Starting phenix.real_space_refine on Sat Sep 12 19:22:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oo5_20146/09_2026/6oo5_20146.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oo5_20146/09_2026/6oo5_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 { model { file = "/net/cci-nas-00/data/ceres_data/6oo5_20146/09_2026/6oo5_20146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oo5_20146/09_2026/6oo5_20146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oo5_20146/09_2026/6oo5_20146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oo5_20146/09_2026/6oo5_20146.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6oo5_20146/09_2026/6oo5_20146.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oo5_20146/09_2026/6oo5_20146.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ASP:plan': 16, 'ASN:plan1': 10, 'ARG:plan': 15, 'GLU:plan': 25, 'TYR:plan': 2, 'GLN:plan1': 10, 'PHE:plan': 3, 'HIS:plan': 2} 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: {'ASP:plan': 18, 'ARG:plan': 17, 'ASN:plan1': 12, 'GLU:plan': 28, 'GLN:plan1': 13, 'HIS:plan': 1, 'PHE:plan': 4} 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: {'ASP:plan': 16, 'ASN:plan1': 10, 'ARG:plan': 15, 'GLU:plan': 25, 'TYR:plan': 2, 'GLN:plan1': 10, 'PHE:plan': 3, 'HIS:plan': 2} 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: {'ASP:plan': 18, 'ARG:plan': 17, 'ASN:plan1': 12, 'GLU:plan': 28, 'GLN:plan1': 13, 'HIS:plan': 1, 'PHE:plan': 4} 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: 3.83, per 1000 atoms: 0.22 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: 1.68 Conformation dependent library (CDL) restraints added in 795.0 milliseconds 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: 0.45 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: 2.82 Time building geometry restraints manager: 2.23 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 - 15.73: 9890 15.73 - 31.45: 336 31.45 - 47.18: 36 47.18 - 62.91: 2 62.91 - 78.63: 12 Dihedral angle restraints: 10276 sinusoidal: 3148 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 10273 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: 0.04 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: 1.680 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.540 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 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 : 9.226 78.634 5668 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.001 ARG D 456 TYR 0.026 0.003 TYR B 159 PHE 0.034 0.003 PHE C 405 TRP 0.034 0.003 TRP B 349 HIS 0.007 0.002 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.01197 / 0.58 (18004) covalent geometry : angle 1.04701 / 0.54 (24726) hydrogen bonds : bond 0.12798 / 8.80 ( 1086) hydrogen bonds : angle 5.41301 / 3.83 ( 3204) *********************** 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 : 0.595 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: 0.7729 (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: 0.7618 (t80) 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: 0.8862 (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: 0.1175 time to fit residues: 91.9876 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 : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN A 368 HIS A 394 ASN B 154 GLN C 154 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 394 ASN D 154 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.103482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.084110 restraints weight = 60143.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.086061 restraints weight = 35844.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087380 restraints weight = 25062.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088231 restraints weight = 19635.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088796 restraints weight = 16673.223| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1852 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= 0.156 Angle : 0.621 8.234 24726 Z= 0.315 Chirality : 0.039 0.155 2930 Planarity : 0.004 0.045 3072 Dihedral : 6.211 69.450 2624 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2408 helix: 0.64 (0.13), residues: 1472 sheet: -0.39 (0.43), residues: 84 loop : -1.96 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 456 TYR 0.026 0.002 TYR C 542 PHE 0.043 0.002 PHE C 616 TRP 0.016 0.002 TRP C 507 HIS 0.006 0.001 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (18004) covalent geometry : angle 0.62128 / 0.32 (24726) hydrogen bonds : bond 0.04156 / 2.79 ( 1086) hydrogen bonds : angle 4.08412 / 2.90 ( 3204) *********************** 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 373 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.688 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: 0.8824 (tm-30) cc_final: 0.8581 (tm-30) REVERT: A 373 LEU cc_start: 0.8645 (mt) cc_final: 0.8427 (mm) REVERT: A 387 LEU cc_start: 0.8796 (mm) cc_final: 0.8282 (tp) REVERT: A 402 MET cc_start: 0.9066 (mmm) cc_final: 0.8600 (tpt) REVERT: A 523 TYR cc_start: 0.8831 (t80) cc_final: 0.8229 (t80) REVERT: B 402 MET cc_start: 0.7676 (mmm) cc_final: 0.7416 (tpp) REVERT: B 526 MET cc_start: 0.8097 (mmp) cc_final: 0.7489 (mtm) REVERT: B 643 MET cc_start: 0.8458 (mmm) cc_final: 0.7855 (tmm) REVERT: C 135 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8750 (tm-30) REVERT: C 402 MET cc_start: 0.9030 (mmm) cc_final: 0.8651 (tpt) REVERT: C 477 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8401 (tm-30) REVERT: C 523 TYR cc_start: 0.8568 (t80) cc_final: 0.8366 (t80) REVERT: D 120 MET cc_start: 0.8528 (mmm) cc_final: 0.8323 (mmm) REVERT: D 213 SER cc_start: 0.9224 (m) cc_final: 0.8909 (p) REVERT: D 214 LEU cc_start: 0.9386 (tp) cc_final: 0.9024 (tp) REVERT: D 268 MET cc_start: 0.8486 (tpp) cc_final: 0.8224 (tpp) REVERT: D 501 SER cc_start: 0.8551 (t) cc_final: 0.8305 (p) REVERT: D 538 PHE cc_start: 0.8338 (t80) cc_final: 0.8101 (t80) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.1127 time to fit residues: 67.0111 Evaluate side-chains 281 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 215 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 77 optimal weight: 0.0370 chunk 56 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.104685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.085336 restraints weight = 59821.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087300 restraints weight = 35561.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088617 restraints weight = 24893.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089512 restraints weight = 19472.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090141 restraints weight = 16451.469| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18004 Z= 0.122 Angle : 0.559 7.865 24726 Z= 0.281 Chirality : 0.037 0.157 2930 Planarity : 0.003 0.037 3072 Dihedral : 5.729 61.147 2624 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.17), residues: 2408 helix: 1.46 (0.13), residues: 1476 sheet: -0.22 (0.44), residues: 84 loop : -1.67 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 457 TYR 0.018 0.001 TYR C 542 PHE 0.026 0.002 PHE C 454 TRP 0.015 0.001 TRP A 331 HIS 0.005 0.001 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (18004) covalent geometry : angle 0.55949 / 0.28 (24726) hydrogen bonds : bond 0.03642 / 2.44 ( 1086) hydrogen bonds : angle 3.77453 / 2.67 ( 3204) *********************** 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 371 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8498 (tm-30) REVERT: A 360 PHE cc_start: 0.8563 (m-10) cc_final: 0.8285 (m-10) REVERT: B 597 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 627 TYR cc_start: 0.9166 (t80) cc_final: 0.8954 (t80) REVERT: B 686 MET cc_start: 0.8797 (tpp) cc_final: 0.8240 (tpp) REVERT: C 135 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8689 (tm-30) REVERT: C 360 PHE cc_start: 0.8727 (m-80) cc_final: 0.8517 (m-80) REVERT: C 370 MET cc_start: 0.9337 (mtm) cc_final: 0.9116 (mtt) REVERT: C 387 LEU cc_start: 0.8996 (mm) cc_final: 0.8298 (tp) REVERT: C 523 TYR cc_start: 0.8471 (t80) cc_final: 0.8027 (t80) REVERT: D 268 MET cc_start: 0.8495 (tpp) cc_final: 0.8224 (tpp) REVERT: D 402 MET cc_start: 0.7384 (tpp) cc_final: 0.6320 (tpp) REVERT: D 501 SER cc_start: 0.8489 (t) cc_final: 0.8252 (p) REVERT: D 526 MET cc_start: 0.8119 (mmp) cc_final: 0.7549 (mtm) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.1116 time to fit residues: 66.6193 Evaluate side-chains 278 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 243 optimal weight: 20.0000 chunk 172 optimal weight: 0.1980 chunk 143 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 3 optimal weight: 0.0670 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.104865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085645 restraints weight = 59896.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087616 restraints weight = 35566.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088938 restraints weight = 24889.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089798 restraints weight = 19457.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090444 restraints weight = 16464.693| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18004 Z= 0.109 Angle : 0.543 7.496 24726 Z= 0.271 Chirality : 0.037 0.177 2930 Planarity : 0.003 0.036 3072 Dihedral : 5.488 59.405 2624 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2408 helix: 1.88 (0.13), residues: 1476 sheet: 0.07 (0.46), residues: 84 loop : -1.54 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 161 TYR 0.017 0.001 TYR A 542 PHE 0.037 0.002 PHE B 601 TRP 0.017 0.001 TRP A 331 HIS 0.010 0.001 HIS D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (18004) covalent geometry : angle 0.54314 / 0.27 (24726) hydrogen bonds : bond 0.03384 / 2.25 ( 1086) hydrogen bonds : angle 3.62276 / 2.56 ( 3204) *********************** 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 352 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8515 (tm-30) REVERT: A 268 MET cc_start: 0.8516 (mmp) cc_final: 0.8301 (mmp) REVERT: A 387 LEU cc_start: 0.8867 (mm) cc_final: 0.8446 (tp) REVERT: A 523 TYR cc_start: 0.8816 (t80) cc_final: 0.8219 (t80) REVERT: A 686 MET cc_start: 0.9148 (tmm) cc_final: 0.8317 (tpt) REVERT: B 526 MET cc_start: 0.8045 (mmp) cc_final: 0.7397 (mtm) REVERT: B 627 TYR cc_start: 0.9199 (t80) cc_final: 0.8970 (t80) REVERT: B 686 MET cc_start: 0.8736 (tpp) cc_final: 0.8194 (tpp) REVERT: C 135 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8627 (tm-30) REVERT: C 387 LEU cc_start: 0.8985 (mm) cc_final: 0.8324 (tp) REVERT: C 523 TYR cc_start: 0.8410 (t80) cc_final: 0.7892 (t80) REVERT: D 268 MET cc_start: 0.8495 (tpp) cc_final: 0.8227 (tpp) REVERT: D 402 MET cc_start: 0.7379 (tpp) cc_final: 0.6411 (tpp) REVERT: D 501 SER cc_start: 0.8537 (t) cc_final: 0.8287 (p) REVERT: D 686 MET cc_start: 0.9002 (tpp) cc_final: 0.8349 (tpp) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1048 time to fit residues: 59.9033 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 : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 181 optimal weight: 0.0070 chunk 111 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 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 = 0.3610 r_free = 0.3610 target = 0.105722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086482 restraints weight = 59344.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088467 restraints weight = 35106.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.089803 restraints weight = 24543.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090667 restraints weight = 19173.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091320 restraints weight = 16224.590| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18004 Z= 0.103 Angle : 0.532 7.165 24726 Z= 0.262 Chirality : 0.037 0.180 2930 Planarity : 0.003 0.038 3072 Dihedral : 5.252 59.255 2624 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.17), residues: 2408 helix: 2.10 (0.13), residues: 1472 sheet: 0.34 (0.47), residues: 84 loop : -1.47 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 456 TYR 0.019 0.001 TYR A 523 PHE 0.030 0.001 PHE B 360 TRP 0.018 0.001 TRP A 331 HIS 0.012 0.001 HIS B 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (18004) covalent geometry : angle 0.53159 / 0.26 (24726) hydrogen bonds : bond 0.03268 / 2.18 ( 1086) hydrogen bonds : angle 3.48173 / 2.44 ( 3204) *********************** 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 359 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8504 (mtt) cc_final: 0.8194 (mtm) REVERT: A 135 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 268 MET cc_start: 0.8550 (mmp) cc_final: 0.8329 (mmp) REVERT: A 387 LEU cc_start: 0.8901 (mm) cc_final: 0.8442 (tp) REVERT: B 170 ILE cc_start: 0.9223 (mt) cc_final: 0.9023 (tt) REVERT: B 627 TYR cc_start: 0.9158 (t80) cc_final: 0.8940 (t80) REVERT: B 686 MET cc_start: 0.8712 (tpp) cc_final: 0.8189 (tpp) REVERT: C 135 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8628 (tm-30) REVERT: C 387 LEU cc_start: 0.8981 (mm) cc_final: 0.8417 (tp) REVERT: C 523 TYR cc_start: 0.8468 (t80) cc_final: 0.7835 (t80) REVERT: D 268 MET cc_start: 0.8485 (tpp) cc_final: 0.8218 (tpp) REVERT: D 501 SER cc_start: 0.8431 (t) cc_final: 0.8137 (p) REVERT: D 526 MET cc_start: 0.8134 (mmp) cc_final: 0.7547 (mtm) REVERT: D 601 PHE cc_start: 0.8263 (t80) cc_final: 0.7998 (t80) REVERT: D 605 MET cc_start: 0.4513 (mpp) cc_final: 0.4021 (mmm) REVERT: D 686 MET cc_start: 0.8971 (tpp) cc_final: 0.8307 (tpp) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.1015 time to fit residues: 59.3166 Evaluate side-chains 289 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 22 optimal weight: 0.0980 chunk 204 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 206 optimal weight: 0.6980 chunk 181 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3604 r_free = 0.3604 target = 0.105581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086459 restraints weight = 59389.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088440 restraints weight = 35133.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089758 restraints weight = 24541.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090670 restraints weight = 19152.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091234 restraints weight = 16101.965| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18004 Z= 0.104 Angle : 0.538 8.637 24726 Z= 0.262 Chirality : 0.037 0.159 2930 Planarity : 0.003 0.036 3072 Dihedral : 5.109 59.611 2624 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.17), residues: 2408 helix: 2.26 (0.13), residues: 1472 sheet: 0.39 (0.47), residues: 84 loop : -1.35 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 161 TYR 0.013 0.001 TYR A 453 PHE 0.022 0.001 PHE B 454 TRP 0.023 0.001 TRP A 331 HIS 0.011 0.001 HIS B 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (18004) covalent geometry : angle 0.53811 / 0.26 (24726) hydrogen bonds : bond 0.03124 / 2.09 ( 1086) hydrogen bonds : angle 3.42605 / 2.40 ( 3204) *********************** 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 350 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8506 (tm-30) REVERT: A 387 LEU cc_start: 0.8949 (mm) cc_final: 0.8495 (tp) REVERT: A 686 MET cc_start: 0.9182 (tmm) cc_final: 0.8296 (tpt) REVERT: B 120 MET cc_start: 0.8453 (mmm) cc_final: 0.8203 (mmt) REVERT: B 170 ILE cc_start: 0.9239 (mt) cc_final: 0.9023 (tt) REVERT: B 526 MET cc_start: 0.8126 (mmp) cc_final: 0.7559 (mtm) REVERT: B 627 TYR cc_start: 0.9135 (t80) cc_final: 0.8919 (t80) REVERT: B 686 MET cc_start: 0.8672 (tpp) cc_final: 0.8154 (tpp) REVERT: C 135 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8633 (tm-30) REVERT: C 302 LYS cc_start: 0.9337 (tttm) cc_final: 0.9102 (ttmm) REVERT: C 387 LEU cc_start: 0.9045 (mm) cc_final: 0.8563 (tp) REVERT: C 523 TYR cc_start: 0.8435 (t80) cc_final: 0.7841 (t80) REVERT: D 268 MET cc_start: 0.8494 (tpp) cc_final: 0.8255 (tpp) REVERT: D 501 SER cc_start: 0.8457 (t) cc_final: 0.8145 (p) REVERT: D 526 MET cc_start: 0.8163 (mmp) cc_final: 0.7473 (mtm) REVERT: D 601 PHE cc_start: 0.8208 (t80) cc_final: 0.8000 (t80) REVERT: D 686 MET cc_start: 0.8974 (tpp) cc_final: 0.8293 (tpp) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.1027 time to fit residues: 59.5161 Evaluate side-chains 281 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 240 optimal weight: 0.0170 chunk 147 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 79 optimal weight: 0.0470 chunk 241 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS B 661 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.106972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087606 restraints weight = 59420.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089599 restraints weight = 35476.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090867 restraints weight = 24805.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091836 restraints weight = 19559.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092411 restraints weight = 16433.377| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18004 Z= 0.098 Angle : 0.539 8.557 24726 Z= 0.261 Chirality : 0.037 0.158 2930 Planarity : 0.003 0.037 3072 Dihedral : 4.914 59.914 2624 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.07 % Allowed : 1.03 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.17), residues: 2408 helix: 2.34 (0.13), residues: 1476 sheet: 0.54 (0.47), residues: 84 loop : -1.29 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 692 TYR 0.020 0.001 TYR A 523 PHE 0.025 0.001 PHE B 360 TRP 0.025 0.001 TRP A 331 HIS 0.011 0.001 HIS B 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (18004) covalent geometry : angle 0.53927 / 0.26 (24726) hydrogen bonds : bond 0.03035 / 2.03 ( 1086) hydrogen bonds : angle 3.34125 / 2.34 ( 3204) *********************** 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 358 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.564 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: 0.8816 (tm-30) cc_final: 0.8483 (tm-30) REVERT: A 268 MET cc_start: 0.8490 (mmp) cc_final: 0.8284 (mmp) REVERT: A 686 MET cc_start: 0.9251 (tmm) cc_final: 0.8334 (tpt) REVERT: B 120 MET cc_start: 0.8402 (mmm) cc_final: 0.8164 (mmt) REVERT: B 661 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8714 (tp-100) REVERT: B 686 MET cc_start: 0.8638 (tpp) cc_final: 0.8149 (tpp) REVERT: C 135 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8617 (tm-30) REVERT: C 302 LYS cc_start: 0.9307 (tttm) cc_final: 0.9072 (ttmm) REVERT: C 387 LEU cc_start: 0.9106 (mm) cc_final: 0.8546 (tp) REVERT: C 392 CYS cc_start: 0.8505 (m) cc_final: 0.8294 (m) REVERT: C 402 MET cc_start: 0.8563 (tpp) cc_final: 0.8248 (tpp) REVERT: C 523 TYR cc_start: 0.8384 (t80) cc_final: 0.7763 (t80) REVERT: D 268 MET cc_start: 0.8499 (tpp) cc_final: 0.8250 (tpp) REVERT: D 501 SER cc_start: 0.8397 (t) cc_final: 0.8101 (p) REVERT: D 605 MET cc_start: 0.4668 (mpp) cc_final: 0.4315 (mmm) REVERT: D 686 MET cc_start: 0.8976 (tpp) cc_final: 0.8285 (tpp) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.0966 time to fit residues: 57.9211 Evaluate side-chains 291 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 27 optimal weight: 0.0070 chunk 26 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 211 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS B 637 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS D 637 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086640 restraints weight = 60299.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.088605 restraints weight = 36004.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089917 restraints weight = 25223.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090839 restraints weight = 19803.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.091460 restraints weight = 16687.977| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3458 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= 0.111 Angle : 0.553 7.625 24726 Z= 0.267 Chirality : 0.037 0.165 2930 Planarity : 0.003 0.035 3072 Dihedral : 4.808 59.391 2624 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.18), residues: 2408 helix: 2.55 (0.13), residues: 1452 sheet: 0.57 (0.48), residues: 84 loop : -1.20 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.015 0.001 TYR B 632 PHE 0.023 0.001 PHE D 454 TRP 0.027 0.001 TRP B 658 HIS 0.011 0.001 HIS B 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (18004) covalent geometry : angle 0.55254 / 0.27 (24726) hydrogen bonds : bond 0.03079 / 2.07 ( 1086) hydrogen bonds : angle 3.33478 / 2.35 ( 3204) *********************** 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 349 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8509 (tm-30) REVERT: A 268 MET cc_start: 0.8491 (mmp) cc_final: 0.8286 (mmp) REVERT: A 686 MET cc_start: 0.9302 (tmm) cc_final: 0.8409 (tpt) REVERT: B 120 MET cc_start: 0.8377 (mmm) cc_final: 0.8104 (mmt) REVERT: B 630 LEU cc_start: 0.9252 (mm) cc_final: 0.9045 (mm) REVERT: B 686 MET cc_start: 0.8634 (tpp) cc_final: 0.8130 (tpp) REVERT: C 135 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8634 (tm-30) REVERT: C 302 LYS cc_start: 0.9357 (tttm) cc_final: 0.9092 (ttmm) REVERT: C 387 LEU cc_start: 0.9064 (mm) cc_final: 0.8548 (tp) REVERT: C 392 CYS cc_start: 0.8503 (m) cc_final: 0.8286 (m) REVERT: C 523 TYR cc_start: 0.8314 (t80) cc_final: 0.7753 (t80) REVERT: C 686 MET cc_start: 0.9284 (tpp) cc_final: 0.9080 (tpp) REVERT: D 268 MET cc_start: 0.8488 (tpp) cc_final: 0.8241 (tpp) REVERT: D 501 SER cc_start: 0.8361 (t) cc_final: 0.8086 (p) REVERT: D 526 MET cc_start: 0.7998 (mmp) cc_final: 0.7337 (mtm) REVERT: D 597 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8408 (tm-30) REVERT: D 605 MET cc_start: 0.4421 (mpp) cc_final: 0.4187 (mmm) REVERT: D 686 MET cc_start: 0.8977 (tpp) cc_final: 0.8365 (tpp) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.0978 time to fit residues: 57.0756 Evaluate side-chains 278 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 175 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 156 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 170 optimal weight: 0.0670 chunk 73 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS B 661 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS D 637 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.107304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088067 restraints weight = 59123.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090091 restraints weight = 34960.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091417 restraints weight = 24338.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092361 restraints weight = 18984.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092939 restraints weight = 15890.499| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18004 Z= 0.098 Angle : 0.551 7.443 24726 Z= 0.265 Chirality : 0.038 0.208 2930 Planarity : 0.003 0.037 3072 Dihedral : 4.722 59.954 2624 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.18), residues: 2408 helix: 2.51 (0.14), residues: 1472 sheet: 0.62 (0.48), residues: 84 loop : -1.15 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 692 TYR 0.018 0.001 TYR C 453 PHE 0.031 0.001 PHE B 360 TRP 0.028 0.001 TRP A 331 HIS 0.012 0.001 HIS B 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (18004) covalent geometry : angle 0.55129 / 0.26 (24726) hydrogen bonds : bond 0.02987 / 1.99 ( 1086) hydrogen bonds : angle 3.29219 / 2.31 ( 3204) *********************** 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 362 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8461 (tm-30) REVERT: A 268 MET cc_start: 0.8479 (mmp) cc_final: 0.8272 (mmp) REVERT: A 686 MET cc_start: 0.9304 (tmm) cc_final: 0.8284 (tpp) REVERT: B 120 MET cc_start: 0.8365 (mmm) cc_final: 0.8053 (mmt) REVERT: B 630 LEU cc_start: 0.9173 (mm) cc_final: 0.8964 (mm) REVERT: B 686 MET cc_start: 0.8627 (tpp) cc_final: 0.8144 (tpp) REVERT: C 135 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8626 (tm-30) REVERT: C 302 LYS cc_start: 0.9316 (tttm) cc_final: 0.9070 (ttmm) REVERT: C 387 LEU cc_start: 0.9043 (mm) cc_final: 0.8537 (tp) REVERT: C 392 CYS cc_start: 0.8491 (m) cc_final: 0.8273 (m) REVERT: C 523 TYR cc_start: 0.8411 (t80) cc_final: 0.7805 (t80) REVERT: C 686 MET cc_start: 0.9277 (tpp) cc_final: 0.9060 (tpp) REVERT: D 268 MET cc_start: 0.8491 (tpp) cc_final: 0.8256 (tpp) REVERT: D 402 MET cc_start: 0.7036 (tpp) cc_final: 0.5815 (tpp) REVERT: D 526 MET cc_start: 0.8009 (mmp) cc_final: 0.7236 (mtm) REVERT: D 686 MET cc_start: 0.8954 (tpp) cc_final: 0.8351 (tpp) outliers start: 1 outliers final: 1 residues processed: 362 average time/residue: 0.0968 time to fit residues: 58.5909 Evaluate side-chains 288 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 233 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 90 optimal weight: 0.0060 chunk 203 optimal weight: 0.0980 chunk 188 optimal weight: 0.0010 chunk 164 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS B 637 ASN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.107740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088469 restraints weight = 59354.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090489 restraints weight = 35021.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091855 restraints weight = 24400.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092777 restraints weight = 18960.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093406 restraints weight = 15906.634| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18004 Z= 0.096 Angle : 0.553 8.000 24726 Z= 0.261 Chirality : 0.037 0.159 2930 Planarity : 0.003 0.036 3072 Dihedral : 4.598 57.042 2624 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.18), residues: 2408 helix: 2.64 (0.14), residues: 1448 sheet: 0.60 (0.49), residues: 84 loop : -1.10 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 692 TYR 0.015 0.001 TYR A 453 PHE 0.024 0.001 PHE D 454 TRP 0.040 0.001 TRP B 658 HIS 0.012 0.000 HIS B 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 (18004) covalent geometry : angle 0.55334 / 0.26 (24726) hydrogen bonds : bond 0.02879 / 1.94 ( 1086) hydrogen bonds : angle 3.29343 / 2.33 ( 3204) ********************** 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 359 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.681 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: 0.8789 (tm-30) cc_final: 0.8467 (tm-30) REVERT: A 268 MET cc_start: 0.8464 (mmp) cc_final: 0.8257 (mmp) REVERT: A 686 MET cc_start: 0.9321 (tmm) cc_final: 0.8328 (tpp) REVERT: B 120 MET cc_start: 0.8301 (mmm) cc_final: 0.8015 (mmt) REVERT: B 630 LEU cc_start: 0.9116 (mm) cc_final: 0.8808 (mm) REVERT: B 686 MET cc_start: 0.8615 (tpp) cc_final: 0.8114 (tpp) REVERT: C 135 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8627 (tm-30) REVERT: C 302 LYS cc_start: 0.9313 (tttm) cc_final: 0.9061 (ttmm) REVERT: C 387 LEU cc_start: 0.9118 (mm) cc_final: 0.8637 (tp) REVERT: C 392 CYS cc_start: 0.8460 (m) cc_final: 0.8237 (m) REVERT: C 485 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7290 (pt0) REVERT: C 523 TYR cc_start: 0.8339 (t80) cc_final: 0.7677 (t80) REVERT: C 686 MET cc_start: 0.9270 (tpp) cc_final: 0.9060 (tpp) REVERT: D 268 MET cc_start: 0.8508 (tpp) cc_final: 0.8271 (tpp) REVERT: D 402 MET cc_start: 0.7029 (tpp) cc_final: 0.5892 (tpp) REVERT: D 501 SER cc_start: 0.8497 (t) cc_final: 0.8226 (p) REVERT: D 526 MET cc_start: 0.8019 (mmp) cc_final: 0.7245 (mtm) REVERT: D 686 MET cc_start: 0.8934 (tpp) cc_final: 0.8339 (tpp) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.0997 time to fit residues: 59.1274 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 : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 45 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 HIS B 245 ASN B 637 ASN B 661 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS D 232 HIS ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.102175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.082530 restraints weight = 59961.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084413 restraints weight = 35881.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.085680 restraints weight = 25302.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.086567 restraints weight = 19941.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.087161 restraints weight = 16846.196| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18004 Z= 0.199 Angle : 0.651 7.766 24726 Z= 0.322 Chirality : 0.040 0.147 2930 Planarity : 0.004 0.042 3072 Dihedral : 4.907 58.989 2624 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.18), residues: 2408 helix: 2.37 (0.13), residues: 1448 sheet: 0.31 (0.49), residues: 84 loop : -1.04 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 700 TYR 0.019 0.002 TYR D 206 PHE 0.023 0.002 PHE D 454 TRP 0.038 0.002 TRP B 658 HIS 0.006 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (18004) covalent geometry : angle 0.65100 / 0.32 (24726) hydrogen bonds : bond 0.03682 / 2.50 ( 1086) hydrogen bonds : angle 3.66124 / 2.60 ( 3204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.55 seconds wall clock time: 48 minutes 25.66 seconds (2905.66 seconds total)