Starting phenix.real_space_refine on Sat Feb 7 12:37:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k95_36975/02_2026/8k95_36975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k95_36975/02_2026/8k95_36975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k95_36975/02_2026/8k95_36975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k95_36975/02_2026/8k95_36975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k95_36975/02_2026/8k95_36975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k95_36975/02_2026/8k95_36975.map" } resolution = 3.05 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= 0.003 sd= 0.035 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 47 5.16 5 C 21150 2.51 5 N 6000 2.21 5 O 6279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33481 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "F" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.05, per 1000 atoms: 0.21 Number of scatterers: 33481 At special positions: 0 Unit cell: (131.2, 164.82, 179.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 5 15.00 O 6279 8.00 N 6000 7.00 C 21150 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: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 68 sheets defined 53.8% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 97 through 119 removed outlier: 4.287A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 154 Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.820A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.898A pdb=" N SER A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.864A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 543 through 557 Processing helix chain 'A' and resid 584 through 597 Processing helix chain 'A' and resid 621 through 636 Processing helix chain 'A' and resid 649 through 651 No H-bonds generated for 'chain 'A' and resid 649 through 651' Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.646A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 120 removed outlier: 4.308A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 153 removed outlier: 3.820A pdb=" N LEU B 125 " --> pdb=" O GLN B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.122A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 241 Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.802A pdb=" N ARG B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.932A pdb=" N GLU B 368 " --> pdb=" O GLU B 365 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 369 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.773A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.912A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 543 through 557 Processing helix chain 'B' and resid 585 through 597 Processing helix chain 'B' and resid 621 through 636 Processing helix chain 'B' and resid 649 through 651 No H-bonds generated for 'chain 'B' and resid 649 through 651' Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 97 through 119 removed outlier: 3.904A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 153 Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.296A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 372 removed outlier: 4.062A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'C' and resid 393 through 408 Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 436 through 452 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.876A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 543 through 557 Processing helix chain 'C' and resid 584 through 597 Processing helix chain 'C' and resid 621 through 636 Processing helix chain 'C' and resid 649 through 653 removed outlier: 4.027A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 685 Processing helix chain 'C' and resid 694 through 719 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 70 removed outlier: 3.646A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN D 70 " --> pdb=" O TYR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 120 removed outlier: 4.083A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASN D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 153 Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.374A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.936A pdb=" N GLY D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 380 removed outlier: 3.599A pdb=" N SER D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 407 Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.783A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 543 through 557 Processing helix chain 'D' and resid 585 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 653 removed outlier: 4.106A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 719 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.563A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 119 removed outlier: 4.329A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 153 Processing helix chain 'E' and resid 173 through 221 removed outlier: 4.267A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG E 213 " --> pdb=" O TYR E 209 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 241 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 363 through 369 removed outlier: 4.057A pdb=" N GLY E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 379 removed outlier: 3.721A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 408 Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.741A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 532 through 534 No H-bonds generated for 'chain 'E' and resid 532 through 534' Processing helix chain 'E' and resid 543 through 557 removed outlier: 3.594A pdb=" N TYR E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 597 Processing helix chain 'E' and resid 621 through 636 Processing helix chain 'E' and resid 649 through 653 removed outlier: 4.092A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 719 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 70 Processing helix chain 'F' and resid 97 through 120 removed outlier: 4.194A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 152 Processing helix chain 'F' and resid 173 through 221 removed outlier: 4.421A pdb=" N ASN F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG F 213 " --> pdb=" O TYR F 209 " (cutoff:3.500A) Proline residue: F 216 - end of helix Processing helix chain 'F' and resid 224 through 241 Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 293 through 295 No H-bonds generated for 'chain 'F' and resid 293 through 295' Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 314 through 320 removed outlier: 3.857A pdb=" N GLU F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.967A pdb=" N GLY F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 379 removed outlier: 3.619A pdb=" N SER F 377 " --> pdb=" O ASP F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 407 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 436 through 452 Processing helix chain 'F' and resid 456 through 470 Processing helix chain 'F' and resid 471 through 485 removed outlier: 4.659A pdb=" N GLU F 475 " --> pdb=" O SER F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 543 through 557 Processing helix chain 'F' and resid 584 through 597 removed outlier: 3.641A pdb=" N LEU F 588 " --> pdb=" O GLY F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 637 Processing helix chain 'F' and resid 649 through 653 removed outlier: 4.240A pdb=" N ALA F 652 " --> pdb=" O ALA F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 666 Processing helix chain 'F' and resid 676 through 686 Processing helix chain 'F' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 6.481A pdb=" N VAL A 267 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP A 313 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLU A 269 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 310 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 361 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 312 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 50 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 82 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 411 removed outlier: 7.366A pdb=" N GLN A 410 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 504 removed outlier: 6.912A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 604 through 606 removed outlier: 6.521A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL A 644 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL A 674 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 609 through 610 Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.915A pdb=" N ASP B 313 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU B 310 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL B 361 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 312 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA B 49 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLY B 362 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 51 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N HIS B 48 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 382 " --> pdb=" O HIS B 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 77 through 82 Processing sheet with id=AB6, first strand: chain 'B' and resid 156 through 159 Processing sheet with id=AB7, first strand: chain 'B' and resid 280 through 281 Processing sheet with id=AB8, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AB9, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AC1, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AC2, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.288A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AC4, first strand: chain 'B' and resid 528 through 530 removed outlier: 9.941A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 583 through 584 removed outlier: 4.516A pdb=" N ALA B 583 " --> pdb=" O VAL B 610 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 266 through 269 removed outlier: 6.356A pdb=" N VAL C 267 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP C 313 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU C 269 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 310 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL C 361 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU C 312 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N HIS C 48 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 382 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 77 through 82 Processing sheet with id=AC8, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AC9, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AD1, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AD2, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AD3, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AD4, first strand: chain 'C' and resid 410 through 411 removed outlier: 7.388A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AD6, first strand: chain 'C' and resid 529 through 530 removed outlier: 6.809A pdb=" N ILE C 529 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N PHE C 571 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 609 through 610 Processing sheet with id=AD8, first strand: chain 'D' and resid 266 through 269 removed outlier: 4.010A pdb=" N ASP D 313 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA D 49 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLY D 362 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU D 51 " --> pdb=" O GLY D 362 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 77 through 82 Processing sheet with id=AE1, first strand: chain 'D' and resid 156 through 159 Processing sheet with id=AE2, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AE3, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AE4, first strand: chain 'D' and resid 334 through 335 Processing sheet with id=AE5, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AE6, first strand: chain 'D' and resid 410 through 411 removed outlier: 7.192A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AE8, first strand: chain 'D' and resid 529 through 530 removed outlier: 6.831A pdb=" N ILE D 529 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N PHE D 571 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLU D 498 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N VAL D 606 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASN D 500 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL D 644 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL D 674 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 583 through 584 removed outlier: 4.425A pdb=" N ALA D 583 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 266 through 269 removed outlier: 6.463A pdb=" N VAL E 267 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASP E 313 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU E 269 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS E 48 " --> pdb=" O ILE E 382 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA E 384 " --> pdb=" O HIS E 48 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR E 50 " --> pdb=" O ALA E 384 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 77 through 82 Processing sheet with id=AF3, first strand: chain 'E' and resid 156 through 158 Processing sheet with id=AF4, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AF5, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AF6, first strand: chain 'E' and resid 334 through 335 Processing sheet with id=AF7, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AF8, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.189A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AG1, first strand: chain 'E' and resid 528 through 530 removed outlier: 10.140A pdb=" N GLU E 498 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N VAL E 606 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN E 500 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL E 644 " --> pdb=" O TYR E 672 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL E 674 " --> pdb=" O VAL E 644 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU E 646 " --> pdb=" O VAL E 674 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 583 through 584 removed outlier: 4.491A pdb=" N ALA E 583 " --> pdb=" O VAL E 610 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 266 through 268 removed outlier: 6.058A pdb=" N LEU F 310 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL F 361 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU F 312 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N HIS F 48 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE F 382 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 77 through 82 removed outlier: 3.658A pdb=" N VAL F 88 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 156 through 158 Processing sheet with id=AG6, first strand: chain 'F' and resid 280 through 281 removed outlier: 3.739A pdb=" N ARG F 280 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AG8, first strand: chain 'F' and resid 334 through 335 Processing sheet with id=AG9, first strand: chain 'F' and resid 389 through 391 Processing sheet with id=AH1, first strand: chain 'F' and resid 410 through 411 removed outlier: 6.913A pdb=" N GLN F 410 " --> pdb=" O LEU F 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'F' and resid 494 through 496 Processing sheet with id=AH3, first strand: chain 'F' and resid 498 through 503 removed outlier: 7.584A pdb=" N ILE F 529 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N PHE F 571 " --> pdb=" O ILE F 529 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 604 through 606 removed outlier: 6.316A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL F 644 " --> pdb=" O TYR F 672 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL F 674 " --> pdb=" O VAL F 644 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU F 646 " --> pdb=" O VAL F 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'F' and resid 609 through 610 1874 hydrogen bonds defined for protein. 5442 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: 7.65 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 11695 1.35 - 1.50: 8693 1.50 - 1.65: 13677 1.65 - 1.80: 53 1.80 - 1.95: 24 Bond restraints: 34142 Sorted by residual: bond pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 2.275 1.943 0.332 2.00e-02 2.50e+03 2.75e+02 bond pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 2.275 1.944 0.331 2.00e-02 2.50e+03 2.74e+02 bond pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 2.275 1.945 0.330 2.00e-02 2.50e+03 2.73e+02 bond pdb=" P TS6 E 801 " pdb=" S2P TS6 E 801 " ideal model delta sigma weight residual 2.275 1.946 0.329 2.00e-02 2.50e+03 2.71e+02 bond pdb=" P TS6 A 801 " pdb=" S2P TS6 A 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.68e+02 ... (remaining 34137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 46108 3.44 - 6.88: 215 6.88 - 10.32: 13 10.32 - 13.76: 12 13.76 - 17.20: 8 Bond angle restraints: 46356 Sorted by residual: angle pdb=" N PRO A 270 " pdb=" CA PRO A 270 " pdb=" C PRO A 270 " ideal model delta sigma weight residual 113.53 105.27 8.26 1.39e+00 5.18e-01 3.53e+01 angle pdb=" O1P TS6 A 801 " pdb=" P TS6 A 801 " pdb=" S2P TS6 A 801 " ideal model delta sigma weight residual 98.15 115.35 -17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" O1P TS6 D 801 " pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 98.15 115.31 -17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O1P TS6 C 801 " pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 98.15 115.31 -17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O1P TS6 E 801 " pdb=" P TS6 E 801 " pdb=" S2P TS6 E 801 " ideal model delta sigma weight residual 98.15 115.26 -17.11 3.00e+00 1.11e-01 3.25e+01 ... (remaining 46351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 18946 17.93 - 35.86: 1277 35.86 - 53.79: 222 53.79 - 71.72: 155 71.72 - 89.65: 124 Dihedral angle restraints: 20724 sinusoidal: 8394 harmonic: 12330 Sorted by residual: dihedral pdb=" CA PHE B 542 " pdb=" C PHE B 542 " pdb=" N HIS B 543 " pdb=" CA HIS B 543 " ideal model delta harmonic sigma weight residual 180.00 -155.29 -24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA GLY C 154 " pdb=" C GLY C 154 " pdb=" N PHE C 155 " pdb=" CA PHE C 155 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU C 411 " pdb=" C LEU C 411 " pdb=" N THR C 412 " pdb=" CA THR C 412 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 20721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4362 0.056 - 0.112: 697 0.112 - 0.169: 83 0.169 - 0.225: 21 0.225 - 0.281: 3 Chirality restraints: 5166 Sorted by residual: chirality pdb=" CA LEU B 360 " pdb=" N LEU B 360 " pdb=" C LEU B 360 " pdb=" CB LEU B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA LEU D 360 " pdb=" N LEU D 360 " pdb=" C LEU D 360 " pdb=" CB LEU D 360 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ASP B 313 " pdb=" N ASP B 313 " pdb=" C ASP B 313 " pdb=" CB ASP B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 5163 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 172 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.99e+00 pdb=" N PRO F 173 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 173 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 173 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 182 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" CD GLU A 182 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 182 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 182 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 377 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C SER F 377 " -0.031 2.00e-02 2.50e+03 pdb=" O SER F 377 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU F 378 " 0.011 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 424 2.67 - 3.23: 32399 3.23 - 3.78: 55373 3.78 - 4.34: 73458 4.34 - 4.90: 121720 Nonbonded interactions: 283374 Sorted by model distance: nonbonded pdb=" OG SER A 593 " pdb=" O LEU A 598 " model vdw 2.110 3.040 nonbonded pdb=" OE2 GLU C 498 " pdb=" NE ARG C 516 " model vdw 2.137 3.120 nonbonded pdb=" OG SER B 593 " pdb=" O LEU B 598 " model vdw 2.147 3.040 nonbonded pdb=" OG SER D 593 " pdb=" O LEU D 598 " model vdw 2.153 3.040 nonbonded pdb=" O ALA A 447 " pdb=" OG SER A 459 " model vdw 2.185 3.040 ... (remaining 283369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 719) selection = (chain 'B' and resid 1 through 719) selection = (chain 'C' and resid 1 through 719) selection = (chain 'D' and resid 1 through 719) selection = (chain 'E' and resid 1 through 719) selection = chain 'F' } 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=0.00 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: 2.370 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.450 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 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 : 0.007 0.332 34142 Z= 0.360 Angle : 0.765 17.203 46356 Z= 0.444 Chirality : 0.044 0.281 5166 Planarity : 0.005 0.056 6186 Dihedral : 15.737 89.652 12804 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.21 % Allowed : 0.35 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.36 (0.13), residues: 4302 helix: 1.62 (0.11), residues: 2243 sheet: 0.57 (0.22), residues: 537 loop : 0.06 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 134 TYR 0.020 0.002 TYR D 50 PHE 0.019 0.001 PHE A 692 TRP 0.024 0.002 TRP F 511 HIS 0.007 0.001 HIS B 527 Details of bonding type rmsd covalent geometry : bond 0.00686 (34142) covalent geometry : angle 0.76480 (46356) hydrogen bonds : bond 0.13513 ( 1874) hydrogen bonds : angle 5.83015 ( 5442) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 643 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6878 (mmp80) cc_final: 0.6225 (mtt-85) REVERT: A 268 TYR cc_start: 0.5846 (t80) cc_final: 0.5465 (t80) REVERT: A 313 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: A 322 THR cc_start: 0.5471 (m) cc_final: 0.4840 (p) REVERT: A 365 GLU cc_start: 0.6533 (pm20) cc_final: 0.6104 (tp30) REVERT: A 385 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7161 (mm-30) REVERT: A 410 GLN cc_start: 0.6593 (mp10) cc_final: 0.6328 (mt0) REVERT: A 425 ARG cc_start: 0.7153 (ttt90) cc_final: 0.6796 (ttt-90) REVERT: A 554 ARG cc_start: 0.4770 (tpt90) cc_final: 0.4190 (mtm-85) REVERT: A 655 THR cc_start: 0.7807 (p) cc_final: 0.6746 (p) REVERT: A 657 ARG cc_start: 0.6788 (tpp-160) cc_final: 0.6375 (mmm-85) REVERT: A 696 GLN cc_start: 0.7177 (tt0) cc_final: 0.6925 (tm-30) REVERT: B 1 MET cc_start: 0.5282 (tpt) cc_final: 0.5029 (pmm) REVERT: B 91 LEU cc_start: 0.7114 (tp) cc_final: 0.6705 (mt) REVERT: B 280 ARG cc_start: 0.7200 (ptt180) cc_final: 0.6629 (ptm160) REVERT: B 312 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8400 (mt) REVERT: B 410 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6658 (mt0) REVERT: B 544 LYS cc_start: 0.6746 (ttmt) cc_final: 0.6317 (tttm) REVERT: B 678 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6185 (mp0) REVERT: B 697 GLU cc_start: 0.6549 (mm-30) cc_final: 0.6180 (mt-10) REVERT: B 708 ARG cc_start: 0.5492 (mmp80) cc_final: 0.5201 (mtm110) REVERT: C 4 SER cc_start: 0.7987 (m) cc_final: 0.7711 (p) REVERT: C 33 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6487 (mp0) REVERT: C 114 ARG cc_start: 0.7478 (mmt-90) cc_final: 0.7174 (mmt-90) REVERT: C 195 GLU cc_start: 0.8394 (pt0) cc_final: 0.8162 (mm-30) REVERT: C 225 ARG cc_start: 0.6517 (tpt90) cc_final: 0.5948 (tpp-160) REVERT: C 229 GLU cc_start: 0.6011 (mt-10) cc_final: 0.5659 (mt-10) REVERT: C 269 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7153 (mm-30) REVERT: C 271 TYR cc_start: 0.7434 (t80) cc_final: 0.7185 (t80) REVERT: C 348 GLU cc_start: 0.7370 (tt0) cc_final: 0.6982 (mt-10) REVERT: C 461 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6913 (mt-10) REVERT: C 556 ARG cc_start: 0.7168 (tpp80) cc_final: 0.6728 (tpp-160) REVERT: C 659 GLU cc_start: 0.6903 (pt0) cc_final: 0.6587 (pm20) REVERT: C 690 GLU cc_start: 0.7063 (pp20) cc_final: 0.5976 (mp0) REVERT: C 708 ARG cc_start: 0.6453 (mmt-90) cc_final: 0.6029 (mtt180) REVERT: D 1 MET cc_start: 0.6289 (pmm) cc_final: 0.5957 (ptp) REVERT: D 19 GLU cc_start: 0.7621 (tt0) cc_final: 0.6921 (mp0) REVERT: D 33 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6771 (pm20) REVERT: D 110 LEU cc_start: 0.7216 (mm) cc_final: 0.6959 (tp) REVERT: D 219 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7627 (mm110) REVERT: D 476 GLU cc_start: 0.6915 (tt0) cc_final: 0.6605 (tt0) REVERT: D 490 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7284 (mtp180) REVERT: D 496 VAL cc_start: 0.8683 (p) cc_final: 0.8400 (t) REVERT: D 516 ARG cc_start: 0.6756 (ttt-90) cc_final: 0.6536 (tpp80) REVERT: D 556 ARG cc_start: 0.7458 (tpt90) cc_final: 0.6717 (tpp80) REVERT: D 557 TYR cc_start: 0.7200 (m-80) cc_final: 0.6894 (m-80) REVERT: D 651 LEU cc_start: 0.8101 (mt) cc_final: 0.7799 (mt) REVERT: D 659 GLU cc_start: 0.6981 (pt0) cc_final: 0.6779 (pm20) REVERT: D 678 GLU cc_start: 0.6681 (mt-10) cc_final: 0.5835 (mp0) REVERT: D 696 GLN cc_start: 0.6956 (tt0) cc_final: 0.6719 (mm-40) REVERT: D 708 ARG cc_start: 0.6876 (ptp-110) cc_final: 0.6522 (mtm180) REVERT: E 117 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7087 (mt-10) REVERT: E 127 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7882 (mt-10) REVERT: E 137 GLU cc_start: 0.8721 (tt0) cc_final: 0.7876 (tp30) REVERT: E 208 HIS cc_start: 0.7970 (t70) cc_final: 0.7251 (t-90) REVERT: E 368 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6660 (mm-30) REVERT: E 426 MET cc_start: 0.7403 (mtp) cc_final: 0.7151 (mtp) REVERT: E 462 GLN cc_start: 0.7852 (tt0) cc_final: 0.7648 (mt0) REVERT: E 469 HIS cc_start: 0.7878 (t-170) cc_final: 0.7664 (t-170) REVERT: E 510 TYR cc_start: 0.6183 (p90) cc_final: 0.5816 (t80) REVERT: E 516 ARG cc_start: 0.6750 (ttt180) cc_final: 0.6236 (ttp80) REVERT: E 668 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7207 (mm-40) REVERT: E 696 GLN cc_start: 0.7278 (tt0) cc_final: 0.6756 (tt0) REVERT: F 1 MET cc_start: 0.4208 (ppp) cc_final: 0.3785 (mpp) REVERT: F 2 ARG cc_start: 0.5288 (ttp80) cc_final: 0.5087 (ttp-170) REVERT: F 9 GLU cc_start: 0.3637 (tp30) cc_final: 0.3435 (tp30) REVERT: F 11 ARG cc_start: 0.4918 (mtm180) cc_final: 0.4548 (mtm180) REVERT: F 73 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7042 (mp0) REVERT: F 80 TYR cc_start: 0.5352 (m-80) cc_final: 0.5084 (m-80) REVERT: F 98 GLU cc_start: 0.5458 (pt0) cc_final: 0.4801 (pt0) REVERT: F 101 LEU cc_start: 0.6574 (tp) cc_final: 0.6157 (tp) REVERT: F 147 ARG cc_start: 0.5720 (ttm-80) cc_final: 0.5210 (tpt90) REVERT: F 164 LEU cc_start: 0.6085 (mm) cc_final: 0.5815 (tp) REVERT: F 247 PRO cc_start: 0.7375 (Cg_endo) cc_final: 0.7145 (Cg_exo) REVERT: F 251 ARG cc_start: 0.6390 (ttm170) cc_final: 0.5706 (mmm-85) REVERT: F 269 GLU cc_start: 0.6355 (mm-30) cc_final: 0.6144 (mm-30) REVERT: F 280 ARG cc_start: 0.4982 (ptt-90) cc_final: 0.4654 (ptm160) REVERT: F 433 MET cc_start: 0.3950 (ptp) cc_final: 0.3713 (ptm) REVERT: F 491 THR cc_start: 0.1986 (p) cc_final: 0.1672 (p) REVERT: F 500 ASN cc_start: 0.3773 (m110) cc_final: 0.2926 (p0) REVERT: F 520 ARG cc_start: 0.3924 (mmp-170) cc_final: 0.3451 (ttp-170) REVERT: F 606 VAL cc_start: 0.4767 (t) cc_final: 0.4246 (m) REVERT: F 615 LYS cc_start: 0.2139 (tttt) cc_final: 0.1935 (ttpt) REVERT: F 689 MET cc_start: 0.3894 (mmp) cc_final: 0.2683 (ttt) outliers start: 7 outliers final: 1 residues processed: 649 average time/residue: 0.2629 time to fit residues: 252.2900 Evaluate side-chains 315 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 312 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain C residue 57 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 223 GLN A 249 GLN B 208 HIS B 223 GLN B 696 GLN C 141 GLN C 332 ASN C 500 ASN D 429 GLN D 653 ASN ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 HIS E 543 HIS F 100 HIS F 113 ASN ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.193725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117965 restraints weight = 45177.291| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.83 r_work: 0.3270 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34142 Z= 0.232 Angle : 0.611 9.963 46356 Z= 0.310 Chirality : 0.041 0.183 5166 Planarity : 0.005 0.063 6186 Dihedral : 4.292 46.217 4806 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.91 % Favored : 98.07 % Rotamer: Outliers : 1.41 % Allowed : 7.10 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.28 (0.13), residues: 4302 helix: 1.58 (0.11), residues: 2277 sheet: 0.34 (0.22), residues: 532 loop : 0.03 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 2 TYR 0.025 0.002 TYR C 557 PHE 0.017 0.002 PHE D 630 TRP 0.022 0.002 TRP B 250 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00547 (34142) covalent geometry : angle 0.61056 (46356) hydrogen bonds : bond 0.04275 ( 1874) hydrogen bonds : angle 4.71608 ( 5442) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 339 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.8529 (p90) cc_final: 0.8308 (p90) REVERT: A 44 ARG cc_start: 0.6871 (mmp80) cc_final: 0.6126 (mtt-85) REVERT: A 182 GLU cc_start: 0.4641 (OUTLIER) cc_final: 0.4135 (tp30) REVERT: A 269 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6529 (mm-30) REVERT: A 271 TYR cc_start: 0.7026 (p90) cc_final: 0.6559 (p90) REVERT: A 276 ARG cc_start: 0.5951 (mtp85) cc_final: 0.4914 (mtp-110) REVERT: A 303 HIS cc_start: 0.6200 (m90) cc_final: 0.5365 (m90) REVERT: A 365 GLU cc_start: 0.6765 (pm20) cc_final: 0.6175 (tp30) REVERT: A 554 ARG cc_start: 0.4926 (tpt90) cc_final: 0.4301 (mtm-85) REVERT: A 634 LYS cc_start: 0.8036 (tttt) cc_final: 0.7691 (ttpp) REVERT: A 657 ARG cc_start: 0.7431 (tpp-160) cc_final: 0.6986 (mmt-90) REVERT: A 678 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7533 (tt0) REVERT: B 1 MET cc_start: 0.6600 (tpt) cc_final: 0.6392 (tpp) REVERT: B 199 ARG cc_start: 0.7542 (ptp-110) cc_final: 0.7279 (ptp90) REVERT: B 298 ARG cc_start: 0.7629 (mmt180) cc_final: 0.7133 (mmm160) REVERT: B 410 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7793 (mt0) REVERT: B 544 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7433 (tmtt) REVERT: B 678 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7689 (mp0) REVERT: B 697 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7033 (mt-10) REVERT: B 708 ARG cc_start: 0.6483 (mmp80) cc_final: 0.6014 (mtm110) REVERT: C 33 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7690 (mp0) REVERT: C 40 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8202 (mt-10) REVERT: C 86 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7556 (tpt-90) REVERT: C 114 ARG cc_start: 0.7755 (mmt-90) cc_final: 0.7501 (mpt180) REVERT: C 195 GLU cc_start: 0.8552 (pt0) cc_final: 0.8318 (mm-30) REVERT: C 200 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7367 (tpt90) REVERT: C 225 ARG cc_start: 0.7474 (tpt90) cc_final: 0.6828 (tpp-160) REVERT: C 229 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6754 (mt-10) REVERT: C 290 TRP cc_start: 0.7918 (m100) cc_final: 0.7378 (m-10) REVERT: C 348 GLU cc_start: 0.7838 (tt0) cc_final: 0.7492 (mt-10) REVERT: C 659 GLU cc_start: 0.8326 (pt0) cc_final: 0.8053 (pm20) REVERT: C 708 ARG cc_start: 0.7229 (mmt-90) cc_final: 0.6688 (mtt180) REVERT: D 1 MET cc_start: 0.7631 (pmm) cc_final: 0.7247 (ptm) REVERT: D 19 GLU cc_start: 0.7904 (tt0) cc_final: 0.7374 (mp0) REVERT: D 33 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7892 (pm20) REVERT: D 110 LEU cc_start: 0.7975 (mm) cc_final: 0.7640 (tp) REVERT: D 219 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7906 (mm110) REVERT: D 498 GLU cc_start: 0.7237 (tt0) cc_final: 0.6995 (tt0) REVERT: D 556 ARG cc_start: 0.8459 (tpt90) cc_final: 0.7697 (tpp80) REVERT: D 557 TYR cc_start: 0.8157 (m-80) cc_final: 0.7776 (m-80) REVERT: D 651 LEU cc_start: 0.8719 (mt) cc_final: 0.8477 (mt) REVERT: D 678 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7461 (mp0) REVERT: D 696 GLN cc_start: 0.7726 (tt0) cc_final: 0.7482 (tp40) REVERT: D 708 ARG cc_start: 0.7542 (ptp-110) cc_final: 0.7032 (mtm180) REVERT: D 713 HIS cc_start: 0.1654 (OUTLIER) cc_final: 0.0795 (m170) REVERT: E 127 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7951 (mt-10) REVERT: E 137 GLU cc_start: 0.8791 (tt0) cc_final: 0.8015 (tp30) REVERT: E 149 GLU cc_start: 0.7638 (tp30) cc_final: 0.7324 (tp30) REVERT: E 208 HIS cc_start: 0.8091 (t70) cc_final: 0.7408 (t-90) REVERT: E 229 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7419 (mt-10) REVERT: E 241 THR cc_start: 0.8093 (m) cc_final: 0.7858 (p) REVERT: E 510 TYR cc_start: 0.6963 (p90) cc_final: 0.5950 (t80) REVERT: E 516 ARG cc_start: 0.7377 (ttt180) cc_final: 0.6948 (ttp80) REVERT: E 560 HIS cc_start: 0.7247 (m90) cc_final: 0.6444 (m90) REVERT: E 651 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8580 (mt) REVERT: E 696 GLN cc_start: 0.7468 (tt0) cc_final: 0.7016 (tt0) REVERT: F 1 MET cc_start: 0.4319 (ppp) cc_final: 0.3781 (mpp) REVERT: F 9 GLU cc_start: 0.4114 (tp30) cc_final: 0.3599 (tp30) REVERT: F 73 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7070 (mp0) REVERT: F 80 TYR cc_start: 0.6046 (m-80) cc_final: 0.5751 (m-80) REVERT: F 94 PRO cc_start: 0.5775 (Cg_exo) cc_final: 0.5566 (Cg_endo) REVERT: F 101 LEU cc_start: 0.6507 (tp) cc_final: 0.6117 (tp) REVERT: F 164 LEU cc_start: 0.6073 (mm) cc_final: 0.5811 (tp) REVERT: F 243 GLU cc_start: 0.4532 (pt0) cc_final: 0.4202 (tp30) REVERT: F 324 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: F 500 ASN cc_start: 0.3926 (m110) cc_final: 0.3311 (p0) REVERT: F 520 ARG cc_start: 0.4073 (mmp-170) cc_final: 0.3447 (ttm170) REVERT: F 606 VAL cc_start: 0.5144 (t) cc_final: 0.4547 (m) REVERT: F 689 MET cc_start: 0.3545 (mmp) cc_final: 0.2586 (ttt) outliers start: 48 outliers final: 29 residues processed: 374 average time/residue: 0.2424 time to fit residues: 135.8884 Evaluate side-chains 275 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 527 HIS Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 363 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 270 optimal weight: 0.7980 chunk 88 optimal weight: 40.0000 chunk 424 optimal weight: 7.9990 chunk 383 optimal weight: 30.0000 chunk 420 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 338 optimal weight: 0.2980 chunk 246 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 HIS ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.196119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125256 restraints weight = 44270.757| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.11 r_work: 0.3236 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34142 Z= 0.122 Angle : 0.509 7.823 46356 Z= 0.256 Chirality : 0.038 0.215 5166 Planarity : 0.004 0.063 6186 Dihedral : 3.945 45.277 4802 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.72 % Favored : 98.26 % Rotamer: Outliers : 1.47 % Allowed : 8.60 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.51 (0.13), residues: 4302 helix: 1.89 (0.11), residues: 2237 sheet: 0.32 (0.22), residues: 532 loop : 0.03 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 381 TYR 0.023 0.002 TYR C 557 PHE 0.016 0.001 PHE C 124 TRP 0.018 0.001 TRP B 250 HIS 0.008 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00268 (34142) covalent geometry : angle 0.50899 (46356) hydrogen bonds : bond 0.03818 ( 1874) hydrogen bonds : angle 4.35739 ( 5442) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 298 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6914 (mmp80) cc_final: 0.6175 (mtt-85) REVERT: A 182 GLU cc_start: 0.4657 (OUTLIER) cc_final: 0.4135 (tp30) REVERT: A 271 TYR cc_start: 0.6985 (p90) cc_final: 0.6534 (p90) REVERT: A 276 ARG cc_start: 0.6176 (mtp85) cc_final: 0.5301 (mtp-110) REVERT: A 303 HIS cc_start: 0.6112 (m90) cc_final: 0.5354 (m90) REVERT: A 356 MET cc_start: 0.6584 (mtm) cc_final: 0.6376 (mtm) REVERT: A 365 GLU cc_start: 0.6820 (pm20) cc_final: 0.6284 (tp30) REVERT: A 468 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7548 (mm-30) REVERT: A 554 ARG cc_start: 0.4844 (tpt90) cc_final: 0.4187 (mtm-85) REVERT: A 627 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: A 678 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7461 (tm-30) REVERT: B 1 MET cc_start: 0.6509 (tpt) cc_final: 0.6270 (tpp) REVERT: B 199 ARG cc_start: 0.7640 (ptp-110) cc_final: 0.7396 (ptp90) REVERT: B 298 ARG cc_start: 0.7608 (mmt180) cc_final: 0.7099 (mmm160) REVERT: B 350 GLU cc_start: 0.6842 (tt0) cc_final: 0.6502 (mt-10) REVERT: B 381 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7623 (ttm-80) REVERT: B 410 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7734 (mt0) REVERT: B 544 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7299 (tmtt) REVERT: B 678 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7543 (mp0) REVERT: B 697 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6968 (mt-10) REVERT: B 708 ARG cc_start: 0.6438 (mmp80) cc_final: 0.6053 (mtt-85) REVERT: C 33 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7655 (mp0) REVERT: C 86 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7459 (tpt-90) REVERT: C 108 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7730 (mp) REVERT: C 195 GLU cc_start: 0.8546 (pt0) cc_final: 0.8323 (mm-30) REVERT: C 200 ARG cc_start: 0.7945 (mtp85) cc_final: 0.7356 (tpt90) REVERT: C 225 ARG cc_start: 0.7343 (tpt90) cc_final: 0.6662 (tpp-160) REVERT: C 229 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6458 (mt-10) REVERT: C 290 TRP cc_start: 0.7818 (m100) cc_final: 0.6909 (m-10) REVERT: C 320 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8168 (mm-30) REVERT: C 348 GLU cc_start: 0.7862 (tt0) cc_final: 0.7494 (mt-10) REVERT: C 659 GLU cc_start: 0.8250 (pt0) cc_final: 0.7865 (pm20) REVERT: C 708 ARG cc_start: 0.7082 (mmt-90) cc_final: 0.6575 (mtt180) REVERT: D 1 MET cc_start: 0.7709 (pmm) cc_final: 0.7330 (ptm) REVERT: D 19 GLU cc_start: 0.7941 (tt0) cc_final: 0.7252 (mp0) REVERT: D 33 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7830 (pm20) REVERT: D 110 LEU cc_start: 0.7935 (mm) cc_final: 0.7561 (tp) REVERT: D 114 ARG cc_start: 0.7559 (mmp80) cc_final: 0.7220 (mmp-170) REVERT: D 141 GLN cc_start: 0.7853 (mt0) cc_final: 0.7281 (pp30) REVERT: D 199 ARG cc_start: 0.7650 (mtm180) cc_final: 0.7431 (mtp180) REVERT: D 219 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7816 (mm110) REVERT: D 296 LEU cc_start: 0.9070 (mt) cc_final: 0.8825 (mp) REVERT: D 556 ARG cc_start: 0.8338 (tpt90) cc_final: 0.7635 (tpp80) REVERT: D 651 LEU cc_start: 0.8678 (mt) cc_final: 0.8416 (mt) REVERT: D 678 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7584 (mp0) REVERT: D 696 GLN cc_start: 0.7597 (tt0) cc_final: 0.7241 (tp40) REVERT: D 708 ARG cc_start: 0.7534 (ptp-110) cc_final: 0.7086 (mtm180) REVERT: D 713 HIS cc_start: 0.1532 (OUTLIER) cc_final: 0.0700 (m170) REVERT: E 1 MET cc_start: 0.6519 (ppp) cc_final: 0.5993 (ppp) REVERT: E 127 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7965 (mt-10) REVERT: E 137 GLU cc_start: 0.8827 (tt0) cc_final: 0.8036 (tp30) REVERT: E 208 HIS cc_start: 0.8076 (t70) cc_final: 0.7416 (t-90) REVERT: E 219 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: E 229 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7444 (mt-10) REVERT: E 241 THR cc_start: 0.7972 (m) cc_final: 0.7720 (p) REVERT: E 510 TYR cc_start: 0.7100 (p90) cc_final: 0.6114 (t80) REVERT: E 516 ARG cc_start: 0.7341 (ttt180) cc_final: 0.6961 (ttp80) REVERT: E 641 THR cc_start: 0.7951 (p) cc_final: 0.7665 (p) REVERT: E 651 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8495 (mt) REVERT: E 696 GLN cc_start: 0.7349 (tt0) cc_final: 0.6984 (tt0) REVERT: F 1 MET cc_start: 0.4351 (ppp) cc_final: 0.3872 (mpp) REVERT: F 37 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6819 (mt-10) REVERT: F 74 THR cc_start: 0.6241 (t) cc_final: 0.5915 (t) REVERT: F 80 TYR cc_start: 0.6049 (m-80) cc_final: 0.5727 (m-80) REVERT: F 98 GLU cc_start: 0.5539 (pt0) cc_final: 0.4916 (pt0) REVERT: F 147 ARG cc_start: 0.5587 (ttm-80) cc_final: 0.5191 (tpt90) REVERT: F 164 LEU cc_start: 0.5999 (mm) cc_final: 0.5706 (tp) REVERT: F 181 GLU cc_start: 0.7736 (tp30) cc_final: 0.7234 (tt0) REVERT: F 243 GLU cc_start: 0.4739 (pt0) cc_final: 0.4405 (tp30) REVERT: F 324 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: F 450 LEU cc_start: 0.4534 (mt) cc_final: 0.4216 (mp) REVERT: F 520 ARG cc_start: 0.4080 (mmp-170) cc_final: 0.3458 (ttm170) REVERT: F 615 LYS cc_start: 0.3326 (tttt) cc_final: 0.2868 (ttpt) REVERT: F 634 LYS cc_start: 0.6168 (mttm) cc_final: 0.5643 (ptpt) REVERT: F 689 MET cc_start: 0.3491 (mmp) cc_final: 0.2657 (ttt) outliers start: 50 outliers final: 33 residues processed: 338 average time/residue: 0.2480 time to fit residues: 127.5001 Evaluate side-chains 292 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 527 HIS Chi-restraints excluded: chain D residue 560 HIS Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 363 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 307 optimal weight: 9.9990 chunk 292 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 311 optimal weight: 6.9990 chunk 301 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 370 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN F 407 GLN ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.193627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122432 restraints weight = 44185.224| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.00 r_work: 0.3199 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 34142 Z= 0.194 Angle : 0.536 7.748 46356 Z= 0.269 Chirality : 0.039 0.170 5166 Planarity : 0.004 0.062 6186 Dihedral : 3.987 46.693 4802 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.81 % Favored : 98.16 % Rotamer: Outliers : 1.97 % Allowed : 9.60 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.43 (0.13), residues: 4302 helix: 1.82 (0.11), residues: 2234 sheet: 0.19 (0.22), residues: 529 loop : 0.03 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 120 TYR 0.027 0.002 TYR C 557 PHE 0.018 0.001 PHE A 30 TRP 0.020 0.001 TRP B 250 HIS 0.008 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00459 (34142) covalent geometry : angle 0.53575 (46356) hydrogen bonds : bond 0.03815 ( 1874) hydrogen bonds : angle 4.30294 ( 5442) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.4672 (OUTLIER) cc_final: 0.4141 (tp30) REVERT: A 271 TYR cc_start: 0.7020 (p90) cc_final: 0.6293 (p90) REVERT: A 276 ARG cc_start: 0.6230 (mtp85) cc_final: 0.5380 (mtp85) REVERT: A 303 HIS cc_start: 0.6219 (m90) cc_final: 0.5472 (m90) REVERT: A 356 MET cc_start: 0.6703 (mtm) cc_final: 0.6455 (mtm) REVERT: A 554 ARG cc_start: 0.4843 (tpt90) cc_final: 0.4199 (mtm-85) REVERT: A 627 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: A 634 LYS cc_start: 0.8077 (tttt) cc_final: 0.7678 (ttpp) REVERT: A 678 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7564 (tm-30) REVERT: B 199 ARG cc_start: 0.7641 (ptp-110) cc_final: 0.7390 (ptp90) REVERT: B 298 ARG cc_start: 0.7645 (mmt180) cc_final: 0.7091 (mmm160) REVERT: B 350 GLU cc_start: 0.6928 (tt0) cc_final: 0.6589 (mt-10) REVERT: B 410 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7822 (mt0) REVERT: B 542 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.5453 (t80) REVERT: B 544 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7293 (tmtt) REVERT: B 678 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7609 (mp0) REVERT: B 697 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6949 (mt-10) REVERT: B 708 ARG cc_start: 0.6375 (mmp80) cc_final: 0.6054 (mtt-85) REVERT: C 33 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7667 (mp0) REVERT: C 40 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8172 (mt-10) REVERT: C 86 ARG cc_start: 0.8090 (mmm-85) cc_final: 0.7426 (tpt-90) REVERT: C 108 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7768 (mp) REVERT: C 113 ASN cc_start: 0.7791 (m-40) cc_final: 0.7413 (m110) REVERT: C 195 GLU cc_start: 0.8554 (pt0) cc_final: 0.8354 (mm-30) REVERT: C 200 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7373 (tpt90) REVERT: C 225 ARG cc_start: 0.7422 (tpt90) cc_final: 0.6752 (tpp-160) REVERT: C 229 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6479 (mt-10) REVERT: C 281 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7708 (tt) REVERT: C 290 TRP cc_start: 0.7873 (m100) cc_final: 0.6983 (m-10) REVERT: C 348 GLU cc_start: 0.7879 (tt0) cc_final: 0.7571 (mt-10) REVERT: C 385 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: C 659 GLU cc_start: 0.8233 (pt0) cc_final: 0.7866 (pm20) REVERT: C 708 ARG cc_start: 0.7131 (mmt-90) cc_final: 0.6567 (mtt180) REVERT: D 1 MET cc_start: 0.7719 (pmm) cc_final: 0.7355 (ptm) REVERT: D 19 GLU cc_start: 0.7969 (tt0) cc_final: 0.7328 (mp0) REVERT: D 33 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7876 (pm20) REVERT: D 110 LEU cc_start: 0.8008 (mm) cc_final: 0.7604 (tp) REVERT: D 114 ARG cc_start: 0.7656 (mmp80) cc_final: 0.7403 (mmp-170) REVERT: D 199 ARG cc_start: 0.7704 (mtm180) cc_final: 0.7498 (mtp180) REVERT: D 219 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7854 (mm110) REVERT: D 296 LEU cc_start: 0.9134 (mt) cc_final: 0.8900 (mp) REVERT: D 556 ARG cc_start: 0.8428 (tpt90) cc_final: 0.7802 (tpp80) REVERT: D 651 LEU cc_start: 0.8767 (mt) cc_final: 0.8510 (mt) REVERT: D 678 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7455 (mp0) REVERT: D 696 GLN cc_start: 0.7689 (tt0) cc_final: 0.7387 (tp40) REVERT: D 708 ARG cc_start: 0.7613 (ptp-110) cc_final: 0.7135 (mtm180) REVERT: D 713 HIS cc_start: 0.1682 (OUTLIER) cc_final: 0.0849 (m170) REVERT: E 1 MET cc_start: 0.6613 (ppp) cc_final: 0.5921 (ppp) REVERT: E 127 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7982 (mt-10) REVERT: E 137 GLU cc_start: 0.8870 (tt0) cc_final: 0.8103 (tp30) REVERT: E 149 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6950 (mt-10) REVERT: E 207 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7043 (mp) REVERT: E 208 HIS cc_start: 0.8083 (t70) cc_final: 0.7407 (t-90) REVERT: E 219 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8035 (mp10) REVERT: E 229 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7437 (mt-10) REVERT: E 241 THR cc_start: 0.8067 (m) cc_final: 0.7778 (p) REVERT: E 490 ARG cc_start: 0.6956 (mtp-110) cc_final: 0.6638 (mtp85) REVERT: E 510 TYR cc_start: 0.7135 (p90) cc_final: 0.6170 (t80) REVERT: E 516 ARG cc_start: 0.7402 (ttt180) cc_final: 0.7106 (ttp80) REVERT: E 641 THR cc_start: 0.8091 (p) cc_final: 0.7825 (p) REVERT: E 651 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8515 (mt) REVERT: E 696 GLN cc_start: 0.7400 (tt0) cc_final: 0.7017 (tt0) REVERT: F 1 MET cc_start: 0.4216 (ppp) cc_final: 0.3729 (mpp) REVERT: F 80 TYR cc_start: 0.5985 (m-80) cc_final: 0.5727 (m-80) REVERT: F 147 ARG cc_start: 0.5548 (ttm-80) cc_final: 0.5154 (tpt90) REVERT: F 181 GLU cc_start: 0.7860 (tp30) cc_final: 0.7120 (tt0) REVERT: F 243 GLU cc_start: 0.4856 (pt0) cc_final: 0.4551 (tp30) REVERT: F 324 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: F 450 LEU cc_start: 0.4455 (mt) cc_final: 0.4123 (mp) REVERT: F 520 ARG cc_start: 0.4062 (mmp-170) cc_final: 0.3371 (ttm170) REVERT: F 689 MET cc_start: 0.3394 (mmp) cc_final: 0.2523 (ttt) outliers start: 67 outliers final: 38 residues processed: 319 average time/residue: 0.2491 time to fit residues: 122.8911 Evaluate side-chains 296 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 205 TRP Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 527 HIS Chi-restraints excluded: chain D residue 560 HIS Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 363 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 64 optimal weight: 9.9990 chunk 386 optimal weight: 8.9990 chunk 278 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 312 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 chunk 30 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 ASN C 469 HIS F 249 GLN ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.191539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117315 restraints weight = 43941.134| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.86 r_work: 0.3181 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 34142 Z= 0.263 Angle : 0.577 8.181 46356 Z= 0.290 Chirality : 0.041 0.250 5166 Planarity : 0.005 0.064 6186 Dihedral : 4.118 47.569 4802 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.00 % Favored : 97.98 % Rotamer: Outliers : 2.41 % Allowed : 10.68 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.22 (0.13), residues: 4302 helix: 1.66 (0.11), residues: 2242 sheet: 0.01 (0.22), residues: 529 loop : -0.05 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 120 TYR 0.028 0.002 TYR C 557 PHE 0.015 0.002 PHE D 630 TRP 0.023 0.002 TRP B 250 HIS 0.006 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00628 (34142) covalent geometry : angle 0.57734 (46356) hydrogen bonds : bond 0.03958 ( 1874) hydrogen bonds : angle 4.36556 ( 5442) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 257 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.4681 (OUTLIER) cc_final: 0.4190 (tp30) REVERT: A 271 TYR cc_start: 0.6839 (p90) cc_final: 0.6277 (p90) REVERT: A 276 ARG cc_start: 0.6309 (mtp85) cc_final: 0.5458 (mtp85) REVERT: A 303 HIS cc_start: 0.6217 (m90) cc_final: 0.5530 (m90) REVERT: A 365 GLU cc_start: 0.6692 (pm20) cc_final: 0.6259 (tp30) REVERT: A 554 ARG cc_start: 0.4953 (tpt90) cc_final: 0.4273 (mtm-85) REVERT: A 634 LYS cc_start: 0.8059 (tttt) cc_final: 0.7676 (ttpp) REVERT: A 678 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7562 (tm-30) REVERT: B 199 ARG cc_start: 0.7642 (ptp-110) cc_final: 0.7377 (ptp90) REVERT: B 298 ARG cc_start: 0.7611 (mmt180) cc_final: 0.6987 (mmm160) REVERT: B 350 GLU cc_start: 0.6883 (tt0) cc_final: 0.6554 (mt-10) REVERT: B 410 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7763 (mt0) REVERT: B 542 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5388 (t80) REVERT: B 544 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7199 (tmtt) REVERT: B 697 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6817 (mt-10) REVERT: B 708 ARG cc_start: 0.6395 (mmp80) cc_final: 0.6080 (mtt-85) REVERT: C 33 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7656 (mp0) REVERT: C 40 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8142 (mt-10) REVERT: C 86 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7420 (tpt-90) REVERT: C 108 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7843 (mp) REVERT: C 200 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7359 (tpt90) REVERT: C 225 ARG cc_start: 0.7361 (tpt90) cc_final: 0.6762 (tpp-160) REVERT: C 229 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6422 (mt-10) REVERT: C 290 TRP cc_start: 0.7896 (m100) cc_final: 0.7308 (m-10) REVERT: C 348 GLU cc_start: 0.7841 (tt0) cc_final: 0.7532 (mt-10) REVERT: C 659 GLU cc_start: 0.8176 (pt0) cc_final: 0.7797 (pm20) REVERT: C 708 ARG cc_start: 0.7164 (mmt-90) cc_final: 0.6673 (mtt180) REVERT: D 1 MET cc_start: 0.7617 (pmm) cc_final: 0.7321 (ptm) REVERT: D 19 GLU cc_start: 0.8041 (tt0) cc_final: 0.7323 (mp0) REVERT: D 33 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7886 (pm20) REVERT: D 110 LEU cc_start: 0.8021 (mm) cc_final: 0.7757 (tp) REVERT: D 114 ARG cc_start: 0.7583 (mmp80) cc_final: 0.7352 (mmp-170) REVERT: D 199 ARG cc_start: 0.7618 (mtm180) cc_final: 0.7401 (mtp180) REVERT: D 207 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7450 (mm) REVERT: D 219 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7730 (mm110) REVERT: D 296 LEU cc_start: 0.9136 (mt) cc_final: 0.8884 (mp) REVERT: D 651 LEU cc_start: 0.8830 (mt) cc_final: 0.8565 (mt) REVERT: D 678 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7699 (mp0) REVERT: D 696 GLN cc_start: 0.7658 (tt0) cc_final: 0.7211 (tp40) REVERT: D 708 ARG cc_start: 0.7621 (ptp-110) cc_final: 0.6999 (mtm180) REVERT: D 713 HIS cc_start: 0.1722 (OUTLIER) cc_final: 0.1005 (m170) REVERT: E 1 MET cc_start: 0.6547 (ppp) cc_final: 0.5689 (ppp) REVERT: E 127 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7923 (mt-10) REVERT: E 137 GLU cc_start: 0.8897 (tt0) cc_final: 0.8494 (pt0) REVERT: E 207 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.6973 (mp) REVERT: E 208 HIS cc_start: 0.8042 (t70) cc_final: 0.7362 (t-90) REVERT: E 219 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: E 241 THR cc_start: 0.8177 (m) cc_final: 0.7796 (p) REVERT: E 516 ARG cc_start: 0.7428 (ttt180) cc_final: 0.7123 (ttp80) REVERT: E 651 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8492 (mt) REVERT: E 696 GLN cc_start: 0.7413 (tt0) cc_final: 0.7213 (tt0) REVERT: F 1 MET cc_start: 0.3917 (ppp) cc_final: 0.3583 (mpp) REVERT: F 37 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: F 80 TYR cc_start: 0.5855 (m-80) cc_final: 0.5640 (m-80) REVERT: F 164 LEU cc_start: 0.5822 (mm) cc_final: 0.5486 (tp) REVERT: F 243 GLU cc_start: 0.4917 (pt0) cc_final: 0.4560 (tp30) REVERT: F 324 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: F 450 LEU cc_start: 0.4274 (mt) cc_final: 0.3961 (mp) REVERT: F 520 ARG cc_start: 0.4154 (mmp-170) cc_final: 0.3462 (ttm170) REVERT: F 571 PHE cc_start: 0.4942 (m-10) cc_final: 0.4702 (m-10) REVERT: F 689 MET cc_start: 0.3386 (mmp) cc_final: 0.2430 (ttt) REVERT: F 710 GLU cc_start: 0.1617 (mp0) cc_final: 0.1132 (tt0) outliers start: 82 outliers final: 50 residues processed: 320 average time/residue: 0.2381 time to fit residues: 116.4214 Evaluate side-chains 300 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 205 TRP Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 527 HIS Chi-restraints excluded: chain D residue 560 HIS Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 634 LYS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 363 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 205 optimal weight: 0.3980 chunk 201 optimal weight: 0.9980 chunk 324 optimal weight: 0.9990 chunk 384 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 345 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 361 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 199 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN F 100 HIS ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.195860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122574 restraints weight = 43720.022| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.92 r_work: 0.3244 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 34142 Z= 0.107 Angle : 0.483 8.107 46356 Z= 0.242 Chirality : 0.037 0.232 5166 Planarity : 0.004 0.065 6186 Dihedral : 3.850 44.455 4802 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.74 % Favored : 98.21 % Rotamer: Outliers : 1.88 % Allowed : 11.56 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.50 (0.13), residues: 4302 helix: 1.92 (0.11), residues: 2247 sheet: 0.13 (0.22), residues: 532 loop : -0.01 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 120 TYR 0.022 0.001 TYR C 557 PHE 0.015 0.001 PHE D 629 TRP 0.023 0.001 TRP B 250 HIS 0.008 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00235 (34142) covalent geometry : angle 0.48277 (46356) hydrogen bonds : bond 0.03500 ( 1874) hydrogen bonds : angle 4.07363 ( 5442) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 281 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.4668 (OUTLIER) cc_final: 0.4141 (tp30) REVERT: A 271 TYR cc_start: 0.6704 (p90) cc_final: 0.6369 (p90) REVERT: A 276 ARG cc_start: 0.6267 (mtp85) cc_final: 0.5321 (mtp-110) REVERT: A 303 HIS cc_start: 0.6075 (m90) cc_final: 0.5377 (m90) REVERT: A 554 ARG cc_start: 0.4994 (tpt90) cc_final: 0.4280 (mtm-85) REVERT: A 678 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7525 (tt0) REVERT: B 199 ARG cc_start: 0.7650 (ptp-110) cc_final: 0.7344 (ptp90) REVERT: B 298 ARG cc_start: 0.7603 (mmt180) cc_final: 0.7050 (mmm160) REVERT: B 350 GLU cc_start: 0.6830 (tt0) cc_final: 0.6550 (mt-10) REVERT: B 410 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7756 (mt0) REVERT: B 542 PHE cc_start: 0.6373 (OUTLIER) cc_final: 0.5316 (t80) REVERT: B 544 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7125 (tmtt) REVERT: B 697 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6816 (mt-10) REVERT: B 708 ARG cc_start: 0.6372 (mmp80) cc_final: 0.6028 (mtt-85) REVERT: C 33 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7605 (mp0) REVERT: C 86 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7466 (tpt-90) REVERT: C 125 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6823 (mm) REVERT: C 200 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7347 (tpt90) REVERT: C 225 ARG cc_start: 0.7276 (tpt90) cc_final: 0.6671 (tpp-160) REVERT: C 229 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6339 (mt-10) REVERT: C 281 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7571 (tt) REVERT: C 290 TRP cc_start: 0.7814 (m100) cc_final: 0.7245 (m-10) REVERT: C 320 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8238 (mp0) REVERT: C 348 GLU cc_start: 0.7889 (tt0) cc_final: 0.7574 (mt-10) REVERT: C 659 GLU cc_start: 0.8122 (pt0) cc_final: 0.7755 (pm20) REVERT: C 708 ARG cc_start: 0.7140 (mmt-90) cc_final: 0.6679 (mtt180) REVERT: D 1 MET cc_start: 0.7606 (pmm) cc_final: 0.7284 (ptm) REVERT: D 33 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7772 (pm20) REVERT: D 110 LEU cc_start: 0.7924 (mm) cc_final: 0.7536 (tp) REVERT: D 114 ARG cc_start: 0.7544 (mmp80) cc_final: 0.7340 (mmp-170) REVERT: D 141 GLN cc_start: 0.7800 (mt0) cc_final: 0.7296 (pp30) REVERT: D 219 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7647 (mm110) REVERT: D 296 LEU cc_start: 0.9043 (mt) cc_final: 0.8794 (mp) REVERT: D 461 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7559 (mt-10) REVERT: D 556 ARG cc_start: 0.8387 (tpt90) cc_final: 0.7723 (tpp80) REVERT: D 651 LEU cc_start: 0.8716 (mt) cc_final: 0.8454 (mt) REVERT: D 678 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7465 (mp0) REVERT: D 696 GLN cc_start: 0.7611 (tt0) cc_final: 0.7183 (tp40) REVERT: D 708 ARG cc_start: 0.7580 (ptp-110) cc_final: 0.7171 (mtm110) REVERT: D 713 HIS cc_start: 0.1617 (OUTLIER) cc_final: 0.0929 (m170) REVERT: E 1 MET cc_start: 0.6530 (ppp) cc_final: 0.5703 (ppp) REVERT: E 127 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7901 (mt-10) REVERT: E 137 GLU cc_start: 0.8890 (tt0) cc_final: 0.8478 (pt0) REVERT: E 149 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6996 (mt-10) REVERT: E 208 HIS cc_start: 0.8042 (t70) cc_final: 0.7450 (t-90) REVERT: E 219 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8001 (mp10) REVERT: E 241 THR cc_start: 0.8132 (m) cc_final: 0.7882 (p) REVERT: E 490 ARG cc_start: 0.7350 (mtp85) cc_final: 0.6899 (mtp85) REVERT: E 516 ARG cc_start: 0.7305 (ttt180) cc_final: 0.7020 (ttp80) REVERT: E 568 SER cc_start: 0.7626 (m) cc_final: 0.7184 (p) REVERT: E 651 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8446 (mt) REVERT: E 696 GLN cc_start: 0.7406 (tt0) cc_final: 0.7085 (tt0) REVERT: F 1 MET cc_start: 0.3976 (ppp) cc_final: 0.3630 (mpp) REVERT: F 9 GLU cc_start: 0.3505 (tp30) cc_final: 0.2928 (mm-30) REVERT: F 37 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: F 126 ARG cc_start: 0.7090 (ptm-80) cc_final: 0.6384 (mmm160) REVERT: F 164 LEU cc_start: 0.5855 (mm) cc_final: 0.5482 (tp) REVERT: F 243 GLU cc_start: 0.4823 (pt0) cc_final: 0.4595 (tp30) REVERT: F 313 ASP cc_start: 0.6257 (t0) cc_final: 0.5963 (t0) REVERT: F 365 GLU cc_start: 0.7730 (mp0) cc_final: 0.6823 (pp20) REVERT: F 372 GLU cc_start: 0.6373 (mp0) cc_final: 0.5995 (mp0) REVERT: F 450 LEU cc_start: 0.4416 (mt) cc_final: 0.4077 (mp) REVERT: F 520 ARG cc_start: 0.4121 (mmp-170) cc_final: 0.3435 (ttm170) REVERT: F 571 PHE cc_start: 0.4936 (m-10) cc_final: 0.4690 (m-10) REVERT: F 634 LYS cc_start: 0.6341 (mttm) cc_final: 0.5787 (ptpt) REVERT: F 689 MET cc_start: 0.3368 (mmp) cc_final: 0.2429 (ttt) outliers start: 64 outliers final: 33 residues processed: 332 average time/residue: 0.2656 time to fit residues: 132.5874 Evaluate side-chains 292 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 560 HIS Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 363 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 302 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 356 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 406 optimal weight: 30.0000 chunk 320 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS C 113 ASN ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.190946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117908 restraints weight = 44330.376| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.20 r_work: 0.3142 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 34142 Z= 0.301 Angle : 0.620 18.015 46356 Z= 0.309 Chirality : 0.042 0.219 5166 Planarity : 0.005 0.069 6186 Dihedral : 4.107 21.461 4800 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.29 % Allowed : 11.77 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.17 (0.13), residues: 4302 helix: 1.67 (0.11), residues: 2222 sheet: -0.13 (0.21), residues: 547 loop : -0.09 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 120 TYR 0.030 0.002 TYR C 557 PHE 0.019 0.002 PHE A 571 TRP 0.030 0.002 TRP B 250 HIS 0.007 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00722 (34142) covalent geometry : angle 0.62008 (46356) hydrogen bonds : bond 0.04004 ( 1874) hydrogen bonds : angle 4.35804 ( 5442) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 241 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.4821 (OUTLIER) cc_final: 0.4339 (tp30) REVERT: A 271 TYR cc_start: 0.6841 (p90) cc_final: 0.6516 (p90) REVERT: A 276 ARG cc_start: 0.6341 (mtp85) cc_final: 0.5346 (mtp-110) REVERT: A 283 TYR cc_start: 0.3532 (OUTLIER) cc_final: 0.2511 (m-80) REVERT: A 303 HIS cc_start: 0.6143 (m90) cc_final: 0.5425 (m90) REVERT: A 365 GLU cc_start: 0.6723 (pm20) cc_final: 0.6198 (tp30) REVERT: A 554 ARG cc_start: 0.5024 (tpt90) cc_final: 0.4550 (mtm-85) REVERT: A 634 LYS cc_start: 0.8079 (tttt) cc_final: 0.7693 (ttpp) REVERT: A 678 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7563 (tt0) REVERT: A 697 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5308 (mm-30) REVERT: B 199 ARG cc_start: 0.7675 (ptp-110) cc_final: 0.7410 (ptp90) REVERT: B 298 ARG cc_start: 0.7636 (mmt180) cc_final: 0.7014 (mmm160) REVERT: B 350 GLU cc_start: 0.6904 (tt0) cc_final: 0.6568 (mt-10) REVERT: B 410 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7844 (mt0) REVERT: B 542 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5329 (t80) REVERT: B 544 LYS cc_start: 0.7985 (ttmt) cc_final: 0.7297 (tmtt) REVERT: B 708 ARG cc_start: 0.6359 (mmp80) cc_final: 0.6047 (mtt-85) REVERT: C 33 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7746 (mp0) REVERT: C 40 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8229 (mt-10) REVERT: C 86 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7469 (tpt-90) REVERT: C 200 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7437 (tpt90) REVERT: C 225 ARG cc_start: 0.7427 (tpt90) cc_final: 0.6842 (tpp-160) REVERT: C 229 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6821 (mt-10) REVERT: C 281 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7722 (tt) REVERT: C 290 TRP cc_start: 0.7886 (m100) cc_final: 0.7236 (m-10) REVERT: C 348 GLU cc_start: 0.7893 (tt0) cc_final: 0.7624 (mt-10) REVERT: C 659 GLU cc_start: 0.8224 (pt0) cc_final: 0.7882 (pm20) REVERT: C 708 ARG cc_start: 0.7334 (mmt-90) cc_final: 0.6821 (mtt180) REVERT: D 1 MET cc_start: 0.7693 (pmm) cc_final: 0.7389 (ptm) REVERT: D 33 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7938 (pm20) REVERT: D 110 LEU cc_start: 0.8077 (mm) cc_final: 0.7615 (tp) REVERT: D 114 ARG cc_start: 0.7607 (mmp80) cc_final: 0.7351 (mmp-170) REVERT: D 219 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7733 (mm110) REVERT: D 296 LEU cc_start: 0.9174 (mt) cc_final: 0.8924 (mp) REVERT: D 556 ARG cc_start: 0.8537 (tpt90) cc_final: 0.7919 (tpp80) REVERT: D 678 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7636 (mp0) REVERT: D 696 GLN cc_start: 0.7688 (tt0) cc_final: 0.7317 (tp-100) REVERT: D 708 ARG cc_start: 0.7642 (ptp-110) cc_final: 0.7223 (mtm110) REVERT: D 713 HIS cc_start: 0.1900 (OUTLIER) cc_final: 0.1282 (m170) REVERT: E 127 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7911 (mt-10) REVERT: E 207 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.6960 (mp) REVERT: E 208 HIS cc_start: 0.8085 (t70) cc_final: 0.7439 (t-90) REVERT: E 219 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: E 241 THR cc_start: 0.8223 (m) cc_final: 0.7780 (p) REVERT: E 651 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8559 (mt) REVERT: E 688 ARG cc_start: 0.7071 (ttm110) cc_final: 0.6433 (mtp-110) REVERT: E 696 GLN cc_start: 0.7452 (tt0) cc_final: 0.6988 (tt0) REVERT: F 1 MET cc_start: 0.3942 (ppp) cc_final: 0.3611 (mpp) REVERT: F 37 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: F 126 ARG cc_start: 0.7064 (ptm-80) cc_final: 0.6386 (mmm160) REVERT: F 164 LEU cc_start: 0.5661 (mm) cc_final: 0.5285 (tp) REVERT: F 324 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: F 365 GLU cc_start: 0.7726 (mp0) cc_final: 0.6826 (pp20) REVERT: F 450 LEU cc_start: 0.4302 (mt) cc_final: 0.3984 (mp) REVERT: F 520 ARG cc_start: 0.4115 (mmp-170) cc_final: 0.3305 (ttm170) REVERT: F 571 PHE cc_start: 0.4898 (m-10) cc_final: 0.4604 (m-10) REVERT: F 689 MET cc_start: 0.3294 (mmp) cc_final: 0.2427 (ttt) outliers start: 78 outliers final: 47 residues processed: 299 average time/residue: 0.2514 time to fit residues: 113.6566 Evaluate side-chains 288 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 205 TRP Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 527 HIS Chi-restraints excluded: chain D residue 560 HIS Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 660 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 17 optimal weight: 50.0000 chunk 311 optimal weight: 1.9990 chunk 325 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 288 optimal weight: 0.7980 chunk 220 optimal weight: 0.9990 chunk 259 optimal weight: 0.9980 chunk 401 optimal weight: 4.9990 chunk 314 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN F 100 HIS ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.194443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121997 restraints weight = 43987.071| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.12 r_work: 0.3200 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34142 Z= 0.123 Angle : 0.502 10.678 46356 Z= 0.251 Chirality : 0.038 0.377 5166 Planarity : 0.004 0.071 6186 Dihedral : 3.853 21.444 4800 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.61 % Allowed : 12.62 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.42 (0.13), residues: 4302 helix: 1.91 (0.11), residues: 2229 sheet: -0.05 (0.22), residues: 547 loop : -0.03 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG A 44 TYR 0.022 0.001 TYR C 557 PHE 0.014 0.001 PHE D 629 TRP 0.027 0.001 TRP B 250 HIS 0.007 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00277 (34142) covalent geometry : angle 0.50246 (46356) hydrogen bonds : bond 0.03533 ( 1874) hydrogen bonds : angle 4.09527 ( 5442) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.4749 (OUTLIER) cc_final: 0.4228 (tp30) REVERT: A 271 TYR cc_start: 0.6729 (p90) cc_final: 0.6315 (p90) REVERT: A 276 ARG cc_start: 0.6354 (mtp85) cc_final: 0.5245 (mtp85) REVERT: A 303 HIS cc_start: 0.6085 (m90) cc_final: 0.5409 (m90) REVERT: A 365 GLU cc_start: 0.6690 (pm20) cc_final: 0.6145 (tp30) REVERT: A 554 ARG cc_start: 0.5330 (tpt90) cc_final: 0.4380 (mtm-85) REVERT: A 615 LYS cc_start: 0.7442 (tptm) cc_final: 0.6623 (tptp) REVERT: A 634 LYS cc_start: 0.8025 (tttt) cc_final: 0.7616 (ttpp) REVERT: A 678 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7496 (tt0) REVERT: A 697 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5520 (mm-30) REVERT: B 199 ARG cc_start: 0.7649 (ptp-110) cc_final: 0.7404 (ptp90) REVERT: B 298 ARG cc_start: 0.7565 (mmt180) cc_final: 0.6946 (mmm160) REVERT: B 350 GLU cc_start: 0.6731 (tt0) cc_final: 0.6462 (mt-10) REVERT: B 410 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7663 (mt0) REVERT: B 542 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.5220 (t80) REVERT: B 544 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7090 (tmtt) REVERT: B 697 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6885 (mt-10) REVERT: B 708 ARG cc_start: 0.6318 (mmp80) cc_final: 0.6010 (mtt-85) REVERT: C 33 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7537 (mp0) REVERT: C 86 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7404 (tpt-90) REVERT: C 125 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6845 (mm) REVERT: C 200 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7373 (tpt90) REVERT: C 281 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7527 (tt) REVERT: C 290 TRP cc_start: 0.7804 (m100) cc_final: 0.7282 (m-10) REVERT: C 659 GLU cc_start: 0.7894 (pt0) cc_final: 0.7670 (pm20) REVERT: C 708 ARG cc_start: 0.7149 (mmt-90) cc_final: 0.6702 (mtt180) REVERT: D 1 MET cc_start: 0.7600 (pmm) cc_final: 0.7243 (ptm) REVERT: D 33 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7728 (pm20) REVERT: D 110 LEU cc_start: 0.7943 (mm) cc_final: 0.7560 (tp) REVERT: D 114 ARG cc_start: 0.7545 (mmp80) cc_final: 0.7278 (mmp-170) REVERT: D 219 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7682 (mm110) REVERT: D 296 LEU cc_start: 0.8998 (mt) cc_final: 0.8731 (mp) REVERT: D 556 ARG cc_start: 0.8429 (tpt90) cc_final: 0.7768 (tpp80) REVERT: D 678 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7313 (mp0) REVERT: D 696 GLN cc_start: 0.7624 (tt0) cc_final: 0.7273 (tp40) REVERT: D 708 ARG cc_start: 0.7622 (ptp-110) cc_final: 0.7163 (mtm110) REVERT: D 713 HIS cc_start: 0.1760 (OUTLIER) cc_final: 0.1112 (m170) REVERT: E 1 MET cc_start: 0.6512 (ppp) cc_final: 0.5633 (ppp) REVERT: E 207 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6810 (mp) REVERT: E 208 HIS cc_start: 0.8043 (t70) cc_final: 0.7518 (t-90) REVERT: E 219 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: E 241 THR cc_start: 0.8155 (m) cc_final: 0.7884 (p) REVERT: E 568 SER cc_start: 0.7364 (m) cc_final: 0.6937 (p) REVERT: E 651 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8384 (mt) REVERT: E 688 ARG cc_start: 0.7071 (ttm110) cc_final: 0.6446 (mtp-110) REVERT: F 1 MET cc_start: 0.3843 (ppp) cc_final: 0.3621 (mpp) REVERT: F 37 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: F 126 ARG cc_start: 0.7077 (ptm-80) cc_final: 0.6399 (mmm160) REVERT: F 164 LEU cc_start: 0.5676 (mm) cc_final: 0.5333 (tp) REVERT: F 181 GLU cc_start: 0.7797 (tp30) cc_final: 0.7268 (tt0) REVERT: F 225 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6508 (mmm160) REVERT: F 365 GLU cc_start: 0.7778 (mp0) cc_final: 0.6881 (pp20) REVERT: F 450 LEU cc_start: 0.4274 (mt) cc_final: 0.3968 (mp) REVERT: F 571 PHE cc_start: 0.4887 (m-10) cc_final: 0.4557 (m-10) REVERT: F 689 MET cc_start: 0.3323 (mmp) cc_final: 0.2450 (ttt) outliers start: 55 outliers final: 37 residues processed: 292 average time/residue: 0.2567 time to fit residues: 114.0556 Evaluate side-chains 286 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 560 HIS Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 660 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 294 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 25 optimal weight: 40.0000 chunk 293 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 301 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.195785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122799 restraints weight = 44032.648| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.05 r_work: 0.3224 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34142 Z= 0.116 Angle : 0.495 10.272 46356 Z= 0.246 Chirality : 0.037 0.353 5166 Planarity : 0.004 0.072 6186 Dihedral : 3.727 21.367 4800 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.98 % Favored : 98.00 % Rotamer: Outliers : 1.67 % Allowed : 12.91 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.54 (0.13), residues: 4302 helix: 1.98 (0.11), residues: 2242 sheet: 0.09 (0.22), residues: 547 loop : -0.00 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 120 TYR 0.023 0.001 TYR B 557 PHE 0.014 0.001 PHE D 629 TRP 0.025 0.001 TRP B 250 HIS 0.007 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00264 (34142) covalent geometry : angle 0.49454 (46356) hydrogen bonds : bond 0.03409 ( 1874) hydrogen bonds : angle 3.99476 ( 5442) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 270 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.5030 (tp) cc_final: 0.4787 (mp) REVERT: A 182 GLU cc_start: 0.4664 (OUTLIER) cc_final: 0.4142 (tp30) REVERT: A 303 HIS cc_start: 0.6127 (m90) cc_final: 0.5455 (m90) REVERT: A 365 GLU cc_start: 0.6710 (pm20) cc_final: 0.6181 (tp30) REVERT: A 554 ARG cc_start: 0.5252 (tpt90) cc_final: 0.4360 (mtm-85) REVERT: A 634 LYS cc_start: 0.8027 (tttt) cc_final: 0.7646 (ttpp) REVERT: A 678 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7509 (tt0) REVERT: A 697 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5356 (mm-30) REVERT: B 86 ARG cc_start: 0.7598 (mmp80) cc_final: 0.7373 (mmp-170) REVERT: B 199 ARG cc_start: 0.7681 (ptp-110) cc_final: 0.7426 (ptp90) REVERT: B 250 TRP cc_start: 0.7075 (m100) cc_final: 0.6782 (m100) REVERT: B 298 ARG cc_start: 0.7604 (mmt180) cc_final: 0.6981 (mmm160) REVERT: B 350 GLU cc_start: 0.6800 (tt0) cc_final: 0.6532 (mt-10) REVERT: B 377 SER cc_start: 0.8403 (m) cc_final: 0.7886 (p) REVERT: B 410 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7792 (mt0) REVERT: B 542 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.5294 (t80) REVERT: B 544 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7148 (tmtt) REVERT: B 697 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6897 (mt-10) REVERT: B 708 ARG cc_start: 0.6351 (mmp80) cc_final: 0.6003 (mtt-85) REVERT: C 33 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7632 (mp0) REVERT: C 86 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7428 (tpt-90) REVERT: C 125 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6885 (mm) REVERT: C 200 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7523 (tpt170) REVERT: C 229 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6457 (mt-10) REVERT: C 290 TRP cc_start: 0.7803 (m100) cc_final: 0.7232 (m-10) REVERT: C 659 GLU cc_start: 0.8107 (pt0) cc_final: 0.7776 (pm20) REVERT: C 690 GLU cc_start: 0.7565 (pp20) cc_final: 0.6301 (mp0) REVERT: C 708 ARG cc_start: 0.7225 (mmt-90) cc_final: 0.6744 (mtt180) REVERT: D 1 MET cc_start: 0.7684 (pmm) cc_final: 0.7337 (ptm) REVERT: D 33 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7854 (pm20) REVERT: D 97 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7931 (mm-40) REVERT: D 110 LEU cc_start: 0.7943 (mm) cc_final: 0.7575 (tp) REVERT: D 114 ARG cc_start: 0.7545 (mmp80) cc_final: 0.7288 (mmp-170) REVERT: D 195 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7691 (tm-30) REVERT: D 219 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7700 (mm110) REVERT: D 296 LEU cc_start: 0.9075 (mt) cc_final: 0.8845 (mp) REVERT: D 556 ARG cc_start: 0.8472 (tpt90) cc_final: 0.7854 (tpp80) REVERT: D 678 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7479 (mp0) REVERT: D 696 GLN cc_start: 0.7617 (tt0) cc_final: 0.7236 (tp40) REVERT: D 708 ARG cc_start: 0.7615 (ptp-110) cc_final: 0.7179 (mtm110) REVERT: D 713 HIS cc_start: 0.1729 (OUTLIER) cc_final: 0.1141 (m170) REVERT: E 1 MET cc_start: 0.6570 (ppp) cc_final: 0.5712 (ppp) REVERT: E 137 GLU cc_start: 0.8988 (tt0) cc_final: 0.8751 (pt0) REVERT: E 148 ARG cc_start: 0.8193 (ttp-110) cc_final: 0.7924 (mtp-110) REVERT: E 149 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6960 (mt-10) REVERT: E 207 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6879 (mp) REVERT: E 208 HIS cc_start: 0.8072 (t70) cc_final: 0.7551 (t-90) REVERT: E 219 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: E 241 THR cc_start: 0.8175 (m) cc_final: 0.7925 (p) REVERT: E 568 SER cc_start: 0.7568 (m) cc_final: 0.7160 (p) REVERT: E 651 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8485 (mt) REVERT: E 688 ARG cc_start: 0.7065 (ttm110) cc_final: 0.6432 (mtp-110) REVERT: F 1 MET cc_start: 0.3757 (ppp) cc_final: 0.3517 (mpp) REVERT: F 37 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: F 126 ARG cc_start: 0.7031 (ptm-80) cc_final: 0.6283 (mmm160) REVERT: F 164 LEU cc_start: 0.5653 (mm) cc_final: 0.5298 (tp) REVERT: F 181 GLU cc_start: 0.7920 (tp30) cc_final: 0.7346 (tt0) REVERT: F 225 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6563 (mmm160) REVERT: F 324 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: F 365 GLU cc_start: 0.7795 (mp0) cc_final: 0.6906 (pp20) REVERT: F 450 LEU cc_start: 0.4370 (mt) cc_final: 0.4068 (mp) REVERT: F 520 ARG cc_start: 0.4457 (mmm160) cc_final: 0.3420 (ttm-80) REVERT: F 634 LYS cc_start: 0.6386 (mttm) cc_final: 0.5903 (ptpt) REVERT: F 689 MET cc_start: 0.3323 (mmp) cc_final: 0.2380 (ttt) outliers start: 57 outliers final: 37 residues processed: 309 average time/residue: 0.2469 time to fit residues: 116.0039 Evaluate side-chains 292 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 634 LYS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 660 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 261 optimal weight: 0.3980 chunk 325 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 341 optimal weight: 9.9990 chunk 348 optimal weight: 0.7980 chunk 308 optimal weight: 0.0270 chunk 260 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.196143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123100 restraints weight = 44309.463| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.02 r_work: 0.3231 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34142 Z= 0.111 Angle : 0.492 10.680 46356 Z= 0.245 Chirality : 0.037 0.272 5166 Planarity : 0.004 0.072 6186 Dihedral : 3.689 21.714 4800 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.93 % Favored : 98.05 % Rotamer: Outliers : 1.50 % Allowed : 13.32 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.63 (0.13), residues: 4302 helix: 2.06 (0.11), residues: 2230 sheet: 0.13 (0.22), residues: 547 loop : 0.08 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 120 TYR 0.023 0.001 TYR B 557 PHE 0.014 0.001 PHE D 629 TRP 0.019 0.001 TRP B 250 HIS 0.008 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00252 (34142) covalent geometry : angle 0.49202 (46356) hydrogen bonds : bond 0.03363 ( 1874) hydrogen bonds : angle 3.95170 ( 5442) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.5128 (tp) cc_final: 0.4828 (mp) REVERT: A 182 GLU cc_start: 0.4676 (OUTLIER) cc_final: 0.4139 (tp30) REVERT: A 303 HIS cc_start: 0.6165 (m90) cc_final: 0.5684 (m90) REVERT: A 365 GLU cc_start: 0.6761 (pm20) cc_final: 0.6266 (tp30) REVERT: A 554 ARG cc_start: 0.5276 (tpt90) cc_final: 0.4343 (mtm-85) REVERT: A 678 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7521 (tt0) REVERT: A 697 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5357 (mm-30) REVERT: B 86 ARG cc_start: 0.7605 (mmp80) cc_final: 0.7375 (mmp-170) REVERT: B 199 ARG cc_start: 0.7691 (ptp-110) cc_final: 0.7432 (ptp90) REVERT: B 298 ARG cc_start: 0.7619 (mmt180) cc_final: 0.7012 (mmm160) REVERT: B 350 GLU cc_start: 0.6816 (tt0) cc_final: 0.6544 (mt-10) REVERT: B 377 SER cc_start: 0.8398 (m) cc_final: 0.7882 (p) REVERT: B 410 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7819 (mt0) REVERT: B 542 PHE cc_start: 0.6373 (OUTLIER) cc_final: 0.5317 (t80) REVERT: B 544 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7150 (tmtt) REVERT: B 556 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7928 (tpp80) REVERT: B 697 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6882 (mt-10) REVERT: B 708 ARG cc_start: 0.6346 (mmp80) cc_final: 0.6043 (mtt-85) REVERT: C 33 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7665 (mp0) REVERT: C 86 ARG cc_start: 0.7868 (mmm-85) cc_final: 0.7395 (tpt-90) REVERT: C 125 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6856 (mm) REVERT: C 200 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7524 (tpt170) REVERT: C 229 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6381 (mt-10) REVERT: C 250 TRP cc_start: 0.8902 (m100) cc_final: 0.8677 (m100) REVERT: C 290 TRP cc_start: 0.7797 (m100) cc_final: 0.7218 (m-10) REVERT: C 659 GLU cc_start: 0.8120 (pt0) cc_final: 0.7783 (pm20) REVERT: C 690 GLU cc_start: 0.7533 (pp20) cc_final: 0.6316 (mp0) REVERT: C 708 ARG cc_start: 0.7231 (mmt-90) cc_final: 0.6713 (mtt180) REVERT: D 1 MET cc_start: 0.7637 (pmm) cc_final: 0.7331 (ptm) REVERT: D 33 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7854 (pm20) REVERT: D 97 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7936 (mm-40) REVERT: D 110 LEU cc_start: 0.7920 (mm) cc_final: 0.7553 (tp) REVERT: D 114 ARG cc_start: 0.7522 (mmp80) cc_final: 0.7267 (mmp-170) REVERT: D 219 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7693 (mm110) REVERT: D 296 LEU cc_start: 0.9070 (mt) cc_final: 0.8822 (mp) REVERT: D 556 ARG cc_start: 0.8420 (tpt90) cc_final: 0.7748 (tpp80) REVERT: D 678 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7476 (mp0) REVERT: D 696 GLN cc_start: 0.7658 (tt0) cc_final: 0.7251 (tp40) REVERT: D 708 ARG cc_start: 0.7586 (ptp-110) cc_final: 0.7151 (mtm110) REVERT: D 713 HIS cc_start: 0.1726 (OUTLIER) cc_final: 0.1136 (m170) REVERT: E 1 MET cc_start: 0.6585 (ppp) cc_final: 0.5721 (ppp) REVERT: E 148 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7807 (mtp-110) REVERT: E 149 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6919 (mt-10) REVERT: E 208 HIS cc_start: 0.8073 (t70) cc_final: 0.7576 (t-90) REVERT: E 219 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: E 241 THR cc_start: 0.8184 (m) cc_final: 0.7940 (p) REVERT: E 568 SER cc_start: 0.7619 (m) cc_final: 0.7189 (p) REVERT: E 651 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8515 (mt) REVERT: E 688 ARG cc_start: 0.7118 (ttm110) cc_final: 0.6470 (mtp-110) REVERT: F 1 MET cc_start: 0.3750 (ppp) cc_final: 0.3527 (mpp) REVERT: F 37 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: F 126 ARG cc_start: 0.7023 (ptm-80) cc_final: 0.6251 (mmm160) REVERT: F 164 LEU cc_start: 0.5651 (mm) cc_final: 0.5295 (tp) REVERT: F 181 GLU cc_start: 0.7944 (tp30) cc_final: 0.7410 (tt0) REVERT: F 225 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6621 (mmm160) REVERT: F 324 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: F 365 GLU cc_start: 0.7777 (mp0) cc_final: 0.6746 (pp20) REVERT: F 450 LEU cc_start: 0.4390 (mt) cc_final: 0.4087 (mp) REVERT: F 520 ARG cc_start: 0.4518 (mmm160) cc_final: 0.3507 (ttm-80) REVERT: F 689 MET cc_start: 0.3301 (mmp) cc_final: 0.2360 (ttt) outliers start: 51 outliers final: 37 residues processed: 292 average time/residue: 0.2618 time to fit residues: 116.4298 Evaluate side-chains 293 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 660 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 291 optimal weight: 0.9980 chunk 334 optimal weight: 0.0050 chunk 193 optimal weight: 0.7980 chunk 305 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 30 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 379 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 chunk 261 optimal weight: 0.0980 chunk 328 optimal weight: 8.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.197116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124835 restraints weight = 44123.309| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.09 r_work: 0.3251 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 34142 Z= 0.100 Angle : 0.480 9.435 46356 Z= 0.238 Chirality : 0.037 0.321 5166 Planarity : 0.004 0.072 6186 Dihedral : 3.602 21.047 4800 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.77 % Favored : 98.21 % Rotamer: Outliers : 1.41 % Allowed : 13.53 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.13), residues: 4302 helix: 2.14 (0.11), residues: 2232 sheet: 0.24 (0.22), residues: 549 loop : 0.08 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 120 TYR 0.022 0.001 TYR B 557 PHE 0.013 0.001 PHE D 629 TRP 0.027 0.001 TRP F 250 HIS 0.007 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00223 (34142) covalent geometry : angle 0.48028 (46356) hydrogen bonds : bond 0.03262 ( 1874) hydrogen bonds : angle 3.87485 ( 5442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12199.28 seconds wall clock time: 207 minutes 56.00 seconds (12476.00 seconds total)