Starting phenix.real_space_refine on Sat Jul 4 07:55:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6q_25724/07_2026/7t6q_25724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6q_25724/07_2026/7t6q_25724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6q_25724/07_2026/7t6q_25724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6q_25724/07_2026/7t6q_25724.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6q_25724/07_2026/7t6q_25724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6q_25724/07_2026/7t6q_25724.cif" } resolution = 3.4 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= 0.007 sd= 0.045 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 12 5.49 5 S 140 5.16 5 C 12648 2.51 5 N 3284 2.21 5 O 3516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19600 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.51, per 1000 atoms: 0.23 Number of scatterers: 19600 At special positions: 0 Unit cell: (121.9, 122.96, 120.84, 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 140 16.00 P 12 15.00 O 3516 8.00 N 3284 7.00 C 12648 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 854.5 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 8 sheets defined 64.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.645A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 58 through 67 removed outlier: 4.189A pdb=" N ILE A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.500A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.074A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.776A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.716A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.795A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 210 through 223 removed outlier: 3.876A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.861A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.549A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 306' Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.580A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 401 removed outlier: 3.642A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.941A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.665A pdb=" N TYR A 415 " --> pdb=" O GLY A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 removed outlier: 3.664A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.557A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.828A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.948A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 498 removed outlier: 3.711A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.631A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.757A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 587 removed outlier: 4.115A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.604A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.619A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 58 through 67 removed outlier: 4.041A pdb=" N ILE B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 108 removed outlier: 4.066A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.756A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.594A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.749A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 removed outlier: 4.020A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 264 removed outlier: 4.003A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.547A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 306' Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.522A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 401 removed outlier: 3.642A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.954A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.674A pdb=" N TYR B 415 " --> pdb=" O GLY B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 removed outlier: 3.616A pdb=" N ILE B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.844A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.825A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 498 removed outlier: 3.797A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N CYS B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 512 removed outlier: 3.504A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.782A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 587 removed outlier: 3.986A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.550A pdb=" N LEU B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.600A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 58 through 67 removed outlier: 4.117A pdb=" N ILE C 63 " --> pdb=" O ARG C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 108 removed outlier: 4.085A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.747A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.698A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.693A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 210 through 223 removed outlier: 4.018A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.743A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.528A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 301 through 306' Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.531A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 401 removed outlier: 3.611A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 removed outlier: 3.978A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.657A pdb=" N TYR C 415 " --> pdb=" O GLY C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 removed outlier: 3.674A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.832A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.967A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 4.589A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 511 removed outlier: 3.593A pdb=" N THR C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.807A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 587 Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.574A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 58 through 67 removed outlier: 4.307A pdb=" N ILE D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.072A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.748A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.684A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.742A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 Processing helix chain 'D' and resid 210 through 223 removed outlier: 4.042A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.977A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.560A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN D 306 " --> pdb=" O GLU D 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 301 through 306' Processing helix chain 'D' and resid 313 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.582A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 401 removed outlier: 3.654A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 411 removed outlier: 3.963A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.709A pdb=" N TYR D 415 " --> pdb=" O GLY D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 removed outlier: 3.681A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.616A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.854A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 493 removed outlier: 3.689A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 512 removed outlier: 3.539A pdb=" N THR D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.762A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 562 " --> pdb=" O THR D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 587 Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.508A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 5.919A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 5.907A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 5.932A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 removed outlier: 5.961A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 963 hydrogen bonds defined for protein. 2853 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: 3.15 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3116 1.31 - 1.44: 5435 1.44 - 1.56: 11252 1.56 - 1.69: 17 1.69 - 1.82: 228 Bond restraints: 20048 Sorted by residual: bond pdb=" C1B PIO C1001 " pdb=" O3C PIO C1001 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1B PIO B1001 " pdb=" O3C PIO B1001 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1B PIO A1001 " pdb=" O3C PIO A1001 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1B PIO D1001 " pdb=" O3C PIO D1001 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1A PIO A1001 " pdb=" O2C PIO A1001 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 20043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 26603 3.94 - 7.88: 496 7.88 - 11.82: 108 11.82 - 15.77: 12 15.77 - 19.71: 5 Bond angle restraints: 27224 Sorted by residual: angle pdb=" C GLU C 515 " pdb=" N ASP C 516 " pdb=" CA ASP C 516 " ideal model delta sigma weight residual 121.61 136.10 -14.49 1.39e+00 5.18e-01 1.09e+02 angle pdb=" N MET C 491 " pdb=" CA MET C 491 " pdb=" C MET C 491 " ideal model delta sigma weight residual 114.04 104.66 9.38 1.24e+00 6.50e-01 5.72e+01 angle pdb=" N MET A 491 " pdb=" CA MET A 491 " pdb=" C MET A 491 " ideal model delta sigma weight residual 114.56 105.44 9.12 1.27e+00 6.20e-01 5.15e+01 angle pdb=" N MET B 491 " pdb=" CA MET B 491 " pdb=" C MET B 491 " ideal model delta sigma weight residual 114.04 105.29 8.75 1.24e+00 6.50e-01 4.98e+01 angle pdb=" N ILE B 307 " pdb=" CA ILE B 307 " pdb=" C ILE B 307 " ideal model delta sigma weight residual 113.22 105.65 7.57 1.23e+00 6.61e-01 3.79e+01 ... (remaining 27219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10474 17.76 - 35.52: 1191 35.52 - 53.28: 151 53.28 - 71.03: 36 71.03 - 88.79: 28 Dihedral angle restraints: 11880 sinusoidal: 4800 harmonic: 7080 Sorted by residual: dihedral pdb=" CA ILE B 202 " pdb=" C ILE B 202 " pdb=" N LEU B 203 " pdb=" CA LEU B 203 " ideal model delta harmonic sigma weight residual 180.00 149.31 30.69 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA ILE D 202 " pdb=" C ILE D 202 " pdb=" N LEU D 203 " pdb=" CA LEU D 203 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ILE A 202 " pdb=" C ILE A 202 " pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 11877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2435 0.067 - 0.134: 542 0.134 - 0.201: 93 0.201 - 0.268: 18 0.268 - 0.335: 12 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CB VAL C 297 " pdb=" CA VAL C 297 " pdb=" CG1 VAL C 297 " pdb=" CG2 VAL C 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB VAL D 297 " pdb=" CA VAL D 297 " pdb=" CG1 VAL D 297 " pdb=" CG2 VAL D 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 3097 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 574 " 0.026 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE B 574 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 574 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 574 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 574 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 574 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE B 574 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 432 " -0.014 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR B 432 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR B 432 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 432 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 432 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 432 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 432 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 432 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 456 " -0.026 2.00e-02 2.50e+03 2.50e-02 1.09e+01 pdb=" CG PHE A 456 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 456 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 456 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 456 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 456 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 456 " -0.008 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5111 2.81 - 3.33: 17886 3.33 - 3.85: 33274 3.85 - 4.38: 37553 4.38 - 4.90: 64242 Nonbonded interactions: 158066 Sorted by model distance: nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.282 3.040 nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.285 3.040 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.287 3.040 nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" OD1 ASN B 635 " model vdw 2.306 3.040 ... (remaining 158061 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.280 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.006 0.093 20052 Z= 0.285 Angle : 1.356 19.707 27224 Z= 0.663 Chirality : 0.062 0.335 3100 Planarity : 0.009 0.090 3424 Dihedral : 15.188 88.794 7304 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.87 (0.13), residues: 2408 helix: -2.51 (0.10), residues: 1480 sheet: 0.12 (0.77), residues: 56 loop : -2.57 (0.17), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 35 TYR 0.059 0.003 TYR B 432 PHE 0.060 0.003 PHE B 574 TRP 0.021 0.002 TRP D 29 HIS 0.010 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.29 (20048) covalent geometry : angle 1.35583 / 0.66 (27224) hydrogen bonds : bond 0.16139 / 10.72 ( 963) hydrogen bonds : angle 7.57761 / 5.28 ( 2853) Misc. bond : bond 0.00044 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 432 TYR cc_start: 0.8338 (t80) cc_final: 0.7739 (t80) REVERT: A 584 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7208 (ttt180) REVERT: B 592 LEU cc_start: 0.8456 (mt) cc_final: 0.8219 (mt) REVERT: C 588 GLU cc_start: 0.7711 (pp20) cc_final: 0.7191 (pt0) REVERT: D 570 MET cc_start: 0.7821 (tpp) cc_final: 0.7474 (ttt) REVERT: D 584 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.7162 (ttt180) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.1387 time to fit residues: 80.0647 Evaluate side-chains 254 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0030 chunk 235 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN C 513 GLN C 519 ASN D 519 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.172620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148193 restraints weight = 30259.219| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.23 r_work: 0.3742 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20052 Z= 0.117 Angle : 0.652 10.740 27224 Z= 0.313 Chirality : 0.040 0.169 3100 Planarity : 0.005 0.052 3424 Dihedral : 5.814 49.994 2712 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 8.49 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.15), residues: 2408 helix: -0.94 (0.12), residues: 1528 sheet: 0.31 (0.75), residues: 56 loop : -2.30 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 59 TYR 0.020 0.001 TYR B 432 PHE 0.028 0.001 PHE D 574 TRP 0.016 0.001 TRP B 29 HIS 0.003 0.001 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (20048) covalent geometry : angle 0.65209 / 0.31 (27224) hydrogen bonds : bond 0.03581 / 2.44 ( 963) hydrogen bonds : angle 4.73234 / 3.31 ( 2853) Misc. bond : bond 0.00039 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.751 Fit side-chains REVERT: A 584 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7780 (ttt180) REVERT: B 592 LEU cc_start: 0.8669 (mt) cc_final: 0.8412 (mt) REVERT: C 296 VAL cc_start: 0.9038 (t) cc_final: 0.8829 (p) REVERT: C 592 LEU cc_start: 0.8797 (mt) cc_final: 0.8437 (mt) REVERT: D 584 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7759 (ttt180) REVERT: D 588 GLU cc_start: 0.7875 (pp20) cc_final: 0.7554 (pp20) REVERT: D 592 LEU cc_start: 0.8887 (tp) cc_final: 0.8613 (mt) outliers start: 26 outliers final: 19 residues processed: 284 average time/residue: 0.1305 time to fit residues: 59.0170 Evaluate side-chains 265 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 47 optimal weight: 0.9990 chunk 228 optimal weight: 0.3980 chunk 185 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** 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 = 0.4079 r_free = 0.4079 target = 0.166498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141555 restraints weight = 30235.647| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.20 r_work: 0.3660 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20052 Z= 0.143 Angle : 0.636 12.564 27224 Z= 0.306 Chirality : 0.040 0.180 3100 Planarity : 0.005 0.055 3424 Dihedral : 5.361 48.467 2712 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.29 % Allowed : 12.31 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.16), residues: 2408 helix: -0.29 (0.13), residues: 1536 sheet: 0.41 (0.77), residues: 56 loop : -2.06 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 363 TYR 0.014 0.001 TYR B 432 PHE 0.024 0.001 PHE B 574 TRP 0.014 0.001 TRP D 29 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (20048) covalent geometry : angle 0.63617 / 0.31 (27224) hydrogen bonds : bond 0.03399 / 2.31 ( 963) hydrogen bonds : angle 4.28664 / 3.01 ( 2853) Misc. bond : bond 0.00036 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 0.759 Fit side-chains REVERT: A 83 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8463 (tt) REVERT: A 164 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: A 215 MET cc_start: 0.7637 (ttm) cc_final: 0.7425 (ttm) REVERT: A 427 VAL cc_start: 0.8907 (p) cc_final: 0.8680 (t) REVERT: A 570 MET cc_start: 0.7933 (mtp) cc_final: 0.7580 (mtp) REVERT: A 584 ARG cc_start: 0.8122 (ttp-110) cc_final: 0.7807 (ttt180) REVERT: B 51 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7021 (tp-100) REVERT: B 164 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: B 368 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6659 (pp) REVERT: B 592 LEU cc_start: 0.8734 (mt) cc_final: 0.8406 (mt) REVERT: C 164 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: D 90 ASP cc_start: 0.7462 (m-30) cc_final: 0.7228 (t0) REVERT: D 164 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: D 276 THR cc_start: 0.8825 (t) cc_final: 0.8617 (t) REVERT: D 584 ARG cc_start: 0.8265 (ttp-110) cc_final: 0.8054 (ttt-90) outliers start: 48 outliers final: 27 residues processed: 293 average time/residue: 0.1293 time to fit residues: 61.0186 Evaluate side-chains 268 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 585 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 98 optimal weight: 0.7980 chunk 232 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 chunk 6 optimal weight: 6.9990 chunk 117 optimal weight: 0.0980 chunk 123 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** 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 = 0.4108 r_free = 0.4108 target = 0.169251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144212 restraints weight = 30027.168| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.23 r_work: 0.3696 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20052 Z= 0.105 Angle : 0.602 12.368 27224 Z= 0.284 Chirality : 0.039 0.182 3100 Planarity : 0.004 0.051 3424 Dihedral : 5.039 46.429 2712 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.77 % Allowed : 13.74 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.17), residues: 2408 helix: 0.09 (0.13), residues: 1536 sheet: 0.42 (0.77), residues: 56 loop : -1.94 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 363 TYR 0.014 0.001 TYR A 432 PHE 0.023 0.001 PHE B 574 TRP 0.011 0.001 TRP D 29 HIS 0.003 0.000 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (20048) covalent geometry : angle 0.60155 / 0.28 (27224) hydrogen bonds : bond 0.02970 / 2.02 ( 963) hydrogen bonds : angle 4.08554 / 2.87 ( 2853) Misc. bond : bond 0.00024 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.493 Fit side-chains REVERT: A 83 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 215 MET cc_start: 0.7718 (ttm) cc_final: 0.7414 (ttm) REVERT: A 309 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7533 (tm-30) REVERT: A 584 ARG cc_start: 0.8069 (ttp-110) cc_final: 0.7813 (ttt180) REVERT: B 51 GLN cc_start: 0.7628 (tp-100) cc_final: 0.7013 (tp-100) REVERT: B 368 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6611 (pp) REVERT: B 592 LEU cc_start: 0.8741 (mt) cc_final: 0.8415 (mt) REVERT: C 51 GLN cc_start: 0.7643 (tp-100) cc_final: 0.7073 (tp-100) REVERT: C 368 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6936 (pp) REVERT: D 83 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8443 (tt) REVERT: D 90 ASP cc_start: 0.7394 (m-30) cc_final: 0.7176 (t0) REVERT: D 276 THR cc_start: 0.8703 (t) cc_final: 0.8488 (t) REVERT: D 584 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7805 (ttt180) outliers start: 37 outliers final: 23 residues processed: 280 average time/residue: 0.1208 time to fit residues: 54.2106 Evaluate side-chains 258 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 62 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 HIS C 513 GLN ** D 201 HIS ** 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 = 0.4036 r_free = 0.4036 target = 0.162677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137332 restraints weight = 29785.357| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.16 r_work: 0.3560 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20052 Z= 0.172 Angle : 0.670 14.883 27224 Z= 0.319 Chirality : 0.042 0.193 3100 Planarity : 0.004 0.049 3424 Dihedral : 5.243 46.492 2712 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.72 % Allowed : 15.36 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2408 helix: 0.21 (0.13), residues: 1508 sheet: 0.48 (0.77), residues: 56 loop : -1.91 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 363 TYR 0.019 0.002 TYR A 432 PHE 0.022 0.002 PHE B 574 TRP 0.014 0.001 TRP C 495 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (20048) covalent geometry : angle 0.67046 / 0.32 (27224) hydrogen bonds : bond 0.03445 / 2.35 ( 963) hydrogen bonds : angle 4.15900 / 2.93 ( 2853) Misc. bond : bond 0.00043 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 240 time to evaluate : 0.661 Fit side-chains REVERT: A 83 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8448 (tt) REVERT: A 164 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: A 309 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7704 (tm-30) REVERT: A 368 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7074 (pp) REVERT: A 427 VAL cc_start: 0.8979 (p) cc_final: 0.8687 (t) REVERT: A 575 ILE cc_start: 0.8639 (mm) cc_final: 0.8423 (mt) REVERT: A 584 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7794 (ttt180) REVERT: B 51 GLN cc_start: 0.7657 (tp-100) cc_final: 0.7085 (tp-100) REVERT: B 157 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.6172 (m90) REVERT: B 164 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: B 309 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7641 (tm-30) REVERT: B 368 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6765 (pp) REVERT: B 481 MET cc_start: 0.8304 (ttp) cc_final: 0.8098 (ptt) REVERT: B 592 LEU cc_start: 0.8763 (mt) cc_final: 0.8358 (mt) REVERT: B 603 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7119 (tmt) REVERT: C 51 GLN cc_start: 0.7679 (tp-100) cc_final: 0.7128 (tp-100) REVERT: C 83 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8393 (tt) REVERT: C 164 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: C 260 MET cc_start: 0.7760 (mmt) cc_final: 0.7267 (mmt) REVERT: C 309 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7543 (tm-30) REVERT: C 588 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7642 (pp20) REVERT: D 42 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: D 83 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8432 (tt) REVERT: D 164 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: D 276 THR cc_start: 0.8798 (t) cc_final: 0.8530 (t) REVERT: D 309 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7668 (tm-30) REVERT: D 315 GLU cc_start: 0.8297 (mp0) cc_final: 0.7892 (mp0) REVERT: D 584 ARG cc_start: 0.8292 (ttp-110) cc_final: 0.7967 (ttt180) outliers start: 57 outliers final: 32 residues processed: 279 average time/residue: 0.1203 time to fit residues: 53.8754 Evaluate side-chains 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 155 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 13 optimal weight: 0.0570 chunk 122 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 overall best weight: 1.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 157 HIS ** D 201 HIS ** 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 = 0.4061 r_free = 0.4061 target = 0.164844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139419 restraints weight = 29617.863| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.21 r_work: 0.3582 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20052 Z= 0.129 Angle : 0.630 13.742 27224 Z= 0.298 Chirality : 0.041 0.182 3100 Planarity : 0.004 0.050 3424 Dihedral : 5.039 45.142 2712 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.72 % Allowed : 16.27 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2408 helix: 0.38 (0.13), residues: 1504 sheet: 0.48 (0.76), residues: 56 loop : -1.80 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.016 0.001 TYR A 432 PHE 0.026 0.001 PHE C 574 TRP 0.013 0.001 TRP C 495 HIS 0.009 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (20048) covalent geometry : angle 0.62958 / 0.30 (27224) hydrogen bonds : bond 0.03126 / 2.14 ( 963) hydrogen bonds : angle 4.07157 / 2.87 ( 2853) Misc. bond : bond 0.00031 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 0.819 Fit side-chains REVERT: A 83 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8451 (tt) REVERT: A 164 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: A 309 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7676 (tm-30) REVERT: A 368 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7052 (pp) REVERT: A 584 ARG cc_start: 0.8066 (ttp-110) cc_final: 0.7757 (ttt180) REVERT: B 51 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7104 (tp-100) REVERT: B 157 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.6359 (m-70) REVERT: B 164 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: B 309 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7678 (tm-30) REVERT: B 368 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6831 (pp) REVERT: B 481 MET cc_start: 0.8264 (ttp) cc_final: 0.8011 (ptt) REVERT: B 592 LEU cc_start: 0.8832 (mt) cc_final: 0.8448 (mt) REVERT: C 51 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7110 (tp-100) REVERT: C 83 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8465 (tt) REVERT: C 164 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: C 260 MET cc_start: 0.7752 (mmt) cc_final: 0.7214 (mmt) REVERT: C 309 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7579 (tm-30) REVERT: C 588 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7534 (pp20) REVERT: D 42 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: D 83 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8473 (tt) REVERT: D 157 HIS cc_start: 0.6844 (OUTLIER) cc_final: 0.6170 (m90) REVERT: D 164 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: D 300 LYS cc_start: 0.8524 (pttm) cc_final: 0.8130 (ptpp) REVERT: D 309 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7677 (tm-30) REVERT: D 584 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.8049 (ttt-90) outliers start: 57 outliers final: 28 residues processed: 281 average time/residue: 0.1276 time to fit residues: 57.7943 Evaluate side-chains 267 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 143 optimal weight: 0.0770 chunk 98 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 572 ASN D 157 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.158510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133039 restraints weight = 30076.988| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.23 r_work: 0.3521 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20052 Z= 0.147 Angle : 0.647 13.820 27224 Z= 0.306 Chirality : 0.041 0.181 3100 Planarity : 0.004 0.051 3424 Dihedral : 5.041 44.760 2712 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.86 % Allowed : 16.56 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2408 helix: 0.41 (0.13), residues: 1504 sheet: 0.55 (0.75), residues: 56 loop : -1.79 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.014 0.001 TYR B 555 PHE 0.033 0.001 PHE C 574 TRP 0.011 0.001 TRP C 495 HIS 0.006 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (20048) covalent geometry : angle 0.64745 / 0.31 (27224) hydrogen bonds : bond 0.03225 / 2.20 ( 963) hydrogen bonds : angle 4.08311 / 2.88 ( 2853) Misc. bond : bond 0.00037 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 250 time to evaluate : 0.778 Fit side-chains REVERT: A 83 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8430 (tt) REVERT: A 157 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6122 (m90) REVERT: A 164 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: A 309 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7700 (tm-30) REVERT: A 368 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7067 (pp) REVERT: A 584 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7768 (ttt180) REVERT: B 51 GLN cc_start: 0.7689 (tp-100) cc_final: 0.7148 (tp-100) REVERT: B 164 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: B 309 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7575 (tm-30) REVERT: B 368 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6837 (pp) REVERT: B 403 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8268 (mm-30) REVERT: B 481 MET cc_start: 0.8227 (ttp) cc_final: 0.7982 (ptt) REVERT: B 592 LEU cc_start: 0.8828 (mt) cc_final: 0.8416 (mt) REVERT: B 603 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7042 (tmt) REVERT: C 51 GLN cc_start: 0.7685 (tp-100) cc_final: 0.7144 (tp-100) REVERT: C 83 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8466 (tt) REVERT: C 157 HIS cc_start: 0.6653 (OUTLIER) cc_final: 0.6066 (m-70) REVERT: C 164 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: C 260 MET cc_start: 0.7724 (mmt) cc_final: 0.7167 (mmt) REVERT: C 309 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7568 (tm-30) REVERT: C 481 MET cc_start: 0.8190 (ttp) cc_final: 0.7942 (ptt) REVERT: C 575 ILE cc_start: 0.8562 (mm) cc_final: 0.8255 (mt) REVERT: C 588 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7585 (pp20) REVERT: D 42 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: D 51 GLN cc_start: 0.7573 (tp-100) cc_final: 0.7217 (tp-100) REVERT: D 83 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8421 (tt) REVERT: D 157 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6355 (m90) REVERT: D 164 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: D 276 THR cc_start: 0.8812 (t) cc_final: 0.8551 (t) REVERT: D 309 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7683 (tm-30) outliers start: 60 outliers final: 35 residues processed: 290 average time/residue: 0.1173 time to fit residues: 54.4601 Evaluate side-chains 289 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 239 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 131 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 221 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** 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 = 0.3994 r_free = 0.3994 target = 0.159671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134015 restraints weight = 29945.158| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.26 r_work: 0.3535 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20052 Z= 0.125 Angle : 0.632 12.954 27224 Z= 0.298 Chirality : 0.040 0.176 3100 Planarity : 0.004 0.050 3424 Dihedral : 4.925 43.702 2712 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.81 % Allowed : 16.65 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2408 helix: 0.44 (0.13), residues: 1532 sheet: 0.60 (0.75), residues: 56 loop : -1.62 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.013 0.001 TYR B 555 PHE 0.028 0.001 PHE C 574 TRP 0.014 0.001 TRP C 495 HIS 0.006 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (20048) covalent geometry : angle 0.63186 / 0.30 (27224) hydrogen bonds : bond 0.03058 / 2.08 ( 963) hydrogen bonds : angle 4.03494 / 2.85 ( 2853) Misc. bond : bond 0.00031 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 0.738 Fit side-chains REVERT: A 83 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 157 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.6223 (m90) REVERT: A 164 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: A 309 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7693 (tm-30) REVERT: A 368 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7033 (pp) REVERT: A 584 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7702 (ttt180) REVERT: B 164 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: B 309 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7718 (tm-30) REVERT: B 368 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6833 (pp) REVERT: B 403 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8236 (mm-30) REVERT: B 447 MET cc_start: 0.7738 (ptt) cc_final: 0.7419 (ptt) REVERT: B 481 MET cc_start: 0.8189 (ttp) cc_final: 0.7915 (ptt) REVERT: B 592 LEU cc_start: 0.8819 (mt) cc_final: 0.8418 (mt) REVERT: B 603 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7008 (tmt) REVERT: C 51 GLN cc_start: 0.7662 (tp-100) cc_final: 0.7141 (tp-100) REVERT: C 83 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8419 (tt) REVERT: C 157 HIS cc_start: 0.6690 (OUTLIER) cc_final: 0.6071 (m90) REVERT: C 164 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: C 260 MET cc_start: 0.7683 (mmt) cc_final: 0.7141 (mmt) REVERT: C 309 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7565 (tm-30) REVERT: C 481 MET cc_start: 0.8240 (ttp) cc_final: 0.7984 (ptt) REVERT: C 575 ILE cc_start: 0.8509 (mm) cc_final: 0.8239 (mt) REVERT: C 588 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7647 (pp20) REVERT: D 42 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8620 (tm-30) REVERT: D 51 GLN cc_start: 0.7564 (tp-100) cc_final: 0.7222 (tp-100) REVERT: D 83 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8383 (tt) REVERT: D 90 ASP cc_start: 0.7447 (m-30) cc_final: 0.7120 (t0) REVERT: D 157 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6482 (m-70) REVERT: D 164 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: D 300 LYS cc_start: 0.8564 (pttm) cc_final: 0.8219 (ptpt) REVERT: D 309 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7679 (tm-30) outliers start: 59 outliers final: 34 residues processed: 294 average time/residue: 0.1196 time to fit residues: 56.7102 Evaluate side-chains 293 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.5980 chunk 230 optimal weight: 0.0980 chunk 80 optimal weight: 0.5980 chunk 234 optimal weight: 0.6980 chunk 239 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 212 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 157 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.162562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137773 restraints weight = 29794.089| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.22 r_work: 0.3579 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20052 Z= 0.107 Angle : 0.614 12.789 27224 Z= 0.289 Chirality : 0.040 0.174 3100 Planarity : 0.004 0.051 3424 Dihedral : 4.757 42.062 2712 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.34 % Allowed : 17.70 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2408 helix: 0.55 (0.14), residues: 1524 sheet: 0.74 (0.75), residues: 56 loop : -1.70 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.013 0.001 TYR A 432 PHE 0.026 0.001 PHE C 574 TRP 0.012 0.001 TRP C 495 HIS 0.005 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (20048) covalent geometry : angle 0.61379 / 0.29 (27224) hydrogen bonds : bond 0.02898 / 1.97 ( 963) hydrogen bonds : angle 3.97824 / 2.80 ( 2853) Misc. bond : bond 0.00023 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 0.847 Fit side-chains REVERT: A 309 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7615 (tm-30) REVERT: A 368 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6927 (pp) REVERT: A 608 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8658 (mtp) REVERT: B 309 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7639 (tm-30) REVERT: B 368 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6776 (pp) REVERT: B 447 MET cc_start: 0.7705 (ptt) cc_final: 0.7380 (ptt) REVERT: B 481 MET cc_start: 0.8152 (ttp) cc_final: 0.7751 (ptt) REVERT: B 592 LEU cc_start: 0.8814 (mt) cc_final: 0.8419 (mt) REVERT: B 603 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6921 (tmt) REVERT: C 51 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7110 (tp-100) REVERT: C 83 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8364 (tt) REVERT: C 157 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6350 (m90) REVERT: C 260 MET cc_start: 0.7725 (mmt) cc_final: 0.7060 (mmt) REVERT: C 309 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7537 (tm-30) REVERT: C 481 MET cc_start: 0.8226 (ttp) cc_final: 0.7911 (ptt) REVERT: C 575 ILE cc_start: 0.8476 (mm) cc_final: 0.8206 (mt) REVERT: C 588 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7625 (pp20) REVERT: D 42 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: D 83 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8373 (tt) REVERT: D 90 ASP cc_start: 0.7402 (m-30) cc_final: 0.7123 (t0) REVERT: D 300 LYS cc_start: 0.8539 (pttm) cc_final: 0.8206 (ptpt) REVERT: D 309 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7631 (tm-30) REVERT: D 481 MET cc_start: 0.8282 (ttp) cc_final: 0.8069 (ptt) outliers start: 49 outliers final: 36 residues processed: 285 average time/residue: 0.1294 time to fit residues: 59.6732 Evaluate side-chains 289 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 185 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** 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 = 0.4017 r_free = 0.4017 target = 0.161667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136341 restraints weight = 29989.736| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.24 r_work: 0.3562 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20052 Z= 0.121 Angle : 0.653 17.707 27224 Z= 0.300 Chirality : 0.040 0.177 3100 Planarity : 0.004 0.050 3424 Dihedral : 4.729 41.753 2712 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.53 % Allowed : 18.03 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2408 helix: 0.55 (0.14), residues: 1532 sheet: 0.87 (0.75), residues: 56 loop : -1.62 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.023 0.001 TYR D 555 PHE 0.028 0.001 PHE C 574 TRP 0.016 0.001 TRP C 495 HIS 0.005 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (20048) covalent geometry : angle 0.65316 / 0.30 (27224) hydrogen bonds : bond 0.02972 / 2.03 ( 963) hydrogen bonds : angle 3.95848 / 2.79 ( 2853) Misc. bond : bond 0.00030 / 0.01 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 0.802 Fit side-chains REVERT: A 164 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: A 309 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7671 (tm-30) REVERT: A 368 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6919 (pp) REVERT: A 403 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 608 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8710 (mtp) REVERT: B 164 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: B 309 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7737 (tm-30) REVERT: B 368 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6796 (pp) REVERT: B 447 MET cc_start: 0.7731 (ptt) cc_final: 0.7403 (ptt) REVERT: B 481 MET cc_start: 0.8165 (ttp) cc_final: 0.7752 (ptt) REVERT: B 588 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7517 (pp20) REVERT: B 603 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7005 (tmt) REVERT: C 51 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7116 (tp-100) REVERT: C 83 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8364 (tt) REVERT: C 260 MET cc_start: 0.7685 (mmt) cc_final: 0.7092 (mmt) REVERT: C 309 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7532 (tm-30) REVERT: C 481 MET cc_start: 0.8288 (ttp) cc_final: 0.8043 (ptt) REVERT: C 575 ILE cc_start: 0.8503 (mm) cc_final: 0.8241 (mt) REVERT: C 588 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7622 (pp20) REVERT: D 42 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8610 (tm-30) REVERT: D 83 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8370 (tt) REVERT: D 90 ASP cc_start: 0.7376 (m-30) cc_final: 0.7153 (t0) REVERT: D 300 LYS cc_start: 0.8568 (pttm) cc_final: 0.8128 (ptpp) REVERT: D 309 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7638 (tm-30) REVERT: D 481 MET cc_start: 0.8264 (ttp) cc_final: 0.7963 (ptt) outliers start: 53 outliers final: 40 residues processed: 286 average time/residue: 0.1283 time to fit residues: 58.9725 Evaluate side-chains 297 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 65 optimal weight: 0.6980 chunk 118 optimal weight: 0.2980 chunk 237 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 201 optimal weight: 0.0010 chunk 215 optimal weight: 1.9990 chunk 178 optimal weight: 0.0040 chunk 120 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** 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 = 0.4056 r_free = 0.4056 target = 0.165367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140773 restraints weight = 30016.676| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.23 r_work: 0.3619 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20052 Z= 0.101 Angle : 0.634 16.402 27224 Z= 0.289 Chirality : 0.039 0.170 3100 Planarity : 0.004 0.050 3424 Dihedral : 4.538 39.248 2712 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.29 % Allowed : 18.75 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2408 helix: 0.67 (0.14), residues: 1524 sheet: 0.94 (0.73), residues: 56 loop : -1.64 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.021 0.001 TYR B 555 PHE 0.028 0.001 PHE C 574 TRP 0.014 0.001 TRP C 495 HIS 0.004 0.000 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (20048) covalent geometry : angle 0.63395 / 0.29 (27224) hydrogen bonds : bond 0.02719 / 1.85 ( 963) hydrogen bonds : angle 3.91110 / 2.76 ( 2853) Misc. bond : bond 0.00017 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3596.66 seconds wall clock time: 62 minutes 52.00 seconds (3772.00 seconds total)