Starting phenix.real_space_refine on Tue Aug 6 00:59:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc6_44425/08_2024/9bc6_44425.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc6_44425/08_2024/9bc6_44425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc6_44425/08_2024/9bc6_44425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc6_44425/08_2024/9bc6_44425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc6_44425/08_2024/9bc6_44425.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc6_44425/08_2024/9bc6_44425.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 108 5.16 5 C 9868 2.51 5 N 2468 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 438": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 438": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 276": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C ARG 404": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C ARG 438": "NH1" <-> "NH2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C ARG 554": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D ARG 270": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 276": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ARG 554": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14972 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3695 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 167 Chain: "B" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3695 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 167 Chain: "C" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3695 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 167 Chain: "D" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3695 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 167 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'PCW': 2, 'PFL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'PCW': 2, 'PFL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'PCW': 2, 'PFL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'PCW': 2, 'PFL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 8.74, per 1000 atoms: 0.58 Number of scatterers: 14972 At special positions: 0 Unit cell: (115.868, 115.868, 115.268, 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 108 16.00 O 2528 8.00 N 2468 7.00 C 9868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 2.7 seconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 71.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 94 through 102 removed outlier: 3.816A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 139 through 167 removed outlier: 3.607A pdb=" N VAL A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.672A pdb=" N PHE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.830A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.304A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.807A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 removed outlier: 3.865A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 421 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 471 removed outlier: 5.560A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 4.014A pdb=" N ASN A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.861A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 545 removed outlier: 4.232A pdb=" N THR A 545 " --> pdb=" O CYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 removed outlier: 3.945A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 584 removed outlier: 3.529A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.816A pdb=" N LEU B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 139 through 167 removed outlier: 3.607A pdb=" N VAL B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Proline residue: B 161 - end of helix removed outlier: 3.672A pdb=" N PHE B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 193 Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.831A pdb=" N ARG B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.304A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.807A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.866A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 421 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 471 removed outlier: 5.560A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 4.014A pdb=" N ASN B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.861A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 545 removed outlier: 4.232A pdb=" N THR B 545 " --> pdb=" O CYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 575 removed outlier: 3.945A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 removed outlier: 3.529A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.815A pdb=" N LEU C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 139 through 167 removed outlier: 3.607A pdb=" N VAL C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Proline residue: C 161 - end of helix removed outlier: 3.671A pdb=" N PHE C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 193 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.830A pdb=" N ARG C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.304A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP C 290 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.807A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 removed outlier: 3.866A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 421 Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 471 removed outlier: 5.560A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 4.014A pdb=" N ASN C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.861A pdb=" N ALA C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 545 removed outlier: 4.232A pdb=" N THR C 545 " --> pdb=" O CYS C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 575 removed outlier: 3.944A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 584 removed outlier: 3.529A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.816A pdb=" N LEU D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 139 through 167 removed outlier: 3.607A pdb=" N VAL D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Proline residue: D 161 - end of helix removed outlier: 3.671A pdb=" N PHE D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 193 Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.830A pdb=" N ARG D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.304A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 288 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.807A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 removed outlier: 3.866A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 421 Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 471 removed outlier: 5.560A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 478 removed outlier: 4.014A pdb=" N ASN D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.860A pdb=" N ALA D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 545 removed outlier: 4.232A pdb=" N THR D 545 " --> pdb=" O CYS D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 575 removed outlier: 3.945A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 584 removed outlier: 3.529A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.644A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.439A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 503 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.643A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.439A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 503 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.645A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.440A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 503 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.644A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.439A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 503 " --> pdb=" O VAL D 553 " (cutoff:3.500A) 989 hydrogen bonds defined for protein. 2871 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: 5.14 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2288 1.28 - 1.41: 4222 1.41 - 1.55: 8610 1.55 - 1.68: 20 1.68 - 1.82: 188 Bond restraints: 15328 Sorted by residual: bond pdb=" C ARG D 142 " pdb=" O ARG D 142 " ideal model delta sigma weight residual 1.237 1.144 0.092 1.19e-02 7.06e+03 6.01e+01 bond pdb=" C ARG A 142 " pdb=" O ARG A 142 " ideal model delta sigma weight residual 1.237 1.145 0.091 1.19e-02 7.06e+03 5.91e+01 bond pdb=" C ARG C 142 " pdb=" O ARG C 142 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.19e-02 7.06e+03 5.86e+01 bond pdb=" C ARG B 142 " pdb=" O ARG B 142 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.19e-02 7.06e+03 5.85e+01 bond pdb=" CA ARG C 142 " pdb=" CB ARG C 142 " ideal model delta sigma weight residual 1.528 1.463 0.065 1.59e-02 3.96e+03 1.67e+01 ... (remaining 15323 not shown) Histogram of bond angle deviations from ideal: 97.57 - 104.99: 263 104.99 - 112.40: 6529 112.40 - 119.81: 6584 119.81 - 127.23: 7300 127.23 - 134.64: 112 Bond angle restraints: 20788 Sorted by residual: angle pdb=" C ILE A 159 " pdb=" N ILE A 160 " pdb=" CA ILE A 160 " ideal model delta sigma weight residual 120.33 124.36 -4.03 8.00e-01 1.56e+00 2.54e+01 angle pdb=" C ILE C 159 " pdb=" N ILE C 160 " pdb=" CA ILE C 160 " ideal model delta sigma weight residual 120.33 124.36 -4.03 8.00e-01 1.56e+00 2.54e+01 angle pdb=" C ILE D 159 " pdb=" N ILE D 160 " pdb=" CA ILE D 160 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C ILE B 159 " pdb=" N ILE B 160 " pdb=" CA ILE B 160 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" CB HIS D 437 " pdb=" CG HIS D 437 " pdb=" CD2 HIS D 437 " ideal model delta sigma weight residual 131.20 125.10 6.10 1.30e+00 5.92e-01 2.20e+01 ... (remaining 20783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8382 17.07 - 34.14: 502 34.14 - 51.21: 96 51.21 - 68.27: 24 68.27 - 85.34: 4 Dihedral angle restraints: 9008 sinusoidal: 3304 harmonic: 5704 Sorted by residual: dihedral pdb=" CA TYR C 361 " pdb=" C TYR C 361 " pdb=" N GLY C 362 " pdb=" CA GLY C 362 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA TYR D 361 " pdb=" C TYR D 361 " pdb=" N GLY D 362 " pdb=" CA GLY D 362 " ideal model delta harmonic sigma weight residual 180.00 -157.06 -22.94 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA TYR A 361 " pdb=" C TYR A 361 " pdb=" N GLY A 362 " pdb=" CA GLY A 362 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 9005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1457 0.075 - 0.149: 673 0.149 - 0.224: 162 0.224 - 0.299: 28 0.299 - 0.373: 28 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ARG B 258 " pdb=" N ARG B 258 " pdb=" C ARG B 258 " pdb=" CB ARG B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA ARG D 258 " pdb=" N ARG D 258 " pdb=" C ARG D 258 " pdb=" CB ARG D 258 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA ARG A 258 " pdb=" N ARG A 258 " pdb=" C ARG A 258 " pdb=" CB ARG A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 2345 not shown) Planarity restraints: 2596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 281 " 0.158 2.00e-02 2.50e+03 7.47e-02 1.39e+02 pdb=" CG TRP B 281 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 281 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP B 281 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP B 281 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP B 281 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 281 " -0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 281 " 0.085 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 281 " -0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP B 281 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.158 2.00e-02 2.50e+03 7.46e-02 1.39e+02 pdb=" CG TRP A 281 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " -0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 281 " -0.158 2.00e-02 2.50e+03 7.45e-02 1.39e+02 pdb=" CG TRP C 281 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP C 281 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP C 281 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP C 281 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP C 281 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 281 " 0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 281 " -0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 281 " 0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP C 281 " -0.064 2.00e-02 2.50e+03 ... (remaining 2593 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1317 2.78 - 3.31: 15196 3.31 - 3.84: 24045 3.84 - 4.37: 29358 4.37 - 4.90: 49284 Nonbonded interactions: 119200 Sorted by model distance: nonbonded pdb=" O LEU C 254 " pdb=" NE ARG C 258 " model vdw 2.247 3.120 nonbonded pdb=" O LEU D 254 " pdb=" NE ARG D 258 " model vdw 2.247 3.120 nonbonded pdb=" O LEU A 254 " pdb=" NE ARG A 258 " model vdw 2.247 3.120 nonbonded pdb=" O LEU B 254 " pdb=" NE ARG B 258 " model vdw 2.248 3.120 nonbonded pdb=" ND1 HIS D 310 " pdb=" OH TYR D 345 " model vdw 2.381 3.120 ... (remaining 119195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 94 through 586 or resid 702)) selection = (chain 'B' and (resid 94 through 586 or (resid 702 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27)))) selection = (chain 'C' and (resid 94 through 586 or (resid 702 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27)))) selection = (chain 'D' and (resid 94 through 586 or (resid 702 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27)))) } 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: 12.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 39.070 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.240 ------------------------------------------------------------------------------- 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 0.092 15328 Z= 0.753 Angle : 1.767 12.741 20788 Z= 1.208 Chirality : 0.093 0.373 2348 Planarity : 0.014 0.092 2596 Dihedral : 12.254 85.343 5320 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.56 % Allowed : 2.51 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1920 helix: -0.35 (0.13), residues: 1288 sheet: -0.78 (0.47), residues: 112 loop : -0.00 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.158 0.027 TRP B 281 HIS 0.019 0.005 HIS D 286 PHE 0.066 0.013 PHE A 186 TYR 0.119 0.022 TYR D 407 ARG 0.008 0.001 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 323 time to evaluate : 1.630 Fit side-chains REVERT: A 101 MET cc_start: 0.6371 (mmt) cc_final: 0.5967 (tpp) REVERT: A 195 ARG cc_start: 0.6185 (OUTLIER) cc_final: 0.5852 (mmp-170) REVERT: A 283 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6314 (mm-30) REVERT: A 287 MET cc_start: 0.5024 (ttp) cc_final: 0.3847 (tpt) REVERT: A 304 MET cc_start: 0.8000 (tpp) cc_final: 0.7668 (tpp) REVERT: A 308 LEU cc_start: 0.7955 (mt) cc_final: 0.7632 (mm) REVERT: A 343 LYS cc_start: 0.7879 (mtmm) cc_final: 0.6899 (tptm) REVERT: A 388 MET cc_start: 0.8256 (mmm) cc_final: 0.7978 (mmt) REVERT: A 401 ASP cc_start: 0.6121 (p0) cc_final: 0.5548 (t0) REVERT: A 408 GLN cc_start: 0.7768 (mm110) cc_final: 0.7452 (mm-40) REVERT: A 411 TYR cc_start: 0.6253 (t80) cc_final: 0.5859 (t80) REVERT: A 415 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7129 (mt-10) REVERT: A 459 GLU cc_start: 0.8410 (pt0) cc_final: 0.7656 (mt-10) REVERT: A 483 PHE cc_start: 0.7226 (t80) cc_final: 0.6773 (t80) REVERT: B 101 MET cc_start: 0.6374 (mmt) cc_final: 0.5970 (tpp) REVERT: B 195 ARG cc_start: 0.6168 (OUTLIER) cc_final: 0.5845 (mmp-170) REVERT: B 283 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6334 (mm-30) REVERT: B 287 MET cc_start: 0.5024 (ttp) cc_final: 0.3836 (tpt) REVERT: B 304 MET cc_start: 0.8015 (tpp) cc_final: 0.7675 (tpp) REVERT: B 308 LEU cc_start: 0.7974 (mt) cc_final: 0.7653 (mm) REVERT: B 343 LYS cc_start: 0.7866 (mtmm) cc_final: 0.6882 (tptm) REVERT: B 388 MET cc_start: 0.8262 (mmm) cc_final: 0.7982 (mmt) REVERT: B 401 ASP cc_start: 0.6087 (p0) cc_final: 0.5547 (t0) REVERT: B 408 GLN cc_start: 0.7783 (mm110) cc_final: 0.7472 (mm-40) REVERT: B 411 TYR cc_start: 0.6259 (t80) cc_final: 0.5863 (t80) REVERT: B 415 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7138 (mt-10) REVERT: B 459 GLU cc_start: 0.8399 (pt0) cc_final: 0.7654 (mt-10) REVERT: B 483 PHE cc_start: 0.7240 (t80) cc_final: 0.6843 (t80) REVERT: C 101 MET cc_start: 0.6359 (mmt) cc_final: 0.5959 (tpp) REVERT: C 195 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5855 (mmp-170) REVERT: C 283 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6318 (mm-30) REVERT: C 287 MET cc_start: 0.5023 (ttp) cc_final: 0.3831 (tpt) REVERT: C 304 MET cc_start: 0.8030 (tpp) cc_final: 0.7702 (tpp) REVERT: C 308 LEU cc_start: 0.7967 (mt) cc_final: 0.7651 (mm) REVERT: C 343 LYS cc_start: 0.7855 (mtmm) cc_final: 0.6876 (tptm) REVERT: C 388 MET cc_start: 0.8254 (mmm) cc_final: 0.7973 (mmt) REVERT: C 401 ASP cc_start: 0.6125 (p0) cc_final: 0.5539 (t0) REVERT: C 408 GLN cc_start: 0.7736 (mm110) cc_final: 0.7419 (mm-40) REVERT: C 411 TYR cc_start: 0.6261 (t80) cc_final: 0.5869 (t80) REVERT: C 415 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7125 (mt-10) REVERT: C 459 GLU cc_start: 0.8413 (pt0) cc_final: 0.7665 (mt-10) REVERT: C 483 PHE cc_start: 0.7224 (t80) cc_final: 0.6823 (t80) REVERT: D 101 MET cc_start: 0.6363 (mmt) cc_final: 0.5961 (tpp) REVERT: D 195 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5838 (mmp-170) REVERT: D 283 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6316 (mm-30) REVERT: D 287 MET cc_start: 0.5024 (ttp) cc_final: 0.3834 (tpt) REVERT: D 304 MET cc_start: 0.8020 (tpp) cc_final: 0.7691 (tpp) REVERT: D 308 LEU cc_start: 0.7958 (mt) cc_final: 0.7638 (mm) REVERT: D 343 LYS cc_start: 0.7875 (mtmm) cc_final: 0.6885 (tptm) REVERT: D 388 MET cc_start: 0.8254 (mmm) cc_final: 0.7973 (mmt) REVERT: D 401 ASP cc_start: 0.6122 (p0) cc_final: 0.5538 (t0) REVERT: D 408 GLN cc_start: 0.7735 (mm110) cc_final: 0.7418 (mm-40) REVERT: D 411 TYR cc_start: 0.6263 (t80) cc_final: 0.5842 (t80) REVERT: D 415 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7131 (mt-10) REVERT: D 459 GLU cc_start: 0.8407 (pt0) cc_final: 0.7654 (mt-10) REVERT: D 483 PHE cc_start: 0.7214 (t80) cc_final: 0.6810 (t80) outliers start: 8 outliers final: 8 residues processed: 327 average time/residue: 1.2422 time to fit residues: 444.8210 Evaluate side-chains 303 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 291 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 344 GLN A 355 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN A 421 HIS B 156 ASN B 344 GLN B 355 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 421 HIS C 156 ASN C 344 GLN C 355 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 GLN C 421 HIS D 156 ASN D 344 GLN D 355 HIS ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 GLN D 421 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15328 Z= 0.179 Angle : 0.552 6.459 20788 Z= 0.301 Chirality : 0.042 0.152 2348 Planarity : 0.004 0.026 2596 Dihedral : 8.068 51.918 2236 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 7.68 % Favored : 90.36 % 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: 1.47 (0.19), residues: 1920 helix: 1.37 (0.14), residues: 1300 sheet: -0.20 (0.49), residues: 112 loop : 0.47 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 281 HIS 0.005 0.001 HIS B 421 PHE 0.017 0.002 PHE B 569 TYR 0.014 0.002 TYR B 407 ARG 0.003 0.001 ARG C 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 296 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 VAL cc_start: 0.5740 (t) cc_final: 0.5519 (t) REVERT: A 257 VAL cc_start: 0.7588 (t) cc_final: 0.7199 (p) REVERT: A 283 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6414 (tp30) REVERT: A 287 MET cc_start: 0.4194 (ttp) cc_final: 0.3156 (tpt) REVERT: A 304 MET cc_start: 0.7808 (tpp) cc_final: 0.7429 (tpp) REVERT: A 339 ASP cc_start: 0.6954 (m-30) cc_final: 0.6731 (m-30) REVERT: A 343 LYS cc_start: 0.7758 (mtmm) cc_final: 0.6892 (tptm) REVERT: A 369 MET cc_start: 0.7966 (mmm) cc_final: 0.7725 (tpp) REVERT: A 388 MET cc_start: 0.8117 (mmm) cc_final: 0.7848 (mmt) REVERT: A 408 GLN cc_start: 0.7633 (mm110) cc_final: 0.7311 (mm-40) REVERT: A 411 TYR cc_start: 0.6354 (t80) cc_final: 0.5893 (t80) REVERT: A 412 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7857 (mtpt) REVERT: A 422 LYS cc_start: 0.8092 (mttp) cc_final: 0.7808 (mttt) REVERT: A 433 ASP cc_start: 0.7744 (t70) cc_final: 0.7067 (m-30) REVERT: A 436 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 459 GLU cc_start: 0.8177 (pt0) cc_final: 0.7303 (mt-10) REVERT: A 483 PHE cc_start: 0.7223 (t80) cc_final: 0.6909 (t80) REVERT: B 101 MET cc_start: 0.6406 (mmt) cc_final: 0.6085 (tpp) REVERT: B 212 VAL cc_start: 0.5705 (t) cc_final: 0.5501 (t) REVERT: B 257 VAL cc_start: 0.7583 (t) cc_final: 0.7190 (p) REVERT: B 283 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6430 (tp30) REVERT: B 287 MET cc_start: 0.4210 (ttp) cc_final: 0.3192 (tpt) REVERT: B 304 MET cc_start: 0.7818 (tpp) cc_final: 0.7447 (tpp) REVERT: B 339 ASP cc_start: 0.6946 (m-30) cc_final: 0.6724 (m-30) REVERT: B 343 LYS cc_start: 0.7774 (mtmm) cc_final: 0.6900 (tptm) REVERT: B 388 MET cc_start: 0.8107 (mmm) cc_final: 0.7838 (mmt) REVERT: B 408 GLN cc_start: 0.7637 (mm110) cc_final: 0.7314 (mm-40) REVERT: B 411 TYR cc_start: 0.6339 (t80) cc_final: 0.5925 (t80) REVERT: B 412 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7869 (mtpt) REVERT: B 422 LYS cc_start: 0.8087 (mttp) cc_final: 0.7802 (mttt) REVERT: B 433 ASP cc_start: 0.7751 (t70) cc_final: 0.7086 (m-30) REVERT: B 436 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 459 GLU cc_start: 0.8178 (pt0) cc_final: 0.7303 (mt-10) REVERT: B 483 PHE cc_start: 0.7221 (t80) cc_final: 0.6913 (t80) REVERT: C 187 LEU cc_start: 0.7291 (tp) cc_final: 0.7077 (tt) REVERT: C 212 VAL cc_start: 0.5743 (t) cc_final: 0.5528 (t) REVERT: C 257 VAL cc_start: 0.7580 (t) cc_final: 0.7193 (p) REVERT: C 283 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6409 (tp30) REVERT: C 287 MET cc_start: 0.4218 (ttp) cc_final: 0.3195 (tpt) REVERT: C 304 MET cc_start: 0.7814 (tpp) cc_final: 0.7444 (tpp) REVERT: C 339 ASP cc_start: 0.6931 (m-30) cc_final: 0.6719 (m-30) REVERT: C 343 LYS cc_start: 0.7757 (mtmm) cc_final: 0.6876 (tptm) REVERT: C 388 MET cc_start: 0.8102 (mmm) cc_final: 0.7833 (mmt) REVERT: C 408 GLN cc_start: 0.7590 (mm110) cc_final: 0.7267 (mm-40) REVERT: C 411 TYR cc_start: 0.6357 (t80) cc_final: 0.5926 (t80) REVERT: C 412 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7866 (mtpt) REVERT: C 422 LYS cc_start: 0.8072 (mttp) cc_final: 0.7788 (mttt) REVERT: C 433 ASP cc_start: 0.7743 (t70) cc_final: 0.7074 (m-30) REVERT: C 436 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7652 (mt-10) REVERT: C 459 GLU cc_start: 0.8195 (pt0) cc_final: 0.7330 (mt-10) REVERT: C 483 PHE cc_start: 0.7211 (t80) cc_final: 0.6902 (t80) REVERT: D 212 VAL cc_start: 0.5691 (t) cc_final: 0.5482 (t) REVERT: D 257 VAL cc_start: 0.7577 (t) cc_final: 0.7184 (p) REVERT: D 283 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6406 (tp30) REVERT: D 287 MET cc_start: 0.4192 (ttp) cc_final: 0.3169 (tpt) REVERT: D 304 MET cc_start: 0.7807 (tpp) cc_final: 0.7438 (tpp) REVERT: D 339 ASP cc_start: 0.6947 (m-30) cc_final: 0.6729 (m-30) REVERT: D 343 LYS cc_start: 0.7767 (mtmm) cc_final: 0.6817 (tptt) REVERT: D 388 MET cc_start: 0.8105 (mmm) cc_final: 0.7835 (mmt) REVERT: D 408 GLN cc_start: 0.7587 (mm110) cc_final: 0.7266 (mm-40) REVERT: D 411 TYR cc_start: 0.6359 (t80) cc_final: 0.5926 (t80) REVERT: D 412 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7865 (mtpt) REVERT: D 422 LYS cc_start: 0.8070 (mttp) cc_final: 0.7787 (mttt) REVERT: D 433 ASP cc_start: 0.7738 (t70) cc_final: 0.7072 (m-30) REVERT: D 436 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7652 (mt-10) REVERT: D 459 GLU cc_start: 0.8196 (pt0) cc_final: 0.7332 (mt-10) REVERT: D 483 PHE cc_start: 0.7201 (t80) cc_final: 0.6890 (t80) outliers start: 28 outliers final: 4 residues processed: 308 average time/residue: 1.2697 time to fit residues: 430.6107 Evaluate side-chains 269 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 265 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN A 568 ASN B 398 GLN B 568 ASN C 398 GLN C 568 ASN D 398 GLN D 568 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15328 Z= 0.314 Angle : 0.611 6.963 20788 Z= 0.331 Chirality : 0.046 0.162 2348 Planarity : 0.004 0.032 2596 Dihedral : 8.189 59.881 2212 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.44 % Allowed : 8.87 % Favored : 88.69 % 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: 1.71 (0.19), residues: 1920 helix: 1.61 (0.14), residues: 1272 sheet: 0.57 (0.54), residues: 88 loop : 0.28 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 281 HIS 0.005 0.002 HIS C 437 PHE 0.022 0.003 PHE B 186 TYR 0.028 0.003 TYR C 347 ARG 0.004 0.001 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 276 time to evaluate : 1.536 Fit side-chains REVERT: A 187 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6889 (tt) REVERT: A 257 VAL cc_start: 0.7588 (t) cc_final: 0.7188 (p) REVERT: A 283 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6389 (tp30) REVERT: A 287 MET cc_start: 0.4503 (ttp) cc_final: 0.3469 (tpt) REVERT: A 343 LYS cc_start: 0.7713 (mtmm) cc_final: 0.6873 (tptm) REVERT: A 369 MET cc_start: 0.8024 (mmm) cc_final: 0.7767 (tpp) REVERT: A 388 MET cc_start: 0.8120 (mmm) cc_final: 0.7904 (mmt) REVERT: A 408 GLN cc_start: 0.7592 (mm110) cc_final: 0.7221 (mm-40) REVERT: A 433 ASP cc_start: 0.7949 (t70) cc_final: 0.7057 (m-30) REVERT: A 436 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 459 GLU cc_start: 0.8233 (pt0) cc_final: 0.7377 (mt-10) REVERT: A 483 PHE cc_start: 0.7150 (t80) cc_final: 0.6843 (t80) REVERT: B 187 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6894 (tt) REVERT: B 257 VAL cc_start: 0.7588 (t) cc_final: 0.7190 (p) REVERT: B 283 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6390 (tp30) REVERT: B 287 MET cc_start: 0.4503 (ttp) cc_final: 0.3469 (tpt) REVERT: B 343 LYS cc_start: 0.7719 (mtmm) cc_final: 0.6871 (tptm) REVERT: B 388 MET cc_start: 0.8120 (mmm) cc_final: 0.7904 (mmt) REVERT: B 408 GLN cc_start: 0.7592 (mm110) cc_final: 0.7220 (mm-40) REVERT: B 433 ASP cc_start: 0.7973 (t70) cc_final: 0.7075 (m-30) REVERT: B 436 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7713 (mt-10) REVERT: B 459 GLU cc_start: 0.8232 (pt0) cc_final: 0.7379 (mt-10) REVERT: B 483 PHE cc_start: 0.7149 (t80) cc_final: 0.6831 (t80) REVERT: C 257 VAL cc_start: 0.7598 (t) cc_final: 0.7197 (p) REVERT: C 283 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6389 (tp30) REVERT: C 287 MET cc_start: 0.4476 (ttp) cc_final: 0.3458 (tpt) REVERT: C 343 LYS cc_start: 0.7716 (mtmm) cc_final: 0.6871 (tptm) REVERT: C 388 MET cc_start: 0.8118 (mmm) cc_final: 0.7902 (mmt) REVERT: C 408 GLN cc_start: 0.7595 (mm110) cc_final: 0.7224 (mm-40) REVERT: C 422 LYS cc_start: 0.8112 (mttp) cc_final: 0.7901 (mttp) REVERT: C 433 ASP cc_start: 0.7953 (t70) cc_final: 0.7047 (m-30) REVERT: C 436 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7709 (mt-10) REVERT: C 459 GLU cc_start: 0.8220 (pt0) cc_final: 0.7367 (mt-10) REVERT: C 483 PHE cc_start: 0.7157 (t80) cc_final: 0.6852 (t80) REVERT: D 187 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6886 (tt) REVERT: D 257 VAL cc_start: 0.7589 (t) cc_final: 0.7188 (p) REVERT: D 283 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6388 (tp30) REVERT: D 287 MET cc_start: 0.4474 (ttp) cc_final: 0.3455 (tpt) REVERT: D 343 LYS cc_start: 0.7713 (mtmm) cc_final: 0.6805 (tptt) REVERT: D 388 MET cc_start: 0.8118 (mmm) cc_final: 0.7902 (mmt) REVERT: D 408 GLN cc_start: 0.7593 (mm110) cc_final: 0.7223 (mm-40) REVERT: D 422 LYS cc_start: 0.8114 (mttp) cc_final: 0.7904 (mttp) REVERT: D 433 ASP cc_start: 0.7954 (t70) cc_final: 0.7045 (m-30) REVERT: D 436 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7712 (mt-10) REVERT: D 459 GLU cc_start: 0.8223 (pt0) cc_final: 0.7366 (mt-10) REVERT: D 483 PHE cc_start: 0.7148 (t80) cc_final: 0.6844 (t80) outliers start: 35 outliers final: 17 residues processed: 300 average time/residue: 1.2996 time to fit residues: 427.7301 Evaluate side-chains 258 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 238 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 523 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 185 optimal weight: 0.0270 chunk 91 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15328 Z= 0.143 Angle : 0.470 5.227 20788 Z= 0.251 Chirality : 0.040 0.164 2348 Planarity : 0.003 0.026 2596 Dihedral : 6.282 45.219 2212 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.23 % Allowed : 9.99 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.20), residues: 1920 helix: 1.95 (0.15), residues: 1284 sheet: 0.48 (0.53), residues: 88 loop : 0.48 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 281 HIS 0.003 0.001 HIS D 437 PHE 0.013 0.001 PHE A 514 TYR 0.016 0.001 TYR A 411 ARG 0.003 0.000 ARG D 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 265 time to evaluate : 1.507 Fit side-chains REVERT: A 257 VAL cc_start: 0.7454 (t) cc_final: 0.7033 (p) REVERT: A 283 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6335 (tp30) REVERT: A 287 MET cc_start: 0.3980 (ttp) cc_final: 0.2998 (tpt) REVERT: A 343 LYS cc_start: 0.7674 (mtmm) cc_final: 0.6836 (tptm) REVERT: A 369 MET cc_start: 0.7880 (mmm) cc_final: 0.7583 (tpp) REVERT: A 388 MET cc_start: 0.8144 (mmm) cc_final: 0.7902 (mmt) REVERT: A 408 GLN cc_start: 0.7608 (mm110) cc_final: 0.7274 (mm-40) REVERT: A 412 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7876 (mttt) REVERT: A 429 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6988 (tp40) REVERT: A 433 ASP cc_start: 0.7766 (t70) cc_final: 0.7104 (m-30) REVERT: A 436 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 459 GLU cc_start: 0.8095 (pt0) cc_final: 0.7272 (mt-10) REVERT: A 483 PHE cc_start: 0.7145 (t80) cc_final: 0.6806 (t80) REVERT: B 257 VAL cc_start: 0.7420 (t) cc_final: 0.7007 (p) REVERT: B 283 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6337 (tp30) REVERT: B 287 MET cc_start: 0.3972 (ttp) cc_final: 0.2995 (tpt) REVERT: B 343 LYS cc_start: 0.7681 (mtmm) cc_final: 0.6841 (tptm) REVERT: B 388 MET cc_start: 0.8141 (mmm) cc_final: 0.7899 (mmt) REVERT: B 408 GLN cc_start: 0.7610 (mm110) cc_final: 0.7265 (mm-40) REVERT: B 429 GLN cc_start: 0.7409 (mm-40) cc_final: 0.6981 (tp40) REVERT: B 433 ASP cc_start: 0.7771 (t70) cc_final: 0.7103 (m-30) REVERT: B 436 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7611 (mt-10) REVERT: B 459 GLU cc_start: 0.8103 (pt0) cc_final: 0.7277 (mt-10) REVERT: B 483 PHE cc_start: 0.7155 (t80) cc_final: 0.6819 (t80) REVERT: B 512 MET cc_start: 0.8358 (ttp) cc_final: 0.7940 (ttt) REVERT: C 257 VAL cc_start: 0.7425 (t) cc_final: 0.7011 (p) REVERT: C 283 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6338 (tp30) REVERT: C 287 MET cc_start: 0.3987 (ttp) cc_final: 0.2995 (tpt) REVERT: C 343 LYS cc_start: 0.7669 (mtmm) cc_final: 0.6863 (tptm) REVERT: C 388 MET cc_start: 0.8142 (mmm) cc_final: 0.7898 (mmt) REVERT: C 408 GLN cc_start: 0.7605 (mm110) cc_final: 0.7264 (mm-40) REVERT: C 429 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6982 (tp40) REVERT: C 433 ASP cc_start: 0.7778 (t70) cc_final: 0.7093 (m-30) REVERT: C 436 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7593 (mt-10) REVERT: C 459 GLU cc_start: 0.8087 (pt0) cc_final: 0.7270 (mt-10) REVERT: C 483 PHE cc_start: 0.7149 (t80) cc_final: 0.6816 (t80) REVERT: D 257 VAL cc_start: 0.7423 (t) cc_final: 0.7008 (p) REVERT: D 283 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6337 (tp30) REVERT: D 287 MET cc_start: 0.3990 (ttp) cc_final: 0.2992 (tpt) REVERT: D 343 LYS cc_start: 0.7679 (mtmm) cc_final: 0.6802 (tptt) REVERT: D 388 MET cc_start: 0.8139 (mmm) cc_final: 0.7899 (mmt) REVERT: D 408 GLN cc_start: 0.7605 (mm110) cc_final: 0.7265 (mm-40) REVERT: D 429 GLN cc_start: 0.7422 (mm-40) cc_final: 0.6982 (tp40) REVERT: D 433 ASP cc_start: 0.7777 (t70) cc_final: 0.7092 (m-30) REVERT: D 436 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7590 (mt-10) REVERT: D 459 GLU cc_start: 0.8087 (pt0) cc_final: 0.7269 (mt-10) REVERT: D 483 PHE cc_start: 0.7149 (t80) cc_final: 0.6827 (t80) outliers start: 32 outliers final: 4 residues processed: 281 average time/residue: 1.3037 time to fit residues: 402.8776 Evaluate side-chains 247 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15328 Z= 0.372 Angle : 0.622 7.447 20788 Z= 0.334 Chirality : 0.046 0.176 2348 Planarity : 0.004 0.030 2596 Dihedral : 7.993 58.810 2212 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.09 % Allowed : 12.22 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 1920 helix: 1.80 (0.14), residues: 1280 sheet: 0.37 (0.54), residues: 88 loop : 0.04 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 281 HIS 0.005 0.002 HIS D 421 PHE 0.020 0.003 PHE B 186 TYR 0.026 0.003 TYR A 411 ARG 0.004 0.001 ARG D 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 258 time to evaluate : 1.688 Fit side-chains REVERT: A 208 LEU cc_start: 0.6903 (mt) cc_final: 0.6702 (mt) REVERT: A 257 VAL cc_start: 0.7520 (t) cc_final: 0.7101 (p) REVERT: A 283 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6380 (tp30) REVERT: A 287 MET cc_start: 0.4397 (ttp) cc_final: 0.3345 (tpt) REVERT: A 343 LYS cc_start: 0.7657 (mtmm) cc_final: 0.6836 (tptm) REVERT: A 388 MET cc_start: 0.8131 (mmm) cc_final: 0.7923 (mmt) REVERT: A 408 GLN cc_start: 0.7619 (mm110) cc_final: 0.7267 (mm-40) REVERT: A 415 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 433 ASP cc_start: 0.7925 (t70) cc_final: 0.7102 (m-30) REVERT: A 436 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 459 GLU cc_start: 0.8124 (pt0) cc_final: 0.7337 (mt-10) REVERT: A 483 PHE cc_start: 0.7032 (t80) cc_final: 0.6758 (t80) REVERT: B 208 LEU cc_start: 0.6903 (mt) cc_final: 0.6701 (mt) REVERT: B 257 VAL cc_start: 0.7509 (t) cc_final: 0.7083 (p) REVERT: B 283 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6367 (tp30) REVERT: B 287 MET cc_start: 0.4424 (ttp) cc_final: 0.3372 (tpt) REVERT: B 343 LYS cc_start: 0.7655 (mtmm) cc_final: 0.6839 (tptm) REVERT: B 388 MET cc_start: 0.8121 (mmm) cc_final: 0.7914 (mmt) REVERT: B 408 GLN cc_start: 0.7623 (mm110) cc_final: 0.7268 (mm-40) REVERT: B 433 ASP cc_start: 0.7920 (t70) cc_final: 0.7087 (m-30) REVERT: B 436 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7714 (mt-10) REVERT: B 459 GLU cc_start: 0.8130 (pt0) cc_final: 0.7338 (mt-10) REVERT: B 483 PHE cc_start: 0.7033 (t80) cc_final: 0.6763 (t80) REVERT: C 257 VAL cc_start: 0.7504 (t) cc_final: 0.7081 (p) REVERT: C 283 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6358 (tp30) REVERT: C 287 MET cc_start: 0.4398 (ttp) cc_final: 0.3345 (tpt) REVERT: C 343 LYS cc_start: 0.7673 (mtmm) cc_final: 0.6838 (tptm) REVERT: C 388 MET cc_start: 0.8127 (mmm) cc_final: 0.7919 (mmt) REVERT: C 408 GLN cc_start: 0.7618 (mm110) cc_final: 0.7261 (mm-40) REVERT: C 433 ASP cc_start: 0.7940 (t70) cc_final: 0.7060 (m-30) REVERT: C 436 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7734 (mt-10) REVERT: C 459 GLU cc_start: 0.8126 (pt0) cc_final: 0.7340 (mt-10) REVERT: C 473 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4255 (tmm) REVERT: C 483 PHE cc_start: 0.7038 (t80) cc_final: 0.6767 (t80) REVERT: D 257 VAL cc_start: 0.7508 (t) cc_final: 0.7089 (p) REVERT: D 283 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6360 (tp30) REVERT: D 287 MET cc_start: 0.4399 (ttp) cc_final: 0.3343 (tpt) REVERT: D 343 LYS cc_start: 0.7676 (mtmm) cc_final: 0.6838 (tptm) REVERT: D 388 MET cc_start: 0.8127 (mmm) cc_final: 0.7920 (mmt) REVERT: D 408 GLN cc_start: 0.7617 (mm110) cc_final: 0.7265 (mm-40) REVERT: D 433 ASP cc_start: 0.7931 (t70) cc_final: 0.7053 (m-30) REVERT: D 436 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7740 (mt-10) REVERT: D 459 GLU cc_start: 0.8124 (pt0) cc_final: 0.7339 (mt-10) REVERT: D 473 MET cc_start: 0.5214 (OUTLIER) cc_final: 0.4267 (tmm) REVERT: D 483 PHE cc_start: 0.7029 (t80) cc_final: 0.6768 (t80) outliers start: 30 outliers final: 21 residues processed: 280 average time/residue: 1.3295 time to fit residues: 408.5907 Evaluate side-chains 278 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 255 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 494 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 1.9990 chunk 167 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15328 Z= 0.166 Angle : 0.492 5.581 20788 Z= 0.263 Chirality : 0.041 0.178 2348 Planarity : 0.003 0.023 2596 Dihedral : 6.724 52.946 2212 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.26 % Allowed : 13.62 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1920 helix: 2.10 (0.14), residues: 1284 sheet: 0.28 (0.53), residues: 88 loop : 0.23 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 281 HIS 0.003 0.001 HIS A 437 PHE 0.010 0.001 PHE B 389 TYR 0.022 0.002 TYR A 411 ARG 0.002 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 252 time to evaluate : 1.713 Fit side-chains REVERT: A 257 VAL cc_start: 0.7396 (t) cc_final: 0.6950 (p) REVERT: A 283 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6369 (tp30) REVERT: A 287 MET cc_start: 0.4059 (ttp) cc_final: 0.3029 (tpt) REVERT: A 343 LYS cc_start: 0.7679 (mtmm) cc_final: 0.6865 (tptm) REVERT: A 369 MET cc_start: 0.7951 (mmm) cc_final: 0.7655 (tpp) REVERT: A 388 MET cc_start: 0.8165 (mmm) cc_final: 0.7928 (mmt) REVERT: A 408 GLN cc_start: 0.7636 (mm110) cc_final: 0.7289 (mm-40) REVERT: A 415 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7395 (mt-10) REVERT: A 429 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7000 (tp40) REVERT: A 433 ASP cc_start: 0.7793 (t70) cc_final: 0.7148 (m-30) REVERT: A 436 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 459 GLU cc_start: 0.8103 (pt0) cc_final: 0.7300 (mt-10) REVERT: A 483 PHE cc_start: 0.7078 (t80) cc_final: 0.6801 (t80) REVERT: B 257 VAL cc_start: 0.7383 (t) cc_final: 0.6933 (p) REVERT: B 283 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6372 (tp30) REVERT: B 287 MET cc_start: 0.4048 (ttp) cc_final: 0.3024 (tpt) REVERT: B 343 LYS cc_start: 0.7678 (mtmm) cc_final: 0.6865 (tptm) REVERT: B 388 MET cc_start: 0.8167 (mmm) cc_final: 0.7933 (mmt) REVERT: B 408 GLN cc_start: 0.7643 (mm110) cc_final: 0.7293 (mm-40) REVERT: B 429 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7002 (tp40) REVERT: B 433 ASP cc_start: 0.7821 (t70) cc_final: 0.7139 (m-30) REVERT: B 436 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 459 GLU cc_start: 0.8091 (pt0) cc_final: 0.7283 (mt-10) REVERT: B 483 PHE cc_start: 0.7061 (t80) cc_final: 0.6782 (t80) REVERT: C 257 VAL cc_start: 0.7408 (t) cc_final: 0.6958 (p) REVERT: C 283 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6364 (tp30) REVERT: C 287 MET cc_start: 0.4060 (ttp) cc_final: 0.3025 (tpt) REVERT: C 343 LYS cc_start: 0.7678 (mtmm) cc_final: 0.6864 (tptm) REVERT: C 388 MET cc_start: 0.8166 (mmm) cc_final: 0.7929 (mmt) REVERT: C 408 GLN cc_start: 0.7638 (mm110) cc_final: 0.7282 (mm-40) REVERT: C 429 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6984 (tp40) REVERT: C 433 ASP cc_start: 0.7829 (t70) cc_final: 0.7142 (m-30) REVERT: C 436 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7683 (mt-10) REVERT: C 459 GLU cc_start: 0.8095 (pt0) cc_final: 0.7301 (mt-10) REVERT: C 473 MET cc_start: 0.5145 (OUTLIER) cc_final: 0.4314 (tmm) REVERT: C 483 PHE cc_start: 0.7055 (t80) cc_final: 0.6782 (t80) REVERT: D 257 VAL cc_start: 0.7401 (t) cc_final: 0.6958 (p) REVERT: D 283 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6366 (tp30) REVERT: D 287 MET cc_start: 0.4063 (ttp) cc_final: 0.3023 (tpt) REVERT: D 343 LYS cc_start: 0.7688 (mtmm) cc_final: 0.6801 (tptt) REVERT: D 388 MET cc_start: 0.8165 (mmm) cc_final: 0.7928 (mmt) REVERT: D 408 GLN cc_start: 0.7638 (mm110) cc_final: 0.7286 (mm-40) REVERT: D 429 GLN cc_start: 0.7415 (mm-40) cc_final: 0.6981 (tp40) REVERT: D 433 ASP cc_start: 0.7831 (t70) cc_final: 0.7141 (m-30) REVERT: D 436 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7684 (mt-10) REVERT: D 459 GLU cc_start: 0.8093 (pt0) cc_final: 0.7306 (mt-10) REVERT: D 473 MET cc_start: 0.5164 (OUTLIER) cc_final: 0.4329 (tmm) REVERT: D 483 PHE cc_start: 0.7061 (t80) cc_final: 0.6793 (t80) outliers start: 18 outliers final: 5 residues processed: 265 average time/residue: 1.2159 time to fit residues: 356.0618 Evaluate side-chains 248 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 241 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 473 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15328 Z= 0.134 Angle : 0.460 6.448 20788 Z= 0.242 Chirality : 0.040 0.180 2348 Planarity : 0.003 0.023 2596 Dihedral : 5.721 46.839 2212 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.61 % Allowed : 13.69 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.20), residues: 1920 helix: 2.33 (0.15), residues: 1288 sheet: 0.28 (0.52), residues: 88 loop : 0.53 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 281 HIS 0.003 0.001 HIS D 437 PHE 0.008 0.001 PHE A 514 TYR 0.016 0.001 TYR A 411 ARG 0.002 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 258 time to evaluate : 2.007 Fit side-chains REVERT: A 257 VAL cc_start: 0.7290 (t) cc_final: 0.6834 (p) REVERT: A 283 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6319 (tp30) REVERT: A 287 MET cc_start: 0.3769 (ttp) cc_final: 0.2670 (tpt) REVERT: A 343 LYS cc_start: 0.7630 (mtmm) cc_final: 0.6787 (tptm) REVERT: A 369 MET cc_start: 0.7879 (mmm) cc_final: 0.7578 (tpp) REVERT: A 388 MET cc_start: 0.8166 (mmm) cc_final: 0.7889 (mmt) REVERT: A 408 GLN cc_start: 0.7634 (mm110) cc_final: 0.7340 (mm-40) REVERT: A 429 GLN cc_start: 0.7415 (mm-40) cc_final: 0.6989 (tp40) REVERT: A 433 ASP cc_start: 0.7815 (t70) cc_final: 0.7181 (m-30) REVERT: A 436 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7699 (mt-10) REVERT: A 459 GLU cc_start: 0.8066 (pt0) cc_final: 0.7292 (mt-10) REVERT: A 483 PHE cc_start: 0.7110 (t80) cc_final: 0.6861 (t80) REVERT: B 257 VAL cc_start: 0.7285 (t) cc_final: 0.6826 (p) REVERT: B 283 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6290 (tp30) REVERT: B 287 MET cc_start: 0.3777 (ttp) cc_final: 0.2682 (tpt) REVERT: B 343 LYS cc_start: 0.7634 (mtmm) cc_final: 0.6792 (tptm) REVERT: B 388 MET cc_start: 0.8163 (mmm) cc_final: 0.7887 (mmt) REVERT: B 408 GLN cc_start: 0.7620 (mm110) cc_final: 0.7267 (mm-40) REVERT: B 429 GLN cc_start: 0.7408 (mm-40) cc_final: 0.6991 (tp40) REVERT: B 433 ASP cc_start: 0.7811 (t70) cc_final: 0.7156 (m-30) REVERT: B 436 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 459 GLU cc_start: 0.8061 (pt0) cc_final: 0.7285 (mt-10) REVERT: B 483 PHE cc_start: 0.7110 (t80) cc_final: 0.6867 (t80) REVERT: C 257 VAL cc_start: 0.7281 (t) cc_final: 0.6814 (p) REVERT: C 283 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6309 (tp30) REVERT: C 287 MET cc_start: 0.3778 (ttp) cc_final: 0.2671 (tpt) REVERT: C 343 LYS cc_start: 0.7629 (mtmm) cc_final: 0.6786 (tptm) REVERT: C 388 MET cc_start: 0.8164 (mmm) cc_final: 0.7886 (mmt) REVERT: C 408 GLN cc_start: 0.7609 (mm110) cc_final: 0.7307 (mm-40) REVERT: C 429 GLN cc_start: 0.7407 (mm-40) cc_final: 0.6999 (tp40) REVERT: C 433 ASP cc_start: 0.7814 (t70) cc_final: 0.7152 (m-30) REVERT: C 436 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7703 (mt-10) REVERT: C 459 GLU cc_start: 0.8069 (pt0) cc_final: 0.7291 (mt-10) REVERT: C 473 MET cc_start: 0.4979 (OUTLIER) cc_final: 0.4342 (tmm) REVERT: C 483 PHE cc_start: 0.7107 (t80) cc_final: 0.6830 (t80) REVERT: D 257 VAL cc_start: 0.7280 (t) cc_final: 0.6819 (p) REVERT: D 283 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6311 (tp30) REVERT: D 287 MET cc_start: 0.3779 (ttp) cc_final: 0.2669 (tpt) REVERT: D 343 LYS cc_start: 0.7630 (mtmm) cc_final: 0.6756 (tptt) REVERT: D 388 MET cc_start: 0.8164 (mmm) cc_final: 0.7887 (mmt) REVERT: D 408 GLN cc_start: 0.7609 (mm110) cc_final: 0.7308 (mm-40) REVERT: D 429 GLN cc_start: 0.7412 (mm-40) cc_final: 0.6998 (tp40) REVERT: D 433 ASP cc_start: 0.7814 (t70) cc_final: 0.7152 (m-30) REVERT: D 459 GLU cc_start: 0.8061 (pt0) cc_final: 0.7289 (mt-10) REVERT: D 473 MET cc_start: 0.4984 (OUTLIER) cc_final: 0.4349 (tmm) REVERT: D 483 PHE cc_start: 0.7128 (t80) cc_final: 0.6856 (t80) outliers start: 23 outliers final: 9 residues processed: 273 average time/residue: 1.2548 time to fit residues: 376.9191 Evaluate side-chains 257 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 473 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15328 Z= 0.166 Angle : 0.487 7.466 20788 Z= 0.257 Chirality : 0.041 0.187 2348 Planarity : 0.003 0.021 2596 Dihedral : 5.994 49.111 2212 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.82 % Allowed : 13.55 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.19), residues: 1920 helix: 2.36 (0.14), residues: 1288 sheet: 0.25 (0.53), residues: 88 loop : 0.54 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 281 HIS 0.003 0.001 HIS C 421 PHE 0.010 0.001 PHE D 569 TYR 0.025 0.002 TYR A 411 ARG 0.002 0.000 ARG D 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 250 time to evaluate : 1.563 Fit side-chains REVERT: A 257 VAL cc_start: 0.7293 (t) cc_final: 0.6846 (p) REVERT: A 283 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6285 (tp30) REVERT: A 287 MET cc_start: 0.3934 (ttp) cc_final: 0.2891 (tpt) REVERT: A 343 LYS cc_start: 0.7622 (mtmm) cc_final: 0.6832 (tptm) REVERT: A 369 MET cc_start: 0.7897 (mmm) cc_final: 0.7591 (tpp) REVERT: A 388 MET cc_start: 0.8172 (mmm) cc_final: 0.7941 (mmt) REVERT: A 408 GLN cc_start: 0.7618 (mm110) cc_final: 0.7310 (mm-40) REVERT: A 429 GLN cc_start: 0.7440 (mm-40) cc_final: 0.6999 (tp40) REVERT: A 433 ASP cc_start: 0.7807 (t70) cc_final: 0.7147 (m-30) REVERT: A 436 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 459 GLU cc_start: 0.8086 (pt0) cc_final: 0.7326 (mt-10) REVERT: B 257 VAL cc_start: 0.7290 (t) cc_final: 0.6840 (p) REVERT: B 283 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6260 (tp30) REVERT: B 287 MET cc_start: 0.3932 (ttp) cc_final: 0.2887 (tpt) REVERT: B 343 LYS cc_start: 0.7623 (mtmm) cc_final: 0.6842 (tptm) REVERT: B 388 MET cc_start: 0.8168 (mmm) cc_final: 0.7940 (mmt) REVERT: B 408 GLN cc_start: 0.7652 (mm110) cc_final: 0.7336 (mm-40) REVERT: B 429 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7017 (tp40) REVERT: B 433 ASP cc_start: 0.7858 (t70) cc_final: 0.7169 (m-30) REVERT: B 436 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 459 GLU cc_start: 0.8075 (pt0) cc_final: 0.7313 (mt-10) REVERT: C 257 VAL cc_start: 0.7301 (t) cc_final: 0.6846 (p) REVERT: C 283 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6263 (tp30) REVERT: C 287 MET cc_start: 0.3933 (ttp) cc_final: 0.2886 (tpt) REVERT: C 343 LYS cc_start: 0.7619 (mtmm) cc_final: 0.6833 (tptm) REVERT: C 388 MET cc_start: 0.8166 (mmm) cc_final: 0.7934 (mmt) REVERT: C 408 GLN cc_start: 0.7628 (mm110) cc_final: 0.7315 (mm-40) REVERT: C 429 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7013 (tp40) REVERT: C 433 ASP cc_start: 0.7853 (t70) cc_final: 0.7141 (m-30) REVERT: C 436 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 459 GLU cc_start: 0.8075 (pt0) cc_final: 0.7307 (mt-10) REVERT: C 473 MET cc_start: 0.4961 (OUTLIER) cc_final: 0.4415 (tmm) REVERT: D 257 VAL cc_start: 0.7293 (t) cc_final: 0.6844 (p) REVERT: D 283 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6266 (tp30) REVERT: D 287 MET cc_start: 0.3931 (ttp) cc_final: 0.2883 (tpt) REVERT: D 343 LYS cc_start: 0.7646 (mtmm) cc_final: 0.6772 (tptt) REVERT: D 388 MET cc_start: 0.8167 (mmm) cc_final: 0.7936 (mmt) REVERT: D 408 GLN cc_start: 0.7627 (mm110) cc_final: 0.7316 (mm-40) REVERT: D 429 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7027 (tp40) REVERT: D 433 ASP cc_start: 0.7849 (t70) cc_final: 0.7144 (m-30) REVERT: D 459 GLU cc_start: 0.8071 (pt0) cc_final: 0.7306 (mt-10) REVERT: D 473 MET cc_start: 0.4966 (OUTLIER) cc_final: 0.4300 (tmm) outliers start: 26 outliers final: 12 residues processed: 264 average time/residue: 1.2722 time to fit residues: 369.4798 Evaluate side-chains 257 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 243 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 473 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 103 optimal weight: 0.0010 chunk 75 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15328 Z= 0.137 Angle : 0.467 7.980 20788 Z= 0.243 Chirality : 0.040 0.188 2348 Planarity : 0.003 0.022 2596 Dihedral : 5.590 45.950 2212 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.40 % Allowed : 14.04 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.20), residues: 1920 helix: 2.44 (0.14), residues: 1288 sheet: 0.22 (0.52), residues: 88 loop : 0.59 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 373 HIS 0.003 0.001 HIS D 437 PHE 0.009 0.001 PHE D 483 TYR 0.019 0.001 TYR A 411 ARG 0.002 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 255 time to evaluate : 1.807 Fit side-chains REVERT: A 257 VAL cc_start: 0.7251 (t) cc_final: 0.6795 (p) REVERT: A 265 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7472 (mm) REVERT: A 283 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6267 (tp30) REVERT: A 285 PHE cc_start: 0.6491 (m-10) cc_final: 0.6260 (m-80) REVERT: A 287 MET cc_start: 0.3645 (ttp) cc_final: 0.2709 (tpt) REVERT: A 343 LYS cc_start: 0.7647 (mtmm) cc_final: 0.6785 (tptm) REVERT: A 369 MET cc_start: 0.7903 (mmm) cc_final: 0.7601 (tpp) REVERT: A 388 MET cc_start: 0.8167 (mmm) cc_final: 0.7888 (mmt) REVERT: A 408 GLN cc_start: 0.7580 (mm110) cc_final: 0.7298 (mm-40) REVERT: A 429 GLN cc_start: 0.7422 (mm-40) cc_final: 0.6988 (tp40) REVERT: A 433 ASP cc_start: 0.7785 (t70) cc_final: 0.7155 (m-30) REVERT: A 436 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 459 GLU cc_start: 0.8076 (pt0) cc_final: 0.7317 (mt-10) REVERT: B 257 VAL cc_start: 0.7247 (t) cc_final: 0.6786 (p) REVERT: B 283 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6220 (tp30) REVERT: B 285 PHE cc_start: 0.6478 (m-10) cc_final: 0.6249 (m-80) REVERT: B 287 MET cc_start: 0.3655 (ttp) cc_final: 0.2700 (tpt) REVERT: B 343 LYS cc_start: 0.7646 (mtmm) cc_final: 0.6787 (tptm) REVERT: B 388 MET cc_start: 0.8171 (mmm) cc_final: 0.7895 (mmt) REVERT: B 408 GLN cc_start: 0.7619 (mm110) cc_final: 0.7313 (mm-40) REVERT: B 429 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7010 (tp40) REVERT: B 433 ASP cc_start: 0.7824 (t70) cc_final: 0.7169 (m-30) REVERT: B 436 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 459 GLU cc_start: 0.8062 (pt0) cc_final: 0.7292 (mt-10) REVERT: C 257 VAL cc_start: 0.7238 (t) cc_final: 0.6780 (p) REVERT: C 265 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7473 (mm) REVERT: C 283 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6214 (tp30) REVERT: C 285 PHE cc_start: 0.6487 (m-10) cc_final: 0.6255 (m-80) REVERT: C 287 MET cc_start: 0.3645 (ttp) cc_final: 0.2693 (tpt) REVERT: C 343 LYS cc_start: 0.7644 (mtmm) cc_final: 0.6785 (tptm) REVERT: C 388 MET cc_start: 0.8167 (mmm) cc_final: 0.7890 (mmt) REVERT: C 408 GLN cc_start: 0.7603 (mm110) cc_final: 0.7316 (mm-40) REVERT: C 429 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7006 (tp40) REVERT: C 433 ASP cc_start: 0.7819 (t70) cc_final: 0.7158 (m-30) REVERT: C 436 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 459 GLU cc_start: 0.8062 (pt0) cc_final: 0.7293 (mt-10) REVERT: C 473 MET cc_start: 0.4887 (OUTLIER) cc_final: 0.4243 (tmm) REVERT: D 257 VAL cc_start: 0.7246 (t) cc_final: 0.6789 (p) REVERT: D 283 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6203 (tp30) REVERT: D 285 PHE cc_start: 0.6491 (m-10) cc_final: 0.6252 (m-80) REVERT: D 287 MET cc_start: 0.3646 (ttp) cc_final: 0.2690 (tpt) REVERT: D 343 LYS cc_start: 0.7646 (mtmm) cc_final: 0.6759 (tptt) REVERT: D 388 MET cc_start: 0.8164 (mmm) cc_final: 0.7887 (mmt) REVERT: D 408 GLN cc_start: 0.7609 (mm110) cc_final: 0.7320 (mm-40) REVERT: D 429 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7036 (tp40) REVERT: D 433 ASP cc_start: 0.7819 (t70) cc_final: 0.7156 (m-30) REVERT: D 459 GLU cc_start: 0.8039 (pt0) cc_final: 0.7276 (mt-10) REVERT: D 473 MET cc_start: 0.4883 (OUTLIER) cc_final: 0.4248 (tmm) outliers start: 20 outliers final: 8 residues processed: 264 average time/residue: 1.2636 time to fit residues: 368.4681 Evaluate side-chains 256 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 244 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 473 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 191 optimal weight: 0.4980 chunk 176 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15328 Z= 0.249 Angle : 0.550 9.204 20788 Z= 0.290 Chirality : 0.043 0.202 2348 Planarity : 0.003 0.024 2596 Dihedral : 6.731 54.617 2212 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.77 % Allowed : 14.66 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.19), residues: 1920 helix: 2.29 (0.14), residues: 1284 sheet: 0.27 (0.53), residues: 88 loop : 0.34 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 281 HIS 0.004 0.001 HIS C 421 PHE 0.014 0.002 PHE C 186 TYR 0.031 0.002 TYR A 411 ARG 0.004 0.001 ARG D 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 1.661 Fit side-chains REVERT: A 257 VAL cc_start: 0.7298 (t) cc_final: 0.6845 (p) REVERT: A 283 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6279 (tp30) REVERT: A 285 PHE cc_start: 0.6500 (m-10) cc_final: 0.6270 (m-80) REVERT: A 287 MET cc_start: 0.4127 (ttp) cc_final: 0.3109 (tpt) REVERT: A 343 LYS cc_start: 0.7649 (mtmm) cc_final: 0.6817 (tptm) REVERT: A 369 MET cc_start: 0.8024 (mmm) cc_final: 0.7757 (tpp) REVERT: A 388 MET cc_start: 0.8156 (mmm) cc_final: 0.7915 (mmt) REVERT: A 408 GLN cc_start: 0.7593 (mm110) cc_final: 0.7305 (mm-40) REVERT: A 433 ASP cc_start: 0.7861 (t70) cc_final: 0.7132 (m-30) REVERT: A 436 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 459 GLU cc_start: 0.8103 (pt0) cc_final: 0.7339 (mt-10) REVERT: B 257 VAL cc_start: 0.7304 (t) cc_final: 0.6849 (p) REVERT: B 283 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6292 (tp30) REVERT: B 285 PHE cc_start: 0.6500 (m-10) cc_final: 0.6274 (m-80) REVERT: B 287 MET cc_start: 0.4126 (ttp) cc_final: 0.3106 (tpt) REVERT: B 343 LYS cc_start: 0.7654 (mtmm) cc_final: 0.6824 (tptm) REVERT: B 388 MET cc_start: 0.8151 (mmm) cc_final: 0.7914 (mmt) REVERT: B 408 GLN cc_start: 0.7624 (mm110) cc_final: 0.7264 (mm-40) REVERT: B 433 ASP cc_start: 0.7855 (t70) cc_final: 0.7125 (m-30) REVERT: B 436 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7656 (mt-10) REVERT: B 459 GLU cc_start: 0.8086 (pt0) cc_final: 0.7330 (mt-10) REVERT: C 257 VAL cc_start: 0.7296 (t) cc_final: 0.6838 (p) REVERT: C 283 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6297 (tp30) REVERT: C 285 PHE cc_start: 0.6492 (m-10) cc_final: 0.6270 (m-80) REVERT: C 287 MET cc_start: 0.4120 (ttp) cc_final: 0.3105 (tpt) REVERT: C 343 LYS cc_start: 0.7651 (mtmm) cc_final: 0.6851 (tptm) REVERT: C 388 MET cc_start: 0.8151 (mmm) cc_final: 0.7912 (mmt) REVERT: C 408 GLN cc_start: 0.7602 (mm110) cc_final: 0.7234 (mm-40) REVERT: C 433 ASP cc_start: 0.7849 (t70) cc_final: 0.7106 (m-30) REVERT: C 436 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7687 (mt-10) REVERT: C 459 GLU cc_start: 0.8084 (pt0) cc_final: 0.7333 (mt-10) REVERT: C 473 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.4331 (tmm) REVERT: D 257 VAL cc_start: 0.7295 (t) cc_final: 0.6843 (p) REVERT: D 283 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6300 (tp30) REVERT: D 285 PHE cc_start: 0.6497 (m-10) cc_final: 0.6271 (m-80) REVERT: D 287 MET cc_start: 0.4126 (ttp) cc_final: 0.3105 (tpt) REVERT: D 343 LYS cc_start: 0.7662 (mtmm) cc_final: 0.6779 (tptt) REVERT: D 388 MET cc_start: 0.8151 (mmm) cc_final: 0.7912 (mmt) REVERT: D 408 GLN cc_start: 0.7600 (mm110) cc_final: 0.7303 (mm-40) REVERT: D 433 ASP cc_start: 0.7855 (t70) cc_final: 0.7112 (m-30) REVERT: D 459 GLU cc_start: 0.8065 (pt0) cc_final: 0.7323 (mt-10) REVERT: D 473 MET cc_start: 0.4956 (OUTLIER) cc_final: 0.4342 (tmm) outliers start: 11 outliers final: 8 residues processed: 251 average time/residue: 1.2813 time to fit residues: 353.6716 Evaluate side-chains 253 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 243 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 473 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 63 optimal weight: 0.0870 chunk 156 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.169709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121932 restraints weight = 15024.491| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.62 r_work: 0.3131 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15328 Z= 0.184 Angle : 0.512 9.248 20788 Z= 0.270 Chirality : 0.041 0.196 2348 Planarity : 0.003 0.022 2596 Dihedral : 6.356 53.478 2212 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.91 % Allowed : 14.73 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.19), residues: 1920 helix: 2.30 (0.14), residues: 1288 sheet: 0.21 (0.53), residues: 88 loop : 0.33 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 373 HIS 0.004 0.001 HIS D 421 PHE 0.011 0.002 PHE A 389 TYR 0.028 0.002 TYR A 411 ARG 0.003 0.000 ARG C 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6843.54 seconds wall clock time: 123 minutes 11.54 seconds (7391.54 seconds total)