Starting phenix.real_space_refine on Sun Jun 15 22:49:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oo5_20146/06_2025/6oo5_20146.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oo5_20146/06_2025/6oo5_20146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oo5_20146/06_2025/6oo5_20146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oo5_20146/06_2025/6oo5_20146.map" model { file = "/net/cci-nas-00/data/ceres_data/6oo5_20146/06_2025/6oo5_20146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oo5_20146/06_2025/6oo5_20146.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 11512 2.51 5 N 2980 2.21 5 O 2968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17548 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4394 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 648 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 25, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 335 Chain: "B" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4288 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 622 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 18, 'ASN:plan1': 12, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 28, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 366 Chain: "C" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4394 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 648 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 25, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 335 Chain: "D" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4288 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 622 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 18, 'ASN:plan1': 12, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 28, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 366 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.87, per 1000 atoms: 0.62 Number of scatterers: 17548 At special positions: 0 Unit cell: (156.6, 156.6, 114.48, 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 88 16.00 O 2968 8.00 N 2980 7.00 C 11512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.8 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 4 sheets defined 62.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.638A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.994A pdb=" N VAL A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.546A pdb=" N ALA A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 280 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.760A pdb=" N ILE A 288 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.959A pdb=" N GLN A 322 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 373 through 387 removed outlier: 4.296A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 411 removed outlier: 3.770A pdb=" N PHE A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 457 Processing helix chain 'A' and resid 468 through 491 Processing helix chain 'A' and resid 494 through 509 removed outlier: 4.693A pdb=" N LEU A 498 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 removed outlier: 4.578A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 514 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 515 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 516 " --> pdb=" O TYR A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 516' Processing helix chain 'A' and resid 517 through 557 removed outlier: 5.550A pdb=" N LEU A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARG A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.810A pdb=" N THR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 648 removed outlier: 3.565A pdb=" N ASN A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 672 removed outlier: 3.595A pdb=" N GLY A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 85 Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.516A pdb=" N LYS B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.584A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.629A pdb=" N VAL B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 220 through 230 removed outlier: 3.501A pdb=" N VAL B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.571A pdb=" N ALA B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 280 removed outlier: 3.746A pdb=" N SER B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.619A pdb=" N ILE B 288 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 373 through 387 removed outlier: 4.071A pdb=" N LYS B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 411 removed outlier: 3.878A pdb=" N PHE B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 457 Processing helix chain 'B' and resid 468 through 491 removed outlier: 3.833A pdb=" N ILE B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 473 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.876A pdb=" N LEU B 498 " --> pdb=" O TRP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 516 removed outlier: 3.599A pdb=" N THR B 514 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 515 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY B 516 " --> pdb=" O TYR B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 534 removed outlier: 4.154A pdb=" N TYR B 523 " --> pdb=" O HIS B 519 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 557 Processing helix chain 'B' and resid 590 through 604 removed outlier: 4.243A pdb=" N GLU B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 648 removed outlier: 3.783A pdb=" N ASN B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 672 Processing helix chain 'C' and resid 74 through 85 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 133 through 145 Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.507A pdb=" N ILE C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.991A pdb=" N VAL C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.555A pdb=" N ALA C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 280 Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.765A pdb=" N ILE C 288 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.979A pdb=" N GLN C 322 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 373 through 387 removed outlier: 4.291A pdb=" N LYS C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 411 removed outlier: 3.770A pdb=" N PHE C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 457 Processing helix chain 'C' and resid 468 through 491 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.695A pdb=" N LEU C 498 " --> pdb=" O TRP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 516 removed outlier: 4.576A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR C 514 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 515 " --> pdb=" O TYR C 512 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY C 516 " --> pdb=" O TYR C 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 510 through 516' Processing helix chain 'C' and resid 517 through 557 removed outlier: 5.551A pdb=" N LEU C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ARG C 537 " --> pdb=" O ARG C 533 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.807A pdb=" N THR C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 648 removed outlier: 3.544A pdb=" N ASN C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 672 removed outlier: 3.594A pdb=" N GLY C 672 " --> pdb=" O GLU C 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 85 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 117 through 125 removed outlier: 3.541A pdb=" N LYS D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 144 Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.594A pdb=" N ILE D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 185 removed outlier: 3.631A pdb=" N VAL D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'D' and resid 220 through 230 removed outlier: 3.500A pdb=" N VAL D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.568A pdb=" N ALA D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 280 removed outlier: 3.736A pdb=" N SER D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.618A pdb=" N ILE D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 373 through 387 removed outlier: 4.104A pdb=" N LYS D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU D 379 " --> pdb=" O PRO D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 411 removed outlier: 3.882A pdb=" N PHE D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 457 Processing helix chain 'D' and resid 468 through 491 removed outlier: 3.834A pdb=" N ILE D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU D 473 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.876A pdb=" N LEU D 498 " --> pdb=" O TRP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 516 removed outlier: 3.601A pdb=" N THR D 514 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 515 " --> pdb=" O TYR D 512 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY D 516 " --> pdb=" O TYR D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 534 removed outlier: 4.255A pdb=" N TYR D 523 " --> pdb=" O HIS D 519 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 534 " --> pdb=" O VAL D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 557 Processing helix chain 'D' and resid 590 through 604 removed outlier: 4.210A pdb=" N GLU D 597 " --> pdb=" O ASP D 593 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE D 603 " --> pdb=" O PHE D 599 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 648 removed outlier: 3.780A pdb=" N ASN D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 672 Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 333 removed outlier: 6.997A pdb=" N VAL A 338 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N CYS A 332 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL A 336 " --> pdb=" O CYS A 332 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP A 698 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 327 through 333 removed outlier: 3.630A pdb=" N PHE B 328 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 338 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N CYS B 332 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 336 " --> pdb=" O CYS B 332 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP B 698 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 328 through 333 removed outlier: 6.996A pdb=" N VAL C 338 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N CYS C 332 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL C 336 " --> pdb=" O CYS C 332 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP C 698 " --> pdb=" O VAL C 689 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 327 through 333 removed outlier: 3.632A pdb=" N PHE D 328 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL D 338 " --> pdb=" O GLU D 330 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N CYS D 332 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL D 336 " --> pdb=" O CYS D 332 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP D 698 " --> pdb=" O VAL D 689 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3204 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: 6.36 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2678 1.29 - 1.42: 4992 1.42 - 1.56: 10154 1.56 - 1.69: 46 1.69 - 1.82: 134 Bond restraints: 18004 Sorted by residual: bond pdb=" CAJ 6EU C1001 " pdb=" OAA 6EU C1001 " ideal model delta sigma weight residual 1.439 1.765 -0.326 2.00e-02 2.50e+03 2.66e+02 bond pdb=" CAJ 6EU A1001 " pdb=" OAA 6EU A1001 " ideal model delta sigma weight residual 1.439 1.765 -0.326 2.00e-02 2.50e+03 2.66e+02 bond pdb=" CAJ 6EU D1001 " pdb=" OAA 6EU D1001 " ideal model delta sigma weight residual 1.439 1.762 -0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" CAJ 6EU B1001 " pdb=" OAA 6EU B1001 " ideal model delta sigma weight residual 1.439 1.762 -0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" CAS 6EU A1001 " pdb=" CAX 6EU A1001 " ideal model delta sigma weight residual 1.334 1.594 -0.260 2.00e-02 2.50e+03 1.69e+02 ... (remaining 17999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 24170 3.00 - 6.01: 447 6.01 - 9.01: 95 9.01 - 12.02: 10 12.02 - 15.02: 4 Bond angle restraints: 24726 Sorted by residual: angle pdb=" N PRO C 413 " pdb=" CA PRO C 413 " pdb=" CB PRO C 413 " ideal model delta sigma weight residual 103.00 110.46 -7.46 1.10e+00 8.26e-01 4.60e+01 angle pdb=" N PRO A 413 " pdb=" CA PRO A 413 " pdb=" CB PRO A 413 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.57e+01 angle pdb=" N PRO B 413 " pdb=" CA PRO B 413 " pdb=" CB PRO B 413 " ideal model delta sigma weight residual 103.00 110.29 -7.29 1.10e+00 8.26e-01 4.40e+01 angle pdb=" N PRO D 413 " pdb=" CA PRO D 413 " pdb=" CB PRO D 413 " ideal model delta sigma weight residual 103.00 110.29 -7.29 1.10e+00 8.26e-01 4.39e+01 angle pdb=" CA GLN A 412 " pdb=" C GLN A 412 " pdb=" N PRO A 413 " ideal model delta sigma weight residual 120.58 116.79 3.79 7.40e-01 1.83e+00 2.62e+01 ... (remaining 24721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 10235 16.84 - 33.69: 285 33.69 - 50.53: 66 50.53 - 67.37: 12 67.37 - 84.22: 22 Dihedral angle restraints: 10620 sinusoidal: 3492 harmonic: 7128 Sorted by residual: dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N GLY A 208 " pdb=" CA GLY A 208 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N GLY C 208 " pdb=" CA GLY C 208 " ideal model delta harmonic sigma weight residual -180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA PRO B 586 " pdb=" C PRO B 586 " pdb=" N PRO B 587 " pdb=" CA PRO B 587 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 10617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2626 0.079 - 0.158: 267 0.158 - 0.237: 16 0.237 - 0.316: 15 0.316 - 0.396: 6 Chirality restraints: 2930 Sorted by residual: chirality pdb=" CAN 6EU B1001 " pdb=" CAJ 6EU B1001 " pdb=" CAP 6EU B1001 " pdb=" CAT 6EU B1001 " both_signs ideal model delta sigma weight residual False -2.48 -2.87 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CAN 6EU D1001 " pdb=" CAJ 6EU D1001 " pdb=" CAP 6EU D1001 " pdb=" CAT 6EU D1001 " both_signs ideal model delta sigma weight residual False -2.48 -2.87 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CAM 6EU B1001 " pdb=" CAL 6EU B1001 " pdb=" CAP 6EU B1001 " pdb=" CAV 6EU B1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.89 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 2927 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 280 " -0.041 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO B 281 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 280 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO D 281 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 281 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 281 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 586 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO B 587 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 587 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 587 " 0.035 5.00e-02 4.00e+02 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3963 2.78 - 3.31: 16087 3.31 - 3.84: 27878 3.84 - 4.37: 29112 4.37 - 4.90: 51855 Nonbonded interactions: 128895 Sorted by model distance: nonbonded pdb=" OG1 THR D 481 " pdb=" OG SER D 502 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR B 481 " pdb=" OG SER B 502 " model vdw 2.249 3.040 nonbonded pdb=" O GLN C 322 " pdb=" OG SER C 325 " model vdw 2.327 3.040 nonbonded pdb=" O THR A 514 " pdb=" OG1 THR A 520 " model vdw 2.346 3.040 nonbonded pdb=" O THR C 514 " pdb=" OG1 THR C 520 " model vdw 2.346 3.040 ... (remaining 128890 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 42.960 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 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 0.326 18004 Z= 0.581 Angle : 1.047 15.020 24726 Z= 0.536 Chirality : 0.055 0.396 2930 Planarity : 0.007 0.063 3072 Dihedral : 10.642 84.216 6012 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -2.74 (0.13), residues: 2408 helix: -1.36 (0.11), residues: 1456 sheet: -1.00 (0.49), residues: 76 loop : -2.54 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 349 HIS 0.007 0.002 HIS B 361 PHE 0.034 0.003 PHE C 405 TYR 0.026 0.003 TYR B 159 ARG 0.006 0.001 ARG D 456 Details of bonding type rmsd hydrogen bonds : bond 0.12798 ( 1086) hydrogen bonds : angle 5.41301 ( 3204) covalent geometry : bond 0.01197 (18004) covalent geometry : angle 1.04701 (24726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9289 (tptp) cc_final: 0.9072 (tppt) REVERT: A 373 LEU cc_start: 0.8232 (mt) cc_final: 0.8003 (mp) REVERT: A 378 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7728 (tmtt) REVERT: A 402 MET cc_start: 0.7739 (mmm) cc_final: 0.7204 (tpt) REVERT: A 469 TYR cc_start: 0.7950 (t80) cc_final: 0.7619 (t80) REVERT: B 117 THR cc_start: 0.8276 (p) cc_final: 0.8025 (t) REVERT: B 172 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8420 (mmmm) REVERT: B 213 SER cc_start: 0.9508 (m) cc_final: 0.9025 (p) REVERT: B 226 TYR cc_start: 0.8459 (t80) cc_final: 0.8123 (t80) REVERT: B 398 TYR cc_start: 0.7554 (t80) cc_final: 0.7338 (t80) REVERT: B 501 SER cc_start: 0.8486 (t) cc_final: 0.8273 (p) REVERT: B 619 VAL cc_start: 0.7786 (t) cc_final: 0.7583 (p) REVERT: B 655 TRP cc_start: 0.7857 (t60) cc_final: 0.7641 (t60) REVERT: C 108 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8486 (pt0) REVERT: C 121 LYS cc_start: 0.9319 (tptp) cc_final: 0.9066 (tppt) REVERT: C 133 CYS cc_start: 0.9510 (t) cc_final: 0.9309 (m) REVERT: C 182 VAL cc_start: 0.9461 (t) cc_final: 0.9181 (p) REVERT: C 213 SER cc_start: 0.9265 (m) cc_final: 0.9044 (m) REVERT: C 377 ASN cc_start: 0.7590 (t0) cc_final: 0.7381 (m-40) REVERT: C 402 MET cc_start: 0.7623 (mmm) cc_final: 0.7120 (tpt) REVERT: C 469 TYR cc_start: 0.7859 (t80) cc_final: 0.7633 (t80) REVERT: C 522 ILE cc_start: 0.8599 (mt) cc_final: 0.8342 (mm) REVERT: C 685 VAL cc_start: 0.7917 (t) cc_final: 0.7668 (p) REVERT: C 686 MET cc_start: 0.8729 (tmm) cc_final: 0.8253 (tpp) REVERT: D 111 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6200 (tm-30) REVERT: D 172 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8187 (mtmt) REVERT: D 183 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8852 (mp0) REVERT: D 213 SER cc_start: 0.9389 (m) cc_final: 0.9132 (p) REVERT: D 214 LEU cc_start: 0.8748 (tp) cc_final: 0.8353 (tp) REVERT: D 217 CYS cc_start: 0.8554 (m) cc_final: 0.8335 (m) REVERT: D 226 TYR cc_start: 0.8502 (t80) cc_final: 0.8117 (t80) REVERT: D 268 MET cc_start: 0.9234 (tpp) cc_final: 0.8861 (mmm) REVERT: D 310 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7910 (ttpp) REVERT: D 330 GLU cc_start: 0.8798 (tt0) cc_final: 0.8336 (tp30) REVERT: D 373 LEU cc_start: 0.8725 (mt) cc_final: 0.8484 (mp) REVERT: D 398 TYR cc_start: 0.7625 (t80) cc_final: 0.7418 (t80) REVERT: D 501 SER cc_start: 0.8636 (t) cc_final: 0.8427 (p) REVERT: D 538 PHE cc_start: 0.7245 (t80) cc_final: 0.7007 (t80) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.2652 time to fit residues: 203.3786 Evaluate side-chains 286 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 0.0570 chunk 98 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 HIS A 394 ASN B 154 GLN C 154 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.103830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.084509 restraints weight = 59602.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086455 restraints weight = 35510.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087779 restraints weight = 24848.253| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18004 Z= 0.147 Angle : 0.605 7.766 24726 Z= 0.307 Chirality : 0.039 0.193 2930 Planarity : 0.004 0.044 3072 Dihedral : 6.870 64.905 2968 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.78 % 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: -0.40 (0.16), residues: 2408 helix: 0.67 (0.13), residues: 1476 sheet: -0.33 (0.43), residues: 84 loop : -1.92 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 507 HIS 0.006 0.001 HIS C 163 PHE 0.040 0.002 PHE C 616 TYR 0.027 0.002 TYR C 542 ARG 0.012 0.001 ARG D 456 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1086) hydrogen bonds : angle 4.01450 ( 3204) covalent geometry : bond 0.00309 (18004) covalent geometry : angle 0.60480 (24726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8601 (tm-30) REVERT: A 373 LEU cc_start: 0.8610 (mt) cc_final: 0.8392 (mm) REVERT: A 387 LEU cc_start: 0.8833 (mm) cc_final: 0.8353 (tp) REVERT: A 402 MET cc_start: 0.9065 (mmm) cc_final: 0.8584 (tpt) REVERT: A 523 TYR cc_start: 0.8835 (t80) cc_final: 0.8255 (t80) REVERT: B 402 MET cc_start: 0.7688 (mmm) cc_final: 0.7455 (tpp) REVERT: B 526 MET cc_start: 0.8104 (mmp) cc_final: 0.7528 (mtm) REVERT: B 643 MET cc_start: 0.8452 (mmm) cc_final: 0.7852 (tmm) REVERT: C 135 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8767 (tm-30) REVERT: C 387 LEU cc_start: 0.8908 (mm) cc_final: 0.8177 (tp) REVERT: C 402 MET cc_start: 0.9044 (mmm) cc_final: 0.8661 (tpt) REVERT: C 477 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8407 (tm-30) REVERT: D 213 SER cc_start: 0.9197 (m) cc_final: 0.8890 (p) REVERT: D 214 LEU cc_start: 0.9371 (tp) cc_final: 0.9005 (tp) REVERT: D 268 MET cc_start: 0.8444 (tpp) cc_final: 0.8190 (tpp) REVERT: D 402 MET cc_start: 0.7673 (mmm) cc_final: 0.7471 (tpp) REVERT: D 501 SER cc_start: 0.8515 (t) cc_final: 0.8278 (p) REVERT: D 538 PHE cc_start: 0.8333 (t80) cc_final: 0.8089 (t80) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.2555 time to fit residues: 151.4954 Evaluate side-chains 287 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 8 optimal weight: 0.0570 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 146 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.085088 restraints weight = 59147.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087007 restraints weight = 35339.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.088296 restraints weight = 24920.273| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18004 Z= 0.130 Angle : 0.560 7.706 24726 Z= 0.284 Chirality : 0.038 0.145 2930 Planarity : 0.003 0.038 3072 Dihedral : 6.110 57.198 2968 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.07 % Allowed : 2.19 % Favored : 97.74 % 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: 0.49 (0.17), residues: 2408 helix: 1.45 (0.13), residues: 1476 sheet: -0.28 (0.44), residues: 84 loop : -1.67 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 507 HIS 0.006 0.001 HIS C 163 PHE 0.024 0.001 PHE C 454 TYR 0.023 0.001 TYR C 523 ARG 0.006 0.000 ARG D 161 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1086) hydrogen bonds : angle 3.79745 ( 3204) covalent geometry : bond 0.00277 (18004) covalent geometry : angle 0.56018 (24726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 387 LEU cc_start: 0.8860 (mm) cc_final: 0.8334 (tp) REVERT: B 597 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8210 (tm-30) REVERT: B 627 TYR cc_start: 0.9170 (t80) cc_final: 0.8960 (t80) REVERT: B 686 MET cc_start: 0.8744 (tpp) cc_final: 0.8164 (tpp) REVERT: C 135 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8692 (tm-30) REVERT: C 686 MET cc_start: 0.8500 (ttt) cc_final: 0.8232 (ttt) REVERT: D 268 MET cc_start: 0.8493 (tpp) cc_final: 0.8216 (tpp) REVERT: D 501 SER cc_start: 0.8489 (t) cc_final: 0.8238 (p) REVERT: D 526 MET cc_start: 0.8170 (mmp) cc_final: 0.7601 (mtm) REVERT: D 669 MET cc_start: 0.8275 (mpp) cc_final: 0.8072 (mpp) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.2513 time to fit residues: 145.5402 Evaluate side-chains 279 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 104 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 HIS B 245 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS D 436 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.102043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.082780 restraints weight = 60609.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.084609 restraints weight = 36451.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085896 restraints weight = 25869.535| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18004 Z= 0.190 Angle : 0.613 7.293 24726 Z= 0.312 Chirality : 0.039 0.157 2930 Planarity : 0.004 0.037 3072 Dihedral : 5.940 56.101 2968 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2408 helix: 1.69 (0.13), residues: 1472 sheet: -0.34 (0.44), residues: 84 loop : -1.53 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 331 HIS 0.009 0.001 HIS D 436 PHE 0.031 0.002 PHE B 601 TYR 0.021 0.002 TYR C 542 ARG 0.006 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 1086) hydrogen bonds : angle 3.93359 ( 3204) covalent geometry : bond 0.00413 (18004) covalent geometry : angle 0.61274 (24726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.8927 (mm) cc_final: 0.8341 (tp) REVERT: A 523 TYR cc_start: 0.8893 (t80) cc_final: 0.8526 (t80) REVERT: B 103 TYR cc_start: 0.7416 (m-80) cc_final: 0.7193 (m-80) REVERT: B 526 MET cc_start: 0.8036 (mmp) cc_final: 0.7329 (mtm) REVERT: B 627 TYR cc_start: 0.9228 (t80) cc_final: 0.8988 (t80) REVERT: B 686 MET cc_start: 0.8752 (tpp) cc_final: 0.8189 (tpp) REVERT: C 387 LEU cc_start: 0.9056 (mm) cc_final: 0.8349 (tp) REVERT: D 268 MET cc_start: 0.8425 (tpp) cc_final: 0.8159 (tpp) REVERT: D 686 MET cc_start: 0.9059 (tpp) cc_final: 0.8402 (tpp) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.2509 time to fit residues: 129.4937 Evaluate side-chains 262 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 188 optimal weight: 0.2980 chunk 67 optimal weight: 0.0970 chunk 12 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 637 ASN D 436 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.105726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.086306 restraints weight = 60000.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088294 restraints weight = 35616.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089618 restraints weight = 24971.486| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18004 Z= 0.103 Angle : 0.544 9.568 24726 Z= 0.268 Chirality : 0.038 0.201 2930 Planarity : 0.003 0.045 3072 Dihedral : 5.448 57.213 2968 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.17), residues: 2408 helix: 2.10 (0.13), residues: 1448 sheet: 0.14 (0.46), residues: 84 loop : -1.39 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 331 HIS 0.010 0.001 HIS D 436 PHE 0.021 0.002 PHE C 454 TYR 0.033 0.001 TYR C 523 ARG 0.009 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 1086) hydrogen bonds : angle 3.55751 ( 3204) covalent geometry : bond 0.00204 (18004) covalent geometry : angle 0.54442 (24726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8491 (mtt) cc_final: 0.8249 (mtm) REVERT: A 135 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 268 MET cc_start: 0.8569 (mmp) cc_final: 0.8341 (mmp) REVERT: A 387 LEU cc_start: 0.8859 (mm) cc_final: 0.8389 (tp) REVERT: B 103 TYR cc_start: 0.7297 (m-80) cc_final: 0.6982 (m-80) REVERT: B 170 ILE cc_start: 0.9216 (mt) cc_final: 0.8975 (tt) REVERT: B 526 MET cc_start: 0.8141 (mmp) cc_final: 0.7540 (mtm) REVERT: B 627 TYR cc_start: 0.9185 (t80) cc_final: 0.8903 (t80) REVERT: B 686 MET cc_start: 0.8716 (tpp) cc_final: 0.8188 (tpp) REVERT: C 135 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8672 (tm-30) REVERT: C 387 LEU cc_start: 0.8948 (mm) cc_final: 0.8366 (tp) REVERT: C 686 MET cc_start: 0.8968 (ttt) cc_final: 0.8252 (tpt) REVERT: D 268 MET cc_start: 0.8438 (tpp) cc_final: 0.8170 (tpp) REVERT: D 501 SER cc_start: 0.8457 (t) cc_final: 0.8217 (p) REVERT: D 526 MET cc_start: 0.8108 (mmp) cc_final: 0.7385 (mtm) REVERT: D 686 MET cc_start: 0.9017 (tpp) cc_final: 0.8343 (tpp) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2492 time to fit residues: 142.0179 Evaluate side-chains 288 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 31 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 199 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 225 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 13 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS B 436 HIS C 637 ASN D 436 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.106077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086710 restraints weight = 59932.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.088683 restraints weight = 35634.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.090030 restraints weight = 24965.895| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18004 Z= 0.099 Angle : 0.542 10.934 24726 Z= 0.262 Chirality : 0.037 0.174 2930 Planarity : 0.003 0.037 3072 Dihedral : 5.183 57.473 2968 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 1.44 (0.17), residues: 2408 helix: 2.23 (0.13), residues: 1472 sheet: 0.38 (0.46), residues: 84 loop : -1.36 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 331 HIS 0.013 0.001 HIS B 436 PHE 0.020 0.001 PHE B 601 TYR 0.020 0.001 TYR B 226 ARG 0.006 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 1086) hydrogen bonds : angle 3.41190 ( 3204) covalent geometry : bond 0.00203 (18004) covalent geometry : angle 0.54223 (24726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8425 (mtt) cc_final: 0.8204 (mtm) REVERT: A 135 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8537 (tm-30) REVERT: A 268 MET cc_start: 0.8559 (mmp) cc_final: 0.8333 (mmp) REVERT: A 387 LEU cc_start: 0.8915 (mm) cc_final: 0.8441 (tp) REVERT: A 686 MET cc_start: 0.9211 (tmm) cc_final: 0.8243 (tpt) REVERT: B 103 TYR cc_start: 0.7146 (m-80) cc_final: 0.6782 (m-80) REVERT: B 170 ILE cc_start: 0.9238 (mt) cc_final: 0.8983 (tt) REVERT: B 669 MET cc_start: 0.8368 (mpp) cc_final: 0.8132 (mpp) REVERT: B 686 MET cc_start: 0.8669 (tpp) cc_final: 0.8160 (tpp) REVERT: C 135 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8646 (tm-30) REVERT: C 387 LEU cc_start: 0.8964 (mm) cc_final: 0.8351 (tp) REVERT: C 686 MET cc_start: 0.8611 (ttt) cc_final: 0.8407 (tpt) REVERT: D 268 MET cc_start: 0.8475 (tpp) cc_final: 0.8214 (tpp) REVERT: D 501 SER cc_start: 0.8417 (t) cc_final: 0.8111 (p) REVERT: D 526 MET cc_start: 0.8141 (mmp) cc_final: 0.7458 (mtm) REVERT: D 686 MET cc_start: 0.8969 (tpp) cc_final: 0.8320 (tpp) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2477 time to fit residues: 140.6036 Evaluate side-chains 279 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN D 436 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.104715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.085387 restraints weight = 59845.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087305 restraints weight = 35898.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088607 restraints weight = 25329.228| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18004 Z= 0.127 Angle : 0.561 7.007 24726 Z= 0.276 Chirality : 0.038 0.162 2930 Planarity : 0.003 0.034 3072 Dihedral : 5.155 57.606 2968 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), residues: 2408 helix: 2.36 (0.14), residues: 1472 sheet: 0.36 (0.47), residues: 84 loop : -1.26 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 658 HIS 0.010 0.001 HIS D 436 PHE 0.021 0.001 PHE D 454 TYR 0.030 0.001 TYR C 523 ARG 0.005 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 1086) hydrogen bonds : angle 3.47212 ( 3204) covalent geometry : bond 0.00274 (18004) covalent geometry : angle 0.56057 (24726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8418 (mtt) cc_final: 0.8206 (mtm) REVERT: A 135 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8548 (tm-30) REVERT: A 387 LEU cc_start: 0.8943 (mm) cc_final: 0.8392 (tp) REVERT: A 605 MET cc_start: 0.7340 (mmm) cc_final: 0.7110 (tpp) REVERT: A 686 MET cc_start: 0.9272 (tmm) cc_final: 0.8327 (tpt) REVERT: B 330 GLU cc_start: 0.8404 (tt0) cc_final: 0.8202 (tt0) REVERT: B 686 MET cc_start: 0.8740 (tpp) cc_final: 0.8196 (tpp) REVERT: C 387 LEU cc_start: 0.8999 (mm) cc_final: 0.8343 (tp) REVERT: C 556 LEU cc_start: 0.7900 (tp) cc_final: 0.7676 (pp) REVERT: C 686 MET cc_start: 0.8719 (ttt) cc_final: 0.8494 (tpt) REVERT: D 268 MET cc_start: 0.8444 (tpp) cc_final: 0.8169 (tpp) REVERT: D 601 PHE cc_start: 0.8292 (t80) cc_final: 0.8080 (t80) REVERT: D 686 MET cc_start: 0.8977 (tpp) cc_final: 0.8395 (tpp) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2410 time to fit residues: 130.5625 Evaluate side-chains 272 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 65 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 HIS D 436 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.104159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084973 restraints weight = 59752.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086865 restraints weight = 35711.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.088157 restraints weight = 25110.473| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18004 Z= 0.134 Angle : 0.583 10.093 24726 Z= 0.285 Chirality : 0.038 0.174 2930 Planarity : 0.003 0.034 3072 Dihedral : 5.188 57.420 2968 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 1.73 (0.17), residues: 2408 helix: 2.46 (0.13), residues: 1448 sheet: 0.32 (0.47), residues: 84 loop : -1.11 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 658 HIS 0.010 0.001 HIS B 436 PHE 0.027 0.002 PHE B 601 TYR 0.028 0.001 TYR A 523 ARG 0.006 0.000 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 1086) hydrogen bonds : angle 3.54704 ( 3204) covalent geometry : bond 0.00292 (18004) covalent geometry : angle 0.58286 (24726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8462 (mtt) cc_final: 0.8227 (mtm) REVERT: A 268 MET cc_start: 0.8625 (mmp) cc_final: 0.8423 (mmp) REVERT: A 387 LEU cc_start: 0.8966 (mm) cc_final: 0.8534 (tp) REVERT: A 686 MET cc_start: 0.9241 (tmm) cc_final: 0.8315 (tpt) REVERT: B 505 MET cc_start: 0.7688 (tmm) cc_final: 0.7487 (tmm) REVERT: B 686 MET cc_start: 0.8718 (tpp) cc_final: 0.8184 (tpp) REVERT: C 268 MET cc_start: 0.8509 (mmp) cc_final: 0.8305 (mmp) REVERT: C 387 LEU cc_start: 0.9058 (mm) cc_final: 0.8513 (tp) REVERT: D 268 MET cc_start: 0.8465 (tpp) cc_final: 0.8181 (tpp) REVERT: D 501 SER cc_start: 0.8448 (t) cc_final: 0.8191 (p) REVERT: D 526 MET cc_start: 0.8014 (mmp) cc_final: 0.7304 (mtm) REVERT: D 601 PHE cc_start: 0.8364 (t80) cc_final: 0.8147 (t80) REVERT: D 686 MET cc_start: 0.8962 (tpp) cc_final: 0.8326 (tpp) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.2341 time to fit residues: 125.9596 Evaluate side-chains 260 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 17 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 7 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS D 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.106223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086818 restraints weight = 59676.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088790 restraints weight = 35649.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.090129 restraints weight = 25001.860| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18004 Z= 0.099 Angle : 0.561 7.628 24726 Z= 0.269 Chirality : 0.037 0.153 2930 Planarity : 0.003 0.036 3072 Dihedral : 5.070 56.955 2968 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 1.84 (0.18), residues: 2408 helix: 2.55 (0.13), residues: 1448 sheet: 0.46 (0.48), residues: 84 loop : -1.09 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 658 HIS 0.012 0.001 HIS D 436 PHE 0.028 0.001 PHE C 360 TYR 0.016 0.001 TYR A 453 ARG 0.005 0.000 ARG A 515 Details of bonding type rmsd hydrogen bonds : bond 0.03031 ( 1086) hydrogen bonds : angle 3.39940 ( 3204) covalent geometry : bond 0.00208 (18004) covalent geometry : angle 0.56089 (24726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8522 (tm-30) REVERT: A 268 MET cc_start: 0.8563 (mmp) cc_final: 0.8332 (mmp) REVERT: A 686 MET cc_start: 0.9308 (tmm) cc_final: 0.8390 (tpt) REVERT: B 217 CYS cc_start: 0.8902 (m) cc_final: 0.8440 (t) REVERT: B 526 MET cc_start: 0.7875 (mmp) cc_final: 0.7037 (mtm) REVERT: B 686 MET cc_start: 0.8645 (tpp) cc_final: 0.8104 (tpp) REVERT: C 268 MET cc_start: 0.8458 (mmp) cc_final: 0.8230 (mmp) REVERT: C 387 LEU cc_start: 0.9063 (mm) cc_final: 0.8544 (tp) REVERT: C 556 LEU cc_start: 0.8981 (pp) cc_final: 0.8272 (tp) REVERT: D 268 MET cc_start: 0.8443 (tpp) cc_final: 0.8202 (tpp) REVERT: D 402 MET cc_start: 0.7163 (tpp) cc_final: 0.5942 (tpp) REVERT: D 526 MET cc_start: 0.7957 (mmp) cc_final: 0.7231 (mtm) REVERT: D 597 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8444 (tm-30) REVERT: D 686 MET cc_start: 0.8906 (tpp) cc_final: 0.8292 (tpp) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.2338 time to fit residues: 130.1770 Evaluate side-chains 262 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 89 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.104562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.085358 restraints weight = 59848.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087305 restraints weight = 35681.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088606 restraints weight = 24894.916| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18004 Z= 0.136 Angle : 0.593 7.425 24726 Z= 0.287 Chirality : 0.038 0.192 2930 Planarity : 0.003 0.037 3072 Dihedral : 5.175 56.365 2968 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.18), residues: 2408 helix: 2.54 (0.13), residues: 1448 sheet: 0.39 (0.48), residues: 84 loop : -1.02 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 658 HIS 0.011 0.001 HIS B 436 PHE 0.032 0.001 PHE C 360 TYR 0.025 0.001 TYR D 627 ARG 0.004 0.000 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 1086) hydrogen bonds : angle 3.51491 ( 3204) covalent geometry : bond 0.00299 (18004) covalent geometry : angle 0.59299 (24726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8560 (tm-30) REVERT: A 268 MET cc_start: 0.8591 (mmp) cc_final: 0.8366 (mmp) REVERT: A 387 LEU cc_start: 0.9037 (mm) cc_final: 0.8619 (tp) REVERT: A 686 MET cc_start: 0.9308 (tmm) cc_final: 0.8378 (tpt) REVERT: B 217 CYS cc_start: 0.8890 (m) cc_final: 0.8494 (t) REVERT: B 402 MET cc_start: 0.7254 (tpp) cc_final: 0.6066 (tpp) REVERT: B 526 MET cc_start: 0.7875 (mmp) cc_final: 0.7029 (mtm) REVERT: B 630 LEU cc_start: 0.9295 (mm) cc_final: 0.9078 (mm) REVERT: B 686 MET cc_start: 0.8668 (tpp) cc_final: 0.8121 (tpp) REVERT: C 268 MET cc_start: 0.8548 (mmp) cc_final: 0.8333 (mmp) REVERT: C 387 LEU cc_start: 0.9058 (mm) cc_final: 0.8548 (tp) REVERT: C 556 LEU cc_start: 0.9012 (pp) cc_final: 0.8272 (tp) REVERT: D 268 MET cc_start: 0.8451 (tpp) cc_final: 0.8178 (tpp) REVERT: D 526 MET cc_start: 0.7941 (mmp) cc_final: 0.7170 (mtm) REVERT: D 686 MET cc_start: 0.8911 (tpp) cc_final: 0.8278 (tpp) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2472 time to fit residues: 134.5685 Evaluate side-chains 264 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.083435 restraints weight = 60293.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085347 restraints weight = 36178.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086617 restraints weight = 25448.097| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18004 Z= 0.185 Angle : 0.642 8.005 24726 Z= 0.316 Chirality : 0.039 0.155 2930 Planarity : 0.004 0.037 3072 Dihedral : 5.553 58.435 2968 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.18), residues: 2408 helix: 2.35 (0.13), residues: 1448 sheet: 0.10 (0.48), residues: 84 loop : -1.01 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 658 HIS 0.010 0.001 HIS B 436 PHE 0.019 0.002 PHE D 601 TYR 0.018 0.002 TYR D 206 ARG 0.005 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 1086) hydrogen bonds : angle 3.76617 ( 3204) covalent geometry : bond 0.00408 (18004) covalent geometry : angle 0.64238 (24726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5493.87 seconds wall clock time: 95 minutes 34.21 seconds (5734.21 seconds total)