Starting phenix.real_space_refine on Sat Sep 12 20:53:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oo3_20143/09_2026/6oo3_20143.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oo3_20143/09_2026/6oo3_20143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6oo3_20143/09_2026/6oo3_20143.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oo3_20143/09_2026/6oo3_20143.cif" model { file = "/net/cci-nas-00/data/ceres_data/6oo3_20143/09_2026/6oo3_20143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oo3_20143/09_2026/6oo3_20143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oo3_20143/09_2026/6oo3_20143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oo3_20143/09_2026/6oo3_20143.map" } resolution = 2.9 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= 0.015 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 112 5.16 5 C 12028 2.51 5 N 3060 2.21 5 O 3036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s 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: 18236 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4513 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 8, 'ARG:plan': 9, 'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 215 Chain: "B" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4513 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 8, 'ARG:plan': 9, 'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 215 Chain: "C" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4513 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 8, 'ARG:plan': 9, 'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 215 Chain: "D" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4513 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 8, 'ARG:plan': 9, 'GLU:plan': 20, 'GLN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 215 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: 3.93, per 1000 atoms: 0.22 Number of scatterers: 18236 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 112 16.00 O 3036 8.00 N 3060 7.00 C 12028 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: 1.44 Conformation dependent library (CDL) restraints added in 686.7 milliseconds 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 4 sheets defined 66.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.679A pdb=" N ASP A 89 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.613A pdb=" N ARG A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.669A pdb=" N SER A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.588A pdb=" N ASN A 152 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 258 through 280 removed outlier: 3.587A pdb=" N ARG A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.525A pdb=" N GLY A 287 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 288 " --> pdb=" O LEU A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 288' Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.506A pdb=" N GLN A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 325 removed outlier: 3.834A pdb=" N GLN A 322 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER A 323 " --> pdb=" O PRO A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.912A pdb=" N VAL A 372 " --> pdb=" O HIS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 removed outlier: 4.320A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 411 removed outlier: 3.628A pdb=" N HIS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 455 Processing helix chain 'A' and resid 470 through 490 Processing helix chain 'A' and resid 494 through 510 removed outlier: 4.499A pdb=" N LEU A 498 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.614A pdb=" N THR A 514 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 515 " --> pdb=" O TYR A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 558 removed outlier: 3.965A pdb=" N TYR A 523 " --> pdb=" O HIS A 519 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 549 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.678A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 648 removed outlier: 3.735A pdb=" N VAL A 620 " --> pdb=" O PHE A 616 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 672 removed outlier: 4.278A pdb=" N TRP A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.643A 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 86 through 90 removed outlier: 3.677A pdb=" N ASP B 89 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.608A pdb=" N ARG B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 133 through 144 removed outlier: 3.652A pdb=" N SER B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.586A pdb=" N ASN B 152 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 220 through 229 Processing helix chain 'B' and resid 246 through 254 Processing helix chain 'B' and resid 258 through 280 removed outlier: 3.640A pdb=" N ARG B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.526A pdb=" N GLY B 287 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE B 288 " --> pdb=" O LEU B 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 284 through 288' Processing helix chain 'B' and resid 295 through 304 Processing helix chain 'B' and resid 305 through 314 removed outlier: 3.520A pdb=" N GLN B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 removed outlier: 3.833A pdb=" N GLN B 322 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N SER B 323 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.939A pdb=" N VAL B 372 " --> pdb=" O HIS B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 removed outlier: 4.315A pdb=" N LYS B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 411 removed outlier: 3.624A pdb=" N HIS B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 455 Processing helix chain 'B' and resid 470 through 490 Processing helix chain 'B' and resid 494 through 510 removed outlier: 4.491A pdb=" N LEU B 498 " --> pdb=" O TRP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 removed outlier: 3.640A pdb=" N THR B 514 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 515 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 516 " --> pdb=" O TYR B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 516' Processing helix chain 'B' and resid 517 through 558 removed outlier: 3.985A pdb=" N TYR B 523 " --> pdb=" O HIS B 519 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG B 537 " --> pdb=" O ARG B 533 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B 538 " --> pdb=" O ASP B 534 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 549 " --> pdb=" O PHE B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 removed outlier: 3.750A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE B 601 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 648 removed outlier: 3.728A pdb=" N VAL B 620 " --> pdb=" O PHE B 616 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 672 removed outlier: 4.306A pdb=" N TRP B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 672 " --> pdb=" O GLU B 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 85 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.676A pdb=" N ASP C 89 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.598A pdb=" N ARG C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 133 through 144 removed outlier: 3.661A pdb=" N SER C 144 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.600A pdb=" N ASN C 152 " --> pdb=" O PRO C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 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 Processing helix chain 'C' and resid 246 through 254 Processing helix chain 'C' and resid 258 through 280 removed outlier: 3.671A pdb=" N ARG C 267 " --> pdb=" O ALA C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.516A pdb=" N GLY C 287 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 288 " --> pdb=" O LEU C 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 288' Processing helix chain 'C' and resid 295 through 304 Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.512A pdb=" N GLN C 314 " --> pdb=" O LYS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 325 removed outlier: 3.838A pdb=" N GLN C 322 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER C 323 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.970A pdb=" N VAL C 372 " --> pdb=" O HIS C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 387 removed outlier: 4.317A pdb=" N LYS C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 411 removed outlier: 3.621A pdb=" N HIS C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 455 Processing helix chain 'C' and resid 470 through 490 Processing helix chain 'C' and resid 494 through 510 removed outlier: 4.501A pdb=" N LEU C 498 " --> pdb=" O TRP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.647A pdb=" N THR C 514 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 515 " --> pdb=" O TYR C 512 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 516 " --> pdb=" O TYR C 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 511 through 516' Processing helix chain 'C' and resid 517 through 558 removed outlier: 3.961A pdb=" N TYR C 523 " --> pdb=" O HIS C 519 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG C 537 " --> pdb=" O ARG C 533 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 548 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.795A pdb=" N LEU C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C 601 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 648 removed outlier: 3.716A pdb=" N VAL C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 672 removed outlier: 4.312A pdb=" N TRP C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) removed outlier: 3.632A 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 86 through 90 removed outlier: 3.678A pdb=" N ASP D 89 " --> pdb=" O ASN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.596A pdb=" N ARG D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 125 Processing helix chain 'D' and resid 133 through 144 removed outlier: 3.648A pdb=" N SER D 144 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.600A pdb=" N ASN D 152 " --> pdb=" O PRO D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 194 through 198 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'D' and resid 220 through 229 Processing helix chain 'D' and resid 246 through 254 Processing helix chain 'D' and resid 258 through 280 removed outlier: 3.617A pdb=" N ARG D 267 " --> pdb=" O ALA D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.514A pdb=" N GLY D 287 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 284 through 288' Processing helix chain 'D' and resid 295 through 304 Processing helix chain 'D' and resid 305 through 314 removed outlier: 3.509A pdb=" N GLN D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 removed outlier: 3.837A pdb=" N GLN D 322 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER D 323 " --> pdb=" O PRO D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.949A pdb=" N VAL D 372 " --> pdb=" O HIS D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 387 removed outlier: 4.337A pdb=" N LYS D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 411 removed outlier: 3.632A pdb=" N HIS D 411 " --> pdb=" O ALA D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 455 Processing helix chain 'D' and resid 470 through 490 Processing helix chain 'D' and resid 494 through 510 removed outlier: 4.512A pdb=" N LEU D 498 " --> pdb=" O TRP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 516 removed outlier: 3.626A pdb=" N THR D 514 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG D 515 " --> pdb=" O TYR D 512 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY D 516 " --> pdb=" O TYR D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 511 through 516' Processing helix chain 'D' and resid 517 through 558 removed outlier: 3.959A pdb=" N TYR D 523 " --> pdb=" O HIS D 519 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG D 537 " --> pdb=" O ARG D 533 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D 538 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 548 " --> pdb=" O VAL D 544 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D 549 " --> pdb=" O PHE D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 604 removed outlier: 3.796A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE D 601 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 648 removed outlier: 3.728A pdb=" N VAL D 620 " --> pdb=" O PHE D 616 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 672 removed outlier: 4.282A pdb=" N TRP D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 672 " --> pdb=" O GLU D 668 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 333 removed outlier: 6.923A pdb=" N VAL A 338 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N CYS A 332 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A 336 " --> pdb=" O CYS A 332 " (cutoff:3.500A) removed outlier: 6.935A 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: 6.903A pdb=" N VAL B 338 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N CYS B 332 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 336 " --> pdb=" O CYS B 332 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP B 698 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 327 through 333 removed outlier: 6.905A pdb=" N VAL C 338 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N CYS C 332 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL C 336 " --> pdb=" O CYS C 332 " (cutoff:3.500A) removed outlier: 6.942A 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: 6.918A pdb=" N VAL D 338 " --> pdb=" O GLU D 330 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N CYS D 332 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL D 336 " --> pdb=" O CYS D 332 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASP D 698 " --> pdb=" O VAL D 689 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 3162 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: 2.99 Time building geometry restraints manager: 1.96 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: 2752 1.29 - 1.42: 5121 1.42 - 1.55: 10622 1.55 - 1.69: 45 1.69 - 1.82: 168 Bond restraints: 18708 Sorted by residual: bond pdb=" CAJ 6EU C1001 " pdb=" OAA 6EU C1001 " ideal model delta sigma weight residual 1.439 1.764 -0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" CAJ 6EU A1001 " pdb=" OAA 6EU A1001 " ideal model delta sigma weight residual 1.439 1.764 -0.325 2.00e-02 2.50e+03 2.63e+02 bond pdb=" CAJ 6EU D1001 " pdb=" OAA 6EU D1001 " ideal model delta sigma weight residual 1.439 1.763 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" CAJ 6EU B1001 " pdb=" OAA 6EU B1001 " ideal model delta sigma weight residual 1.439 1.763 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" CAS 6EU D1001 " pdb=" CAX 6EU D1001 " ideal model delta sigma weight residual 1.334 1.587 -0.253 2.00e-02 2.50e+03 1.60e+02 ... (remaining 18703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 24998 3.51 - 7.02: 498 7.02 - 10.53: 80 10.53 - 14.04: 4 14.04 - 17.55: 4 Bond angle restraints: 25584 Sorted by residual: angle pdb=" N ILE C 306 " pdb=" CA ILE C 306 " pdb=" C ILE C 306 " ideal model delta sigma weight residual 110.72 120.99 -10.27 1.01e+00 9.80e-01 1.03e+02 angle pdb=" N ILE B 306 " pdb=" CA ILE B 306 " pdb=" C ILE B 306 " ideal model delta sigma weight residual 110.72 120.80 -10.08 1.01e+00 9.80e-01 9.96e+01 angle pdb=" N ILE D 306 " pdb=" CA ILE D 306 " pdb=" C ILE D 306 " ideal model delta sigma weight residual 110.72 120.76 -10.04 1.01e+00 9.80e-01 9.88e+01 angle pdb=" N ILE A 306 " pdb=" CA ILE A 306 " pdb=" C ILE A 306 " ideal model delta sigma weight residual 110.72 119.31 -8.59 1.01e+00 9.80e-01 7.24e+01 angle pdb=" N PRO B 413 " pdb=" CA PRO B 413 " pdb=" CB PRO B 413 " ideal model delta sigma weight residual 103.00 110.52 -7.52 1.10e+00 8.26e-01 4.67e+01 ... (remaining 25579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 10241 15.91 - 31.81: 468 31.81 - 47.72: 67 47.72 - 63.63: 0 63.63 - 79.54: 12 Dihedral angle restraints: 10788 sinusoidal: 3764 harmonic: 7024 Sorted by residual: dihedral pdb=" CA GLN C 198 " pdb=" C GLN C 198 " pdb=" N LYS C 199 " pdb=" CA LYS C 199 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA GLN B 198 " pdb=" C GLN B 198 " pdb=" N LYS B 199 " pdb=" CA LYS B 199 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLN D 198 " pdb=" C GLN D 198 " pdb=" N LYS D 199 " pdb=" CA LYS D 199 " ideal model delta harmonic sigma weight residual 180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 10785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2539 0.082 - 0.163: 405 0.163 - 0.245: 31 0.245 - 0.326: 9 0.326 - 0.408: 12 Chirality restraints: 2996 Sorted by residual: chirality pdb=" CAM 6EU D1001 " pdb=" CAL 6EU D1001 " pdb=" CAP 6EU D1001 " pdb=" CAV 6EU D1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.91 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CAM 6EU C1001 " pdb=" CAL 6EU C1001 " pdb=" CAP 6EU C1001 " pdb=" CAV 6EU C1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.90 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CAM 6EU A1001 " pdb=" CAL 6EU A1001 " pdb=" CAP 6EU A1001 " pdb=" CAV 6EU A1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.90 0.40 2.00e-01 2.50e+01 4.10e+00 ... (remaining 2993 not shown) Planarity restraints: 3140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 160 " 0.025 2.00e-02 2.50e+03 1.86e-02 6.92e+00 pdb=" CG TYR D 160 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 160 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 160 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 160 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 160 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 160 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 160 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 160 " -0.023 2.00e-02 2.50e+03 1.78e-02 6.32e+00 pdb=" CG TYR B 160 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 160 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 160 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 160 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 160 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 160 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 160 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 160 " 0.023 2.00e-02 2.50e+03 1.76e-02 6.16e+00 pdb=" CG TYR C 160 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR C 160 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 160 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 160 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 160 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 160 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 160 " 0.004 2.00e-02 2.50e+03 ... (remaining 3137 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.98: 7395 2.98 - 3.46: 17783 3.46 - 3.94: 28441 3.94 - 4.42: 31519 4.42 - 4.90: 54248 Nonbonded interactions: 139386 Sorted by model distance: nonbonded pdb=" CAS 6EU D1001 " pdb=" OAB 6EU D1001 " model vdw 2.495 2.672 nonbonded pdb=" CAS 6EU A1001 " pdb=" OAB 6EU A1001 " model vdw 2.495 2.672 nonbonded pdb=" CAS 6EU B1001 " pdb=" OAB 6EU B1001 " model vdw 2.497 2.672 nonbonded pdb=" CAS 6EU C1001 " pdb=" OAB 6EU C1001 " model vdw 2.498 2.672 nonbonded pdb=" NE2 GLN D 154 " pdb=" O GLY D 162 " model vdw 2.513 3.120 ... (remaining 139381 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.750 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.014 0.325 18708 Z= 0.628 Angle : 1.222 17.546 25584 Z= 0.632 Chirality : 0.064 0.408 2996 Planarity : 0.008 0.058 3140 Dihedral : 9.995 79.537 6252 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -2.84 (0.14), residues: 2372 helix: -1.55 (0.11), residues: 1420 sheet: 0.81 (0.58), residues: 72 loop : -2.53 (0.16), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG C 173 TYR 0.045 0.004 TYR D 160 PHE 0.029 0.005 PHE C 205 TRP 0.019 0.004 TRP D 507 HIS 0.012 0.003 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.01395 / 0.63 (18708) covalent geometry : angle 1.22172 / 0.63 (25584) hydrogen bonds : bond 0.17584 / 11.84 ( 1085) hydrogen bonds : angle 5.55733 / 3.86 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.441 Fit side-chains REVERT: A 125 ASN cc_start: 0.8495 (m110) cc_final: 0.8220 (m-40) REVERT: B 121 LYS cc_start: 0.8207 (tttp) cc_final: 0.7988 (tttm) REVERT: B 125 ASN cc_start: 0.8455 (m110) cc_final: 0.8143 (m110) REVERT: B 140 ILE cc_start: 0.8536 (mt) cc_final: 0.8329 (mt) REVERT: C 179 LYS cc_start: 0.8470 (mttt) cc_final: 0.8233 (mttt) REVERT: D 723 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8069 (mt-10) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.5739 time to fit residues: 215.3245 Evaluate side-chains 212 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 163 HIS A 184 ASN A 613 GLN B 131 ASN B 163 HIS B 184 ASN B 201 GLN B 613 GLN C 131 ASN C 163 HIS C 184 ASN C 201 GLN D 163 HIS D 184 ASN D 201 GLN D 613 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.103227 restraints weight = 22040.088| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.86 r_work: 0.2854 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18708 Z= 0.130 Angle : 0.576 10.925 25584 Z= 0.287 Chirality : 0.037 0.148 2996 Planarity : 0.005 0.046 3140 Dihedral : 5.382 48.007 2608 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.88 % Allowed : 6.88 % Favored : 91.24 % 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: -0.18 (0.16), residues: 2372 helix: 0.77 (0.13), residues: 1456 sheet: 0.67 (0.59), residues: 72 loop : -1.76 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 678 TYR 0.023 0.002 TYR B 445 PHE 0.014 0.002 PHE D 405 TRP 0.010 0.001 TRP C 507 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (18708) covalent geometry : angle 0.57637 / 0.29 (25584) hydrogen bonds : bond 0.05266 / 3.59 ( 1085) hydrogen bonds : angle 3.60539 / 2.46 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.682 Fit side-chains outliers start: 32 outliers final: 8 residues processed: 247 average time/residue: 0.4665 time to fit residues: 132.3025 Evaluate side-chains 207 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 508 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.098467 restraints weight = 22349.465| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.81 r_work: 0.2808 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18708 Z= 0.159 Angle : 0.579 11.489 25584 Z= 0.287 Chirality : 0.038 0.153 2996 Planarity : 0.005 0.048 3140 Dihedral : 5.145 46.596 2608 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.53 % Allowed : 8.12 % Favored : 89.35 % 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: 0.78 (0.17), residues: 2372 helix: 1.68 (0.14), residues: 1456 sheet: 0.83 (0.61), residues: 72 loop : -1.66 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 678 TYR 0.018 0.002 TYR B 445 PHE 0.021 0.002 PHE D 405 TRP 0.009 0.001 TRP B 713 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (18708) covalent geometry : angle 0.57856 / 0.29 (25584) hydrogen bonds : bond 0.05767 / 3.94 ( 1085) hydrogen bonds : angle 3.46111 / 2.35 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.543 Fit side-chains REVERT: A 135 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6215 (tp-100) REVERT: B 135 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6070 (tp-100) REVERT: B 476 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7944 (mt) REVERT: C 135 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6182 (tp-100) REVERT: C 476 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8065 (mt) REVERT: D 135 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6230 (tp-100) REVERT: D 686 MET cc_start: 0.8966 (tpp) cc_final: 0.8640 (tpp) outliers start: 43 outliers final: 10 residues processed: 221 average time/residue: 0.5123 time to fit residues: 128.8860 Evaluate side-chains 208 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 508 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 32 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.096832 restraints weight = 22258.471| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.80 r_work: 0.2799 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18708 Z= 0.146 Angle : 0.559 10.831 25584 Z= 0.276 Chirality : 0.038 0.155 2996 Planarity : 0.004 0.047 3140 Dihedral : 4.957 45.350 2608 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.88 % Allowed : 8.53 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.18), residues: 2372 helix: 2.11 (0.14), residues: 1456 sheet: 1.07 (0.63), residues: 72 loop : -1.56 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 678 TYR 0.018 0.002 TYR B 445 PHE 0.017 0.002 PHE D 405 TRP 0.011 0.001 TRP C 221 HIS 0.004 0.001 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (18708) covalent geometry : angle 0.55931 / 0.28 (25584) hydrogen bonds : bond 0.05349 / 3.66 ( 1085) hydrogen bonds : angle 3.38600 / 2.29 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.550 Fit side-chains REVERT: A 135 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6353 (tp-100) REVERT: A 291 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8921 (mp) REVERT: A 476 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7901 (mt) REVERT: B 135 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6253 (tp-100) REVERT: B 291 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8851 (mp) REVERT: B 347 ASP cc_start: 0.9295 (t0) cc_final: 0.8988 (t70) REVERT: B 476 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7953 (mt) REVERT: C 135 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6112 (tp-100) REVERT: C 476 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7988 (mt) REVERT: D 135 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6281 (tp-100) outliers start: 49 outliers final: 11 residues processed: 229 average time/residue: 0.4846 time to fit residues: 126.3809 Evaluate side-chains 215 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 689 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 208 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 HIS B 314 GLN C 361 HIS D 195 HIS D 361 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.133235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.101965 restraints weight = 22260.368| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.71 r_work: 0.2874 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18708 Z= 0.097 Angle : 0.496 12.008 25584 Z= 0.242 Chirality : 0.036 0.155 2996 Planarity : 0.004 0.045 3140 Dihedral : 4.529 42.123 2608 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.94 % Allowed : 10.18 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.73 (0.18), residues: 2372 helix: 2.51 (0.14), residues: 1452 sheet: 1.14 (0.64), residues: 72 loop : -1.40 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 678 TYR 0.018 0.001 TYR A 445 PHE 0.009 0.001 PHE A 547 TRP 0.010 0.001 TRP A 221 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (18708) covalent geometry : angle 0.49643 / 0.24 (25584) hydrogen bonds : bond 0.03889 / 2.67 ( 1085) hydrogen bonds : angle 3.19595 / 2.15 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.751 Fit side-chains REVERT: A 135 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6399 (tp-100) REVERT: B 135 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6517 (tp-100) REVERT: B 347 ASP cc_start: 0.9299 (t0) cc_final: 0.8995 (t70) REVERT: C 135 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6172 (tp-100) REVERT: D 135 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6406 (tp-100) outliers start: 33 outliers final: 11 residues processed: 226 average time/residue: 0.5410 time to fit residues: 139.3100 Evaluate side-chains 215 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 132 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 235 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS C 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.134482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.101326 restraints weight = 22098.338| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.82 r_work: 0.2869 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18708 Z= 0.091 Angle : 0.481 11.002 25584 Z= 0.233 Chirality : 0.035 0.152 2996 Planarity : 0.004 0.043 3140 Dihedral : 4.309 39.766 2608 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.12 % Allowed : 10.94 % Favored : 86.94 % 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: 1.99 (0.18), residues: 2372 helix: 2.68 (0.14), residues: 1456 sheet: 1.23 (0.66), residues: 72 loop : -1.25 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 678 TYR 0.017 0.001 TYR B 445 PHE 0.008 0.001 PHE B 405 TRP 0.009 0.001 TRP B 713 HIS 0.003 0.001 HIS D 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (18708) covalent geometry : angle 0.48119 / 0.23 (25584) hydrogen bonds : bond 0.03616 / 2.48 ( 1085) hydrogen bonds : angle 3.09483 / 2.08 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.699 Fit side-chains REVERT: A 135 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6426 (tp-100) REVERT: B 135 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6450 (tp-100) REVERT: B 347 ASP cc_start: 0.9327 (t0) cc_final: 0.9039 (t70) REVERT: C 135 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6118 (tp-100) REVERT: D 135 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6379 (tp-100) REVERT: D 476 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7918 (mt) REVERT: D 643 MET cc_start: 0.7858 (mmm) cc_final: 0.7605 (tpp) outliers start: 36 outliers final: 11 residues processed: 226 average time/residue: 0.5399 time to fit residues: 139.1688 Evaluate side-chains 216 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 689 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 225 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 211 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 181 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.135203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.103533 restraints weight = 22314.403| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.84 r_work: 0.2888 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18708 Z= 0.089 Angle : 0.474 10.585 25584 Z= 0.230 Chirality : 0.035 0.151 2996 Planarity : 0.003 0.041 3140 Dihedral : 4.197 38.422 2608 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.94 % Allowed : 11.12 % Favored : 86.94 % 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: 2.15 (0.18), residues: 2372 helix: 2.80 (0.14), residues: 1456 sheet: 1.34 (0.67), residues: 72 loop : -1.16 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 678 TYR 0.016 0.001 TYR A 445 PHE 0.008 0.001 PHE D 405 TRP 0.009 0.001 TRP A 713 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 (18708) covalent geometry : angle 0.47429 / 0.23 (25584) hydrogen bonds : bond 0.03499 / 2.40 ( 1085) hydrogen bonds : angle 3.07914 / 2.07 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.680 Fit side-chains REVERT: A 135 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6436 (tp-100) REVERT: A 476 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7864 (mt) REVERT: B 135 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6474 (tp-100) REVERT: B 347 ASP cc_start: 0.9309 (t0) cc_final: 0.9009 (t70) REVERT: B 476 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7905 (mt) REVERT: C 135 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6177 (tp-100) REVERT: C 643 MET cc_start: 0.7975 (mmm) cc_final: 0.7433 (tpp) REVERT: D 135 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6363 (tp-100) REVERT: D 476 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7838 (mt) REVERT: D 643 MET cc_start: 0.7810 (mmm) cc_final: 0.7523 (tpp) outliers start: 33 outliers final: 14 residues processed: 226 average time/residue: 0.5118 time to fit residues: 132.9385 Evaluate side-chains 216 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 689 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 128 optimal weight: 8.9990 chunk 125 optimal weight: 0.0770 chunk 58 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 94 optimal weight: 10.0000 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 HIS C 366 HIS D 366 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.105230 restraints weight = 22338.853| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.76 r_work: 0.2909 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18708 Z= 0.085 Angle : 0.466 10.050 25584 Z= 0.225 Chirality : 0.035 0.153 2996 Planarity : 0.003 0.038 3140 Dihedral : 4.100 37.031 2608 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.41 % Allowed : 12.00 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.31 (0.18), residues: 2372 helix: 2.87 (0.14), residues: 1464 sheet: 1.42 (0.67), residues: 72 loop : -1.03 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 678 TYR 0.015 0.001 TYR A 445 PHE 0.008 0.001 PHE C 405 TRP 0.008 0.001 TRP B 713 HIS 0.003 0.001 HIS D 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.09 (18708) covalent geometry : angle 0.46614 / 0.23 (25584) hydrogen bonds : bond 0.03289 / 2.26 ( 1085) hydrogen bonds : angle 3.05234 / 2.05 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.733 Fit side-chains REVERT: A 135 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6454 (tp-100) REVERT: A 712 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.7849 (p) REVERT: B 135 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6526 (tp-100) REVERT: B 347 ASP cc_start: 0.9328 (t0) cc_final: 0.9016 (t70) REVERT: B 476 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7922 (mt) REVERT: B 643 MET cc_start: 0.8044 (mmm) cc_final: 0.7310 (tpp) REVERT: B 712 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7798 (p) REVERT: C 135 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6240 (tp-100) REVERT: C 643 MET cc_start: 0.8047 (mmm) cc_final: 0.7466 (tpp) REVERT: D 135 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6403 (tp-100) REVERT: D 643 MET cc_start: 0.7825 (mmm) cc_final: 0.7323 (tpp) outliers start: 24 outliers final: 12 residues processed: 220 average time/residue: 0.5015 time to fit residues: 126.8043 Evaluate side-chains 216 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 712 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 200 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 151 optimal weight: 0.0040 chunk 51 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 366 HIS D 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.132721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.100943 restraints weight = 22104.448| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.81 r_work: 0.2870 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 18708 Z= 0.113 Angle : 0.511 10.933 25584 Z= 0.248 Chirality : 0.036 0.151 2996 Planarity : 0.004 0.039 3140 Dihedral : 4.275 38.522 2608 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.71 % Allowed : 12.00 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.26 (0.18), residues: 2372 helix: 2.86 (0.14), residues: 1460 sheet: 1.42 (0.67), residues: 72 loop : -1.09 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 678 TYR 0.014 0.001 TYR A 445 PHE 0.013 0.001 PHE B 405 TRP 0.007 0.001 TRP C 507 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (18708) covalent geometry : angle 0.51147 / 0.25 (25584) hydrogen bonds : bond 0.04296 / 2.95 ( 1085) hydrogen bonds : angle 3.15301 / 2.13 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.650 Fit side-chains REVERT: A 135 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6485 (tp-100) REVERT: B 135 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.6398 (tp-100) REVERT: B 347 ASP cc_start: 0.9338 (t0) cc_final: 0.9011 (t70) REVERT: B 476 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7890 (mt) REVERT: B 643 MET cc_start: 0.8213 (mmm) cc_final: 0.7471 (tpp) REVERT: B 712 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7849 (p) REVERT: C 135 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6223 (tp-100) REVERT: C 476 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7900 (mt) REVERT: C 643 MET cc_start: 0.7923 (mmm) cc_final: 0.7347 (tpp) REVERT: D 135 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6411 (tp-100) REVERT: D 643 MET cc_start: 0.7952 (mmm) cc_final: 0.7404 (tpp) outliers start: 29 outliers final: 16 residues processed: 222 average time/residue: 0.5101 time to fit residues: 130.0653 Evaluate side-chains 219 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain D residue 712 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 12 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 366 HIS D 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.133711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.103534 restraints weight = 22186.993| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.70 r_work: 0.2853 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18708 Z= 0.121 Angle : 0.516 11.132 25584 Z= 0.252 Chirality : 0.037 0.155 2996 Planarity : 0.004 0.040 3140 Dihedral : 4.385 39.619 2608 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.59 % Allowed : 12.18 % Favored : 86.24 % 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: 2.19 (0.18), residues: 2372 helix: 2.79 (0.14), residues: 1460 sheet: 1.45 (0.66), residues: 72 loop : -1.09 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 678 TYR 0.014 0.001 TYR A 445 PHE 0.015 0.001 PHE C 405 TRP 0.008 0.001 TRP B 221 HIS 0.004 0.001 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (18708) covalent geometry : angle 0.51587 / 0.25 (25584) hydrogen bonds : bond 0.04502 / 3.09 ( 1085) hydrogen bonds : angle 3.20313 / 2.16 ( 3162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.707 Fit side-chains REVERT: A 135 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6541 (tp-100) REVERT: B 135 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6465 (tp-100) REVERT: B 347 ASP cc_start: 0.9318 (t0) cc_final: 0.8966 (t70) REVERT: B 476 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7904 (mt) REVERT: B 643 MET cc_start: 0.8211 (mmm) cc_final: 0.7552 (tpp) REVERT: B 712 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.7889 (p) REVERT: C 135 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6247 (tp-100) REVERT: C 347 ASP cc_start: 0.9317 (t0) cc_final: 0.8945 (t70) REVERT: C 476 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7979 (mt) REVERT: C 643 MET cc_start: 0.8086 (mmm) cc_final: 0.7560 (tpp) REVERT: D 135 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6436 (tp-100) REVERT: D 643 MET cc_start: 0.8027 (mmm) cc_final: 0.7485 (tpp) outliers start: 27 outliers final: 18 residues processed: 217 average time/residue: 0.4997 time to fit residues: 124.2272 Evaluate side-chains 223 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain D residue 712 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 86 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 HIS C 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.099814 restraints weight = 22321.146| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.82 r_work: 0.2818 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18708 Z= 0.137 Angle : 0.545 11.625 25584 Z= 0.265 Chirality : 0.038 0.153 2996 Planarity : 0.004 0.040 3140 Dihedral : 4.502 40.958 2608 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.71 % Allowed : 11.94 % Favored : 86.35 % 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: 2.12 (0.18), residues: 2372 helix: 2.73 (0.14), residues: 1460 sheet: 1.98 (0.64), residues: 68 loop : -1.17 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 678 TYR 0.014 0.002 TYR D 226 PHE 0.016 0.001 PHE B 405 TRP 0.008 0.001 TRP B 221 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (18708) covalent geometry : angle 0.54459 / 0.27 (25584) hydrogen bonds : bond 0.04925 / 3.37 ( 1085) hydrogen bonds : angle 3.26609 / 2.21 ( 3162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5877.75 seconds wall clock time: 100 minutes 47.16 seconds (6047.16 seconds total)