446 ASN B 473 GLN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS C 157 HIS C 206 GLN C 238 HIS C 446 ASN C 473 GLN D 128 GLN D 157 HIS D 206 GLN D 214 GLN D 238 HIS D 265 HIS D 310 GLN D 446 ASN D 518 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20064 Z= 0.208 Angle : 0.707 10.569 27248 Z= 0.359 Chirality : 0.043 0.175 3100 Planarity : 0.006 0.046 3460 Dihedral : 6.313 49.005 2682 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.39 % Favored : 93.57 % Rotamer: Outliers : 4.81 % Allowed : 13.77 % Favored : 81.42 % 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: -3.63 (0.15), residues: 2440 helix: -2.13 (0.11), residues: 1408 sheet: -2.19 (0.68), residues: 56 loop : -2.69 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 613 HIS 0.006 0.001 HIS D 238 PHE 0.019 0.002 PHE B 508 TYR 0.020 0.002 TYR B 559 ARG 0.008 0.001 ARG B 628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 449 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 ILE cc_start: 0.8197 (mp) cc_final: 0.7985 (mt) REVERT: A 442 MET cc_start: 0.8143 (mmt) cc_final: 0.7185 (mmt) REVERT: A 501 ILE cc_start: 0.8262 (pt) cc_final: 0.8055 (mt) REVERT: B 35 ARG cc_start: 0.7155 (mmt90) cc_final: 0.6520 (mmt-90) REVERT: B 208 ASN cc_start: 0.5214 (t0) cc_final: 0.4506 (p0) REVERT: B 637 HIS cc_start: 0.6864 (m-70) cc_final: 0.6654 (m90) REVERT: C 301 LYS cc_start: 0.8256 (tptm) cc_final: 0.8030 (tptp) REVERT: D 38 MET cc_start: 0.8138 (mtp) cc_final: 0.7768 (mtm) REVERT: D 442 MET cc_start: 0.8156 (mmm) cc_final: 0.6885 (mmt) REVERT: D 501 ILE cc_start: 0.8449 (pt) cc_final: 0.8148 (mt) REVERT: D 603 MET cc_start: 0.7892 (tmm) cc_final: 0.7615 (tmm) REVERT: D 622 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: D 623 TYR cc_start: 0.7281 (m-80) cc_final: 0.7028 (m-80) outliers start: 102 outliers final: 29 residues processed: 507 average time/residue: 1.2107 time to fit residues: 696.1514 Evaluate side-chains 379 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 349 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 613 TRP Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 31 GLN B 128 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 257 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS D 214 GLN D 265 HIS D 518 ASN D 582 HIS D 587 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 20064 Z= 0.402 Angle : 0.754 10.985 27248 Z= 0.379 Chirality : 0.047 0.192 3100 Planarity : 0.005 0.049 3460 Dihedral : 5.873 30.773 2674 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.86 % Allowed : 17.74 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.16), residues: 2440 helix: -1.17 (0.13), residues: 1392 sheet: -2.19 (0.65), residues: 56 loop : -2.65 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 613 HIS 0.008 0.001 HIS C 201 PHE 0.017 0.002 PHE B 508 TYR 0.029 0.002 TYR B 559 ARG 0.009 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 385 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.6951 (pm20) cc_final: 0.6746 (pm20) REVERT: A 286 TRP cc_start: 0.7634 (OUTLIER) cc_final: 0.6913 (m100) REVERT: B 139 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6526 (mtm-85) REVERT: B 208 ASN cc_start: 0.6179 (t0) cc_final: 0.5553 (p0) REVERT: D 38 MET cc_start: 0.8289 (mtp) cc_final: 0.8040 (mtm) REVERT: D 80 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7761 (pt0) REVERT: D 286 TRP cc_start: 0.7175 (OUTLIER) cc_final: 0.6842 (m100) REVERT: D 622 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: D 623 TYR cc_start: 0.7351 (m-80) cc_final: 0.7017 (m-80) outliers start: 103 outliers final: 44 residues processed: 441 average time/residue: 1.1901 time to fit residues: 596.3178 Evaluate side-chains 389 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 340 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 222 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN C 519 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS D 518 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20064 Z= 0.198 Angle : 0.632 10.850 27248 Z= 0.317 Chirality : 0.042 0.177 3100 Planarity : 0.004 0.046 3460 Dihedral : 5.387 24.675 2672 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.77 % Allowed : 20.19 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.17), residues: 2440 helix: -0.44 (0.13), residues: 1400 sheet: -2.27 (0.59), residues: 56 loop : -2.45 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 29 HIS 0.013 0.001 HIS D 265 PHE 0.015 0.001 PHE A 553 TYR 0.027 0.002 TYR D 32 ARG 0.006 0.000 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 375 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TRP cc_start: 0.7454 (OUTLIER) cc_final: 0.6685 (m100) REVERT: A 322 LYS cc_start: 0.8250 (mptt) cc_final: 0.7980 (mmtm) REVERT: B 208 ASN cc_start: 0.5917 (t0) cc_final: 0.5498 (p0) REVERT: B 274 THR cc_start: 0.8378 (p) cc_final: 0.8120 (p) REVERT: B 368 LEU cc_start: 0.7703 (mm) cc_final: 0.7408 (mm) REVERT: B 608 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8072 (mtp) REVERT: C 38 MET cc_start: 0.7905 (mtp) cc_final: 0.7643 (mtm) REVERT: D 38 MET cc_start: 0.8254 (mtp) cc_final: 0.7958 (mtm) REVERT: D 622 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7048 (pt0) REVERT: D 623 TYR cc_start: 0.7091 (m-80) cc_final: 0.6817 (m-80) outliers start: 80 outliers final: 33 residues processed: 427 average time/residue: 1.2250 time to fit residues: 598.4397 Evaluate side-chains 367 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 331 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.0670 chunk 133 optimal weight: 0.0970 chunk 3 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 201 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 206 GLN C 310 GLN D 51 GLN D 157 HIS D 265 HIS D 518 ASN D 519 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20064 Z= 0.155 Angle : 0.602 11.685 27248 Z= 0.301 Chirality : 0.041 0.169 3100 Planarity : 0.004 0.048 3460 Dihedral : 5.042 21.755 2672 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.73 % Allowed : 20.75 % Favored : 75.52 % 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: -1.39 (0.17), residues: 2440 helix: 0.03 (0.14), residues: 1412 sheet: -2.07 (0.58), residues: 56 loop : -2.28 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 29 HIS 0.007 0.001 HIS A 157 PHE 0.018 0.001 PHE C 553 TYR 0.024 0.001 TYR D 32 ARG 0.009 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 372 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.7744 (tp30) cc_final: 0.7334 (tp30) REVERT: A 286 TRP cc_start: 0.7098 (OUTLIER) cc_final: 0.6449 (m100) REVERT: A 322 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8039 (mmtm) REVERT: B 208 ASN cc_start: 0.5843 (t0) cc_final: 0.5425 (p0) REVERT: B 368 LEU cc_start: 0.7555 (mm) cc_final: 0.7264 (mm) REVERT: C 474 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7027 (tpp) REVERT: D 38 MET cc_start: 0.8218 (mtp) cc_final: 0.7929 (mtm) REVERT: D 622 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7005 (pt0) REVERT: D 623 TYR cc_start: 0.6955 (m-80) cc_final: 0.6608 (m-80) outliers start: 79 outliers final: 32 residues processed: 418 average time/residue: 1.1182 time to fit residues: 534.2750 Evaluate side-chains 380 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 344 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 58 optimal weight: 0.0000 chunk 236 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS A 158 ASN A 208 ASN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN B 519 ASN C 31 GLN C 51 GLN C 519 ASN ** C 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20064 Z= 0.224 Angle : 0.628 15.013 27248 Z= 0.311 Chirality : 0.043 0.360 3100 Planarity : 0.004 0.048 3460 Dihedral : 5.006 23.245 2672 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.15 % Allowed : 21.18 % Favored : 74.67 % 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: -1.14 (0.17), residues: 2440 helix: 0.24 (0.14), residues: 1400 sheet: -1.93 (0.59), residues: 56 loop : -2.15 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 286 HIS 0.005 0.001 HIS A 201 PHE 0.022 0.001 PHE C 553 TYR 0.023 0.002 TYR C 32 ARG 0.007 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 355 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TRP cc_start: 0.7166 (OUTLIER) cc_final: 0.6496 (m100) REVERT: A 322 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8093 (mmtm) REVERT: A 623 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6747 (m-80) REVERT: B 83 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8796 (tp) REVERT: B 208 ASN cc_start: 0.6091 (t0) cc_final: 0.5564 (p0) REVERT: B 368 LEU cc_start: 0.7615 (mm) cc_final: 0.7350 (mm) REVERT: C 51 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.6511 (tt0) REVERT: C 403 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: D 38 MET cc_start: 0.8298 (mtp) cc_final: 0.7978 (mtm) REVERT: D 403 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6382 (mp0) outliers start: 88 outliers final: 46 residues processed: 404 average time/residue: 1.1448 time to fit residues: 529.1876 Evaluate side-chains 386 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 333 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain D residue 554 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 172 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 131 optimal weight: 0.0970 chunk 235 optimal weight: 0.0060 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN C 51 GLN C 518 ASN C 519 ASN D 157 HIS ** D 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20064 Z= 0.170 Angle : 0.603 10.897 27248 Z= 0.301 Chirality : 0.041 0.167 3100 Planarity : 0.004 0.073 3460 Dihedral : 4.886 21.504 2672 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.10 % Allowed : 22.03 % Favored : 73.87 % 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: -0.93 (0.17), residues: 2440 helix: 0.45 (0.14), residues: 1392 sheet: -1.91 (0.57), residues: 76 loop : -2.11 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 29 HIS 0.004 0.001 HIS B 157 PHE 0.021 0.001 PHE C 553 TYR 0.028 0.002 TYR A 32 ARG 0.009 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 359 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TRP cc_start: 0.7055 (OUTLIER) cc_final: 0.6399 (m100) REVERT: A 474 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6742 (tpp) REVERT: B 208 ASN cc_start: 0.6028 (t0) cc_final: 0.5623 (p0) REVERT: B 368 LEU cc_start: 0.7439 (mm) cc_final: 0.7192 (mm) REVERT: C 403 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: D 38 MET cc_start: 0.8308 (mtp) cc_final: 0.8033 (mtm) REVERT: D 211 PHE cc_start: 0.7659 (m-80) cc_final: 0.7421 (m-80) REVERT: D 286 TRP cc_start: 0.6946 (OUTLIER) cc_final: 0.6479 (m100) REVERT: D 403 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: D 447 MET cc_start: 0.6756 (mpt) cc_final: 0.6535 (mpt) outliers start: 87 outliers final: 40 residues processed: 403 average time/residue: 1.1287 time to fit residues: 520.2659 Evaluate side-chains 375 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 330 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 464 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.0060 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS A 158 ASN A 310 GLN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 518 ASN B 519 ASN C 51 GLN C 518 ASN C 519 ASN D 157 HIS ** D 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20064 Z= 0.199 Angle : 0.616 10.555 27248 Z= 0.307 Chirality : 0.042 0.188 3100 Planarity : 0.004 0.076 3460 Dihedral : 4.839 21.770 2672 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.63 % Allowed : 22.78 % Favored : 73.58 % 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: -0.78 (0.17), residues: 2440 helix: 0.61 (0.14), residues: 1368 sheet: -1.89 (0.55), residues: 76 loop : -2.05 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 29 HIS 0.006 0.001 HIS B 157 PHE 0.023 0.001 PHE C 553 TYR 0.023 0.002 TYR D 555 ARG 0.007 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 358 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.7712 (tp30) cc_final: 0.7341 (tp30) REVERT: A 286 TRP cc_start: 0.7029 (OUTLIER) cc_final: 0.6404 (m100) REVERT: A 403 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: B 139 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6931 (mtm-85) REVERT: B 208 ASN cc_start: 0.6095 (t0) cc_final: 0.5697 (p0) REVERT: B 368 LEU cc_start: 0.7405 (mm) cc_final: 0.7176 (mm) REVERT: C 80 GLU cc_start: 0.8168 (pm20) cc_final: 0.7902 (pp20) REVERT: C 403 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: D 38 MET cc_start: 0.8308 (mtp) cc_final: 0.8022 (mtm) REVERT: D 211 PHE cc_start: 0.7631 (m-80) cc_final: 0.7420 (m-80) REVERT: D 403 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: D 447 MET cc_start: 0.6760 (mpt) cc_final: 0.6521 (mpt) outliers start: 77 outliers final: 48 residues processed: 395 average time/residue: 1.1598 time to fit residues: 523.2389 Evaluate side-chains 382 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 329 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 464 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.7980 chunk 225 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 219 optimal weight: 0.0980 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 198 optimal weight: 0.5980 chunk 207 optimal weight: 0.3980 chunk 218 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS A 158 ASN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 157 HIS B 519 ASN C 128 GLN C 518 ASN C 519 ASN D 157 HIS ** D 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20064 Z= 0.175 Angle : 0.625 9.928 27248 Z= 0.311 Chirality : 0.041 0.162 3100 Planarity : 0.004 0.064 3460 Dihedral : 4.773 20.780 2672 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.07 % Allowed : 24.06 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.64 (0.17), residues: 2440 helix: 0.73 (0.14), residues: 1364 sheet: -1.85 (0.54), residues: 76 loop : -1.98 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 286 HIS 0.004 0.001 HIS B 637 PHE 0.023 0.001 PHE A 553 TYR 0.029 0.002 TYR A 32 ARG 0.015 0.001 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 337 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.7770 (tp30) cc_final: 0.7377 (tp30) REVERT: A 286 TRP cc_start: 0.6957 (OUTLIER) cc_final: 0.6344 (m100) REVERT: A 403 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: A 554 MET cc_start: 0.8529 (tpt) cc_final: 0.8223 (tpt) REVERT: B 139 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6933 (mtm-85) REVERT: B 208 ASN cc_start: 0.6138 (t0) cc_final: 0.5725 (p0) REVERT: B 368 LEU cc_start: 0.7300 (mm) cc_final: 0.7080 (mm) REVERT: C 80 GLU cc_start: 0.8178 (pm20) cc_final: 0.7921 (pp20) REVERT: C 403 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: D 38 MET cc_start: 0.8335 (mtp) cc_final: 0.8049 (mtm) REVERT: D 211 PHE cc_start: 0.7669 (m-80) cc_final: 0.7452 (m-80) REVERT: D 403 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: D 447 MET cc_start: 0.6757 (mpt) cc_final: 0.6524 (mpt) outliers start: 65 outliers final: 39 residues processed: 372 average time/residue: 1.2404 time to fit residues: 528.0217 Evaluate side-chains 375 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 331 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 464 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.5980 chunk 231 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 0.0070 chunk 243 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 157 HIS B 519 ASN C 128 GLN C 157 HIS D 157 HIS D 265 HIS ** D 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20064 Z= 0.188 Angle : 0.641 9.671 27248 Z= 0.317 Chirality : 0.041 0.159 3100 Planarity : 0.004 0.067 3460 Dihedral : 4.772 20.971 2672 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.50 % Allowed : 25.05 % Favored : 72.45 % 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: -0.58 (0.17), residues: 2440 helix: 0.77 (0.14), residues: 1364 sheet: -1.38 (0.58), residues: 56 loop : -1.97 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 268 HIS 0.008 0.001 HIS B 426 PHE 0.024 0.001 PHE A 553 TYR 0.039 0.002 TYR B 415 ARG 0.016 0.000 ARG D 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 338 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8338 (m) cc_final: 0.8102 (m) REVERT: A 177 GLU cc_start: 0.7747 (tp30) cc_final: 0.7348 (tp30) REVERT: A 286 TRP cc_start: 0.6964 (OUTLIER) cc_final: 0.6372 (m100) REVERT: A 403 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: A 447 MET cc_start: 0.6457 (mpt) cc_final: 0.6161 (mpt) REVERT: B 139 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6951 (mtm-85) REVERT: B 208 ASN cc_start: 0.6231 (t0) cc_final: 0.5774 (p0) REVERT: B 368 LEU cc_start: 0.7332 (mm) cc_final: 0.7111 (mm) REVERT: C 80 GLU cc_start: 0.8171 (pm20) cc_final: 0.7926 (pp20) REVERT: C 403 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: C 637 HIS cc_start: 0.6978 (m-70) cc_final: 0.6765 (m90) REVERT: D 38 MET cc_start: 0.8309 (mtp) cc_final: 0.8000 (mtm) REVERT: D 211 PHE cc_start: 0.7668 (m-80) cc_final: 0.7466 (m-80) REVERT: D 403 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: D 447 MET cc_start: 0.6702 (mpt) cc_final: 0.6474 (mpt) outliers start: 53 outliers final: 36 residues processed: 371 average time/residue: 1.2309 time to fit residues: 519.9730 Evaluate side-chains 361 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 320 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 464 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 157 HIS A 158 ASN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 157 HIS B 257 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN C 128 GLN C 157 HIS C 265 HIS D 265 HIS ** D 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123098 restraints weight = 24984.900| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.12 r_work: 0.3188 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20064 Z= 0.195 Angle : 0.650 10.213 27248 Z= 0.321 Chirality : 0.042 0.249 3100 Planarity : 0.004 0.061 3460 Dihedral : 4.754 21.110 2672 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.59 % Allowed : 25.38 % Favored : 72.03 % 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: -0.54 (0.17), residues: 2440 helix: 0.79 (0.14), residues: 1364 sheet: -1.23 (0.59), residues: 56 loop : -1.96 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 286 HIS 0.008 0.001 HIS B 426 PHE 0.025 0.001 PHE A 553 TYR 0.028 0.002 TYR A 32 ARG 0.015 0.000 ARG D 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8624.72 seconds wall clock time: 153 minutes 16.37 seconds (9196.37 seconds total)