Starting phenix.real_space_refine on Thu Mar 5 02:17:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oo3_20143/03_2026/6oo3_20143.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oo3_20143/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6oo3_20143/03_2026/6oo3_20143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oo3_20143/03_2026/6oo3_20143.map" model { file = "/net/cci-nas-00/data/ceres_data/6oo3_20143/03_2026/6oo3_20143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oo3_20143/03_2026/6oo3_20143.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.98, 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: 1.59 Conformation dependent library (CDL) restraints added in 656.0 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: 0.55 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: 2.94 Time building geometry restraints manager: 2.10 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: 10484 15.91 - 31.81: 527 31.81 - 47.72: 85 47.72 - 63.63: 23 63.63 - 79.54: 13 Dihedral angle restraints: 11132 sinusoidal: 4108 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 11129 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: 0.04 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 16.230 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 10.945 79.537 6596 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 covalent geometry : bond 0.01395 (18708) covalent geometry : angle 1.22172 (25584) hydrogen bonds : bond 0.17584 ( 1085) hydrogen bonds : angle 5.55733 ( 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 : 0.607 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: 0.6094 time to fit residues: 228.0631 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 : 0.710 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3431 r_free = 0.3431 target = 0.133729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102403 restraints weight = 22089.850| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.84 r_work: 0.2856 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18708 Z= 0.127 Angle : 0.575 10.926 25584 Z= 0.286 Chirality : 0.037 0.175 2996 Planarity : 0.005 0.047 3140 Dihedral : 5.923 56.456 2952 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: -0.14 (0.16), residues: 2372 helix: 0.81 (0.13), residues: 1456 sheet: 0.67 (0.59), residues: 72 loop : -1.77 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 A 507 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00279 (18708) covalent geometry : angle 0.57499 (25584) hydrogen bonds : bond 0.05262 ( 1085) hydrogen bonds : angle 3.60513 ( 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 : 0.633 Fit side-chains REVERT: D 682 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.8310 (ttt180) outliers start: 32 outliers final: 8 residues processed: 246 average time/residue: 0.5229 time to fit residues: 146.3665 Evaluate side-chains 206 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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: 6.9990 chunk 108 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 168 optimal weight: 0.0970 chunk 141 optimal weight: 0.0470 chunk 70 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 361 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.101513 restraints weight = 22344.372| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.84 r_work: 0.2854 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2157 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= 0.120 Angle : 0.525 10.167 25584 Z= 0.261 Chirality : 0.037 0.156 2996 Planarity : 0.004 0.046 3140 Dihedral : 5.414 51.553 2952 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.59 % Allowed : 8.06 % 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: 1.01 (0.17), residues: 2372 helix: 1.84 (0.14), residues: 1460 sheet: 0.87 (0.61), residues: 72 loop : -1.54 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 678 TYR 0.020 0.001 TYR B 445 PHE 0.015 0.001 PHE D 405 TRP 0.009 0.001 TRP B 713 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00269 (18708) covalent geometry : angle 0.52513 (25584) hydrogen bonds : bond 0.04791 ( 1085) hydrogen bonds : angle 3.34565 ( 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 250 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 0.609 Fit side-chains REVERT: A 135 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6232 (tp-100) REVERT: B 135 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6129 (tp-100) REVERT: C 135 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6133 (tp-100) REVERT: D 135 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6310 (tp-100) outliers start: 44 outliers final: 10 residues processed: 227 average time/residue: 0.5303 time to fit residues: 136.6241 Evaluate side-chains 205 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 133 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 67 optimal weight: 0.0980 chunk 188 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.134262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.102360 restraints weight = 22233.746| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.80 r_work: 0.2866 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18708 Z= 0.098 Angle : 0.484 9.087 25584 Z= 0.239 Chirality : 0.036 0.163 2996 Planarity : 0.004 0.045 3140 Dihedral : 5.089 49.030 2952 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.47 % Allowed : 9.00 % Favored : 88.53 % 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: 1.57 (0.18), residues: 2372 helix: 2.36 (0.14), residues: 1452 sheet: 1.05 (0.64), residues: 72 loop : -1.41 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 161 TYR 0.019 0.001 TYR A 445 PHE 0.010 0.001 PHE B 405 TRP 0.010 0.001 TRP A 221 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00209 (18708) covalent geometry : angle 0.48429 (25584) hydrogen bonds : bond 0.03900 ( 1085) hydrogen bonds : angle 3.18230 ( 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 248 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 0.529 Fit side-chains REVERT: A 135 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6332 (tp-100) REVERT: B 135 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6489 (tp-100) REVERT: B 347 ASP cc_start: 0.9309 (t0) cc_final: 0.9016 (t70) REVERT: C 135 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6186 (tp-100) REVERT: D 135 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6359 (tp-100) outliers start: 42 outliers final: 14 residues processed: 231 average time/residue: 0.4944 time to fit residues: 130.2044 Evaluate side-chains 209 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 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 508 THR Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 681 GLN 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 508 THR Chi-restraints excluded: chain C residue 640 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.130655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.098311 restraints weight = 22239.526| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.79 r_work: 0.2812 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18708 Z= 0.137 Angle : 0.545 13.302 25584 Z= 0.265 Chirality : 0.037 0.162 2996 Planarity : 0.004 0.045 3140 Dihedral : 5.273 49.525 2952 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.12 % Allowed : 9.12 % Favored : 87.76 % 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: 1.70 (0.18), residues: 2372 helix: 2.44 (0.14), residues: 1456 sheet: 1.19 (0.65), residues: 72 loop : -1.36 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 678 TYR 0.015 0.002 TYR B 445 PHE 0.018 0.001 PHE D 405 TRP 0.009 0.001 TRP A 221 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00322 (18708) covalent geometry : angle 0.54525 (25584) hydrogen bonds : bond 0.05028 ( 1085) hydrogen bonds : angle 3.25659 ( 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 244 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 0.700 Fit side-chains REVERT: A 135 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6463 (tp-100) REVERT: A 476 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7905 (mt) REVERT: B 135 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6302 (tp-100) REVERT: B 347 ASP cc_start: 0.9333 (t0) cc_final: 0.9015 (t70) REVERT: C 135 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6172 (tp-100) REVERT: D 135 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6360 (tp-100) REVERT: D 161 ARG cc_start: 0.8607 (ttp-170) cc_final: 0.8381 (ttm-80) REVERT: D 476 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7948 (mt) outliers start: 53 outliers final: 15 residues processed: 220 average time/residue: 0.5159 time to fit residues: 129.1280 Evaluate side-chains 212 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 476 LEU Chi-restraints excluded: chain A residue 508 THR 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 222 ASP Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 508 THR 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 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 476 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 689 VAL 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: 0.9990 chunk 132 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 235 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.133956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.102267 restraints weight = 22071.591| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.84 r_work: 0.2880 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.002 0.021 18708 Z= 0.095 Angle : 0.484 11.336 25584 Z= 0.235 Chirality : 0.036 0.161 2996 Planarity : 0.004 0.043 3140 Dihedral : 4.964 48.015 2952 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.18 % Allowed : 10.82 % Favored : 87.00 % 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: 1452 sheet: 1.19 (0.66), residues: 72 loop : -1.21 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 678 TYR 0.017 0.001 TYR A 445 PHE 0.008 0.001 PHE B 405 TRP 0.008 0.001 TRP D 331 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00202 (18708) covalent geometry : angle 0.48363 (25584) hydrogen bonds : bond 0.03724 ( 1085) hydrogen bonds : angle 3.14689 ( 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 235 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.718 Fit side-chains REVERT: A 135 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6467 (tp-100) REVERT: B 135 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6305 (tp-100) REVERT: B 347 ASP cc_start: 0.9333 (t0) cc_final: 0.9010 (t70) REVERT: C 135 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6202 (tp-100) REVERT: D 135 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6424 (tp-100) outliers start: 37 outliers final: 17 residues processed: 216 average time/residue: 0.4893 time to fit residues: 121.2224 Evaluate side-chains 215 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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 222 ASP Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 640 ILE 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 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 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: 2.9990 chunk 138 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 147 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 151 optimal weight: 0.0060 chunk 43 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 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 = 0.3424 r_free = 0.3424 target = 0.133378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.100566 restraints weight = 22255.064| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.73 r_work: 0.2866 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18708 Z= 0.101 Angle : 0.491 11.327 25584 Z= 0.239 Chirality : 0.036 0.158 2996 Planarity : 0.004 0.041 3140 Dihedral : 4.953 49.726 2952 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.18 % Allowed : 11.41 % Favored : 86.41 % 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: 2.13 (0.18), residues: 2372 helix: 2.75 (0.14), residues: 1460 sheet: 1.30 (0.67), residues: 72 loop : -1.12 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 678 TYR 0.015 0.001 TYR B 445 PHE 0.011 0.001 PHE B 405 TRP 0.009 0.001 TRP A 713 HIS 0.003 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00221 (18708) covalent geometry : angle 0.49110 (25584) hydrogen bonds : bond 0.03986 ( 1085) hydrogen bonds : angle 3.13881 ( 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 234 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.747 Fit side-chains REVERT: A 135 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6500 (tp-100) REVERT: A 476 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7897 (mt) REVERT: B 135 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6356 (tp-100) REVERT: B 347 ASP cc_start: 0.9326 (t0) cc_final: 0.8998 (t70) REVERT: B 712 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7811 (p) REVERT: C 135 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6245 (tp-100) REVERT: C 201 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6476 (mt0) REVERT: C 643 MET cc_start: 0.8020 (mmm) cc_final: 0.7682 (tpp) REVERT: D 135 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6444 (tp-100) REVERT: D 643 MET cc_start: 0.7587 (tpp) cc_final: 0.7383 (mmm) outliers start: 37 outliers final: 19 residues processed: 216 average time/residue: 0.4832 time to fit residues: 119.4799 Evaluate side-chains 217 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 476 LEU 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 222 ASP Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 681 GLN 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 201 GLN Chi-restraints excluded: chain C residue 222 ASP 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 160 TYR Chi-restraints excluded: chain D residue 222 ASP 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: 0.0070 chunk 125 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 224 optimal weight: 0.6980 chunk 195 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 94 optimal weight: 8.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 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 = 0.3441 r_free = 0.3441 target = 0.134719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.103221 restraints weight = 22235.083| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.82 r_work: 0.2896 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18708 Z= 0.091 Angle : 0.472 10.632 25584 Z= 0.230 Chirality : 0.035 0.160 2996 Planarity : 0.004 0.040 3140 Dihedral : 4.849 52.122 2952 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.00 % Allowed : 11.71 % 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: 2.24 (0.18), residues: 2372 helix: 2.84 (0.14), residues: 1456 sheet: 1.40 (0.67), residues: 72 loop : -1.05 (0.21), residues: 844 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 0.009 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 covalent geometry : bond 0.00193 (18708) covalent geometry : angle 0.47189 (25584) hydrogen bonds : bond 0.03563 ( 1085) hydrogen bonds : angle 3.09026 ( 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 235 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.654 Fit side-chains REVERT: A 135 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6497 (tp-100) REVERT: A 712 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7842 (p) REVERT: B 135 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6382 (tp-100) REVERT: B 347 ASP cc_start: 0.9338 (t0) cc_final: 0.9002 (t70) REVERT: B 712 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7785 (p) REVERT: C 135 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6260 (tp-100) REVERT: C 201 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.6432 (mt0) REVERT: C 643 MET cc_start: 0.7924 (mmm) cc_final: 0.7681 (tpp) REVERT: D 135 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6463 (tp-100) REVERT: D 476 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7936 (mt) outliers start: 34 outliers final: 14 residues processed: 217 average time/residue: 0.4845 time to fit residues: 120.5414 Evaluate side-chains 217 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 508 THR Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 268 MET 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 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 689 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 200 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 228 optimal weight: 0.0030 chunk 151 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3418 r_free = 0.3418 target = 0.132789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.101188 restraints weight = 22016.880| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.71 r_work: 0.2852 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2684 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= 0.111 Angle : 0.503 11.185 25584 Z= 0.245 Chirality : 0.036 0.156 2996 Planarity : 0.004 0.039 3140 Dihedral : 4.980 53.889 2952 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.06 % Allowed : 11.65 % 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: 2.24 (0.18), residues: 2372 helix: 2.82 (0.14), residues: 1460 sheet: 1.38 (0.67), residues: 72 loop : -1.05 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 678 TYR 0.014 0.001 TYR B 445 PHE 0.013 0.001 PHE B 405 TRP 0.007 0.001 TRP B 713 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00253 (18708) covalent geometry : angle 0.50259 (25584) hydrogen bonds : bond 0.04236 ( 1085) hydrogen bonds : angle 3.15951 ( 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 237 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.645 Fit side-chains REVERT: A 135 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6501 (tp-100) REVERT: A 476 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7879 (mt) REVERT: A 712 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.7827 (p) REVERT: B 135 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6391 (tp-100) REVERT: B 347 ASP cc_start: 0.9326 (t0) cc_final: 0.8985 (t70) REVERT: B 643 MET cc_start: 0.8152 (mmm) cc_final: 0.7484 (tpp) REVERT: B 712 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7778 (p) REVERT: C 135 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6250 (tp-100) REVERT: C 201 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6509 (mt0) REVERT: C 643 MET cc_start: 0.8051 (mmm) cc_final: 0.7556 (tpp) REVERT: D 135 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6401 (tp-100) REVERT: D 476 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7922 (mt) REVERT: D 643 MET cc_start: 0.7729 (tpp) cc_final: 0.7484 (mmm) outliers start: 35 outliers final: 18 residues processed: 221 average time/residue: 0.5001 time to fit residues: 126.4972 Evaluate side-chains 224 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 268 MET Chi-restraints excluded: chain A residue 476 LEU 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 508 THR 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 201 GLN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 508 THR 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 222 ASP Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 508 THR 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: 9.9990 chunk 165 optimal weight: 0.9990 chunk 237 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 176 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3442 r_free = 0.3442 target = 0.134644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.103147 restraints weight = 22260.775| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.85 r_work: 0.2874 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18708 Z= 0.095 Angle : 0.481 10.484 25584 Z= 0.234 Chirality : 0.036 0.159 2996 Planarity : 0.004 0.039 3140 Dihedral : 4.892 57.066 2952 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.59 % Allowed : 12.24 % Favored : 86.18 % 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: 2.86 (0.14), residues: 1468 sheet: 1.42 (0.67), residues: 72 loop : -1.02 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 678 TYR 0.014 0.001 TYR B 445 PHE 0.010 0.001 PHE B 405 TRP 0.007 0.001 TRP A 331 HIS 0.003 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00204 (18708) covalent geometry : angle 0.48072 (25584) hydrogen bonds : bond 0.03706 ( 1085) hydrogen bonds : angle 3.12813 ( 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 229 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.679 Fit side-chains REVERT: A 135 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6454 (tp-100) REVERT: A 268 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8959 (mmp) REVERT: A 476 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 712 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7766 (p) REVERT: B 135 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6358 (tp-100) REVERT: B 347 ASP cc_start: 0.9341 (t0) cc_final: 0.9019 (t70) REVERT: B 643 MET cc_start: 0.8112 (mmm) cc_final: 0.7404 (tpp) REVERT: B 712 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7749 (p) REVERT: C 135 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6218 (tp-100) REVERT: C 643 MET cc_start: 0.7968 (mmm) cc_final: 0.7374 (tpp) REVERT: D 135 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6417 (tp-100) REVERT: D 476 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7866 (mt) REVERT: D 643 MET cc_start: 0.7616 (tpp) cc_final: 0.7387 (mmm) outliers start: 27 outliers final: 17 residues processed: 216 average time/residue: 0.4877 time to fit residues: 120.7528 Evaluate side-chains 225 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 268 MET Chi-restraints excluded: chain A residue 476 LEU 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 160 TYR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 640 ILE 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 268 MET Chi-restraints excluded: chain C residue 508 THR 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 222 ASP Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 689 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 86 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3423 r_free = 0.3423 target = 0.133076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.100725 restraints weight = 22270.356| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.86 r_work: 0.2854 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2719 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 : 0.503 11.057 25584 Z= 0.246 Chirality : 0.036 0.159 2996 Planarity : 0.004 0.039 3140 Dihedral : 5.007 59.946 2952 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.94 % Allowed : 11.76 % 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: 2.25 (0.18), residues: 2372 helix: 2.81 (0.14), residues: 1468 sheet: 1.39 (0.67), residues: 72 loop : -1.05 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 678 TYR 0.013 0.001 TYR B 445 PHE 0.013 0.001 PHE B 405 TRP 0.007 0.001 TRP B 713 HIS 0.003 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00260 (18708) covalent geometry : angle 0.50312 (25584) hydrogen bonds : bond 0.04264 ( 1085) hydrogen bonds : angle 3.18135 ( 3162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5771.15 seconds wall clock time: 99 minutes 19.20 seconds (5959.20 seconds total)