Starting phenix.real_space_refine on Sun Sep 13 00:59:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6d7t_7825/09_2026/6d7t_7825.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d7t_7825/09_2026/6d7t_7825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d7t_7825/09_2026/6d7t_7825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d7t_7825/09_2026/6d7t_7825.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6d7t_7825/09_2026/6d7t_7825.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6d7t_7825/09_2026/6d7t_7825.cif" model { file = "/net/cci-nas-00/data/ceres_data/6d7t_7825/09_2026/6d7t_7825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d7t_7825/09_2026/6d7t_7825.cif" } resolution = 4.44 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 S 160 5.16 5 B 4 2.79 5 C 12704 2.51 5 N 3324 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19654 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4896 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "B" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4896 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "C" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4896 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "D" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4896 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' CA': 2, 'FZ4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="CA CA A 802 " occ=0.25 residue: pdb="CA CA A 803 " occ=0.25 Time building chain proxies: 4.17, per 1000 atoms: 0.21 Number of scatterers: 19654 At special positions: 0 Unit cell: (132.98, 132.98, 123.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 160 16.00 O 3460 8.00 N 3324 7.00 C 12704 6.00 B 4 5.00 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: 1.39 Conformation dependent library (CDL) restraints added in 688.1 milliseconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4616 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 60.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.912A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.969A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 removed outlier: 4.081A pdb=" N LYS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.728A pdb=" N LEU A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 125 removed outlier: 3.744A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.767A pdb=" N ARG A 153 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.842A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.532A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.530A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.559A pdb=" N ALA A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.114A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.590A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 262 removed outlier: 4.410A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.837A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.606A pdb=" N GLN A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.583A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.554A pdb=" N MET A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 402 removed outlier: 3.949A pdb=" N VAL A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 removed outlier: 3.744A pdb=" N ASP A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.868A pdb=" N ILE A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 446 removed outlier: 4.333A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.584A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.745A pdb=" N ARG A 470 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.923A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 512 removed outlier: 3.693A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.695A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 567 removed outlier: 4.074A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 removed outlier: 4.003A pdb=" N MET A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 removed outlier: 3.811A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.914A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.968A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.081A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.728A pdb=" N LEU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.744A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.767A pdb=" N ARG B 153 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.843A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.531A pdb=" N ILE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.529A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 214 removed outlier: 3.559A pdb=" N ALA B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 removed outlier: 4.114A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.590A pdb=" N ALA B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 4.410A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.837A pdb=" N LEU B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.606A pdb=" N GLN B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.583A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 349 removed outlier: 3.554A pdb=" N MET B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR B 349 " --> pdb=" O MET B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 402 removed outlier: 3.949A pdb=" N VAL B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 411 removed outlier: 3.744A pdb=" N ASP B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.867A pdb=" N ILE B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 446 removed outlier: 4.333A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.584A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 removed outlier: 3.745A pdb=" N ARG B 470 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.923A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 512 removed outlier: 3.693A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.695A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 567 removed outlier: 4.075A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 582 removed outlier: 4.003A pdb=" N MET B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 608 removed outlier: 3.811A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.913A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.969A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 4.081A pdb=" N LYS C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.727A pdb=" N LEU C 105 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.744A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.768A pdb=" N ARG C 153 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.842A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.532A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.530A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.559A pdb=" N ALA C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.115A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.590A pdb=" N ALA C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.409A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.837A pdb=" N LEU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.607A pdb=" N GLN C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 323 removed outlier: 3.583A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.553A pdb=" N MET C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 402 removed outlier: 3.950A pdb=" N VAL C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 411 removed outlier: 3.744A pdb=" N ASP C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.868A pdb=" N ILE C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 446 removed outlier: 4.334A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.584A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 471 removed outlier: 3.745A pdb=" N ARG C 470 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.923A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 512 removed outlier: 3.693A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.695A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 567 removed outlier: 4.075A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 582 removed outlier: 4.003A pdb=" N MET C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 608 removed outlier: 3.810A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.914A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.969A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 removed outlier: 4.081A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.727A pdb=" N LEU D 105 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.744A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.767A pdb=" N ARG D 153 " --> pdb=" O THR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.842A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.531A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.529A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 214 removed outlier: 3.559A pdb=" N ALA D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 221 removed outlier: 4.115A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.591A pdb=" N ALA D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 262 removed outlier: 4.410A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.837A pdb=" N LEU D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.607A pdb=" N GLN D 306 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 323 removed outlier: 3.584A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.554A pdb=" N MET D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 338 " --> pdb=" O ALA D 334 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 402 removed outlier: 3.949A pdb=" N VAL D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 411 removed outlier: 3.745A pdb=" N ASP D 406 " --> pdb=" O VAL D 402 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.868A pdb=" N ILE D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 446 removed outlier: 4.333A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.583A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 471 removed outlier: 3.745A pdb=" N ARG D 470 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 3.923A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 512 removed outlier: 3.693A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.695A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 567 removed outlier: 4.074A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 582 removed outlier: 4.004A pdb=" N MET D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 608 removed outlier: 3.810A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 3.557A pdb=" N GLN A 267 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 276 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 270 removed outlier: 3.556A pdb=" N GLN B 267 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 276 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 265 through 270 removed outlier: 3.555A pdb=" N GLN C 267 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 265 through 270 removed outlier: 3.555A pdb=" N GLN D 267 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR D 276 " --> pdb=" O VAL D 633 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 2831 1.25 - 1.39: 5305 1.39 - 1.54: 11174 1.54 - 1.68: 521 1.68 - 1.82: 273 Bond restraints: 20104 Sorted by residual: bond pdb=" C PRO D 544 " pdb=" N ALA D 545 " ideal model delta sigma weight residual 1.331 1.727 -0.396 1.23e-02 6.61e+03 1.04e+03 bond pdb=" C ILE D 540 " pdb=" N ILE D 541 " ideal model delta sigma weight residual 1.335 1.552 -0.217 1.27e-02 6.20e+03 2.92e+02 bond pdb=" C ILE C 540 " pdb=" N ILE C 541 " ideal model delta sigma weight residual 1.332 1.103 0.229 1.73e-02 3.34e+03 1.76e+02 bond pdb=" C ILE B 540 " pdb=" N ILE B 541 " ideal model delta sigma weight residual 1.332 1.510 -0.178 1.73e-02 3.34e+03 1.06e+02 bond pdb=" C ILE A 540 " pdb=" N ILE A 541 " ideal model delta sigma weight residual 1.332 1.510 -0.178 1.73e-02 3.34e+03 1.06e+02 ... (remaining 20099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 26379 3.51 - 7.02: 748 7.02 - 10.53: 103 10.53 - 14.03: 17 14.03 - 17.54: 21 Bond angle restraints: 27268 Sorted by residual: angle pdb=" O PRO D 544 " pdb=" C PRO D 544 " pdb=" N ALA D 545 " ideal model delta sigma weight residual 123.03 110.57 12.46 1.06e+00 8.90e-01 1.38e+02 angle pdb=" C ILE D 540 " pdb=" N ILE D 541 " pdb=" CA ILE D 541 " ideal model delta sigma weight residual 120.13 102.63 17.50 1.58e+00 4.01e-01 1.23e+02 angle pdb=" CA ILE D 540 " pdb=" C ILE D 540 " pdb=" N ILE D 541 " ideal model delta sigma weight residual 116.60 102.58 14.02 1.45e+00 4.76e-01 9.35e+01 angle pdb=" CA PRO D 544 " pdb=" C PRO D 544 " pdb=" N ALA D 545 " ideal model delta sigma weight residual 116.01 128.14 -12.13 1.27e+00 6.20e-01 9.12e+01 angle pdb=" O ILE D 540 " pdb=" C ILE D 540 " pdb=" N ILE D 541 " ideal model delta sigma weight residual 122.57 132.50 -9.93 1.25e+00 6.40e-01 6.31e+01 ... (remaining 27263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 11736 35.95 - 71.89: 268 71.89 - 107.84: 4 107.84 - 143.78: 0 143.78 - 179.73: 4 Dihedral angle restraints: 12012 sinusoidal: 4868 harmonic: 7144 Sorted by residual: dihedral pdb=" CA ASN A 129 " pdb=" C ASN A 129 " pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta harmonic sigma weight residual 180.00 142.43 37.57 0 5.00e+00 4.00e-02 5.65e+01 dihedral pdb=" CA ASN C 129 " pdb=" C ASN C 129 " pdb=" N MET C 130 " pdb=" CA MET C 130 " ideal model delta harmonic sigma weight residual 180.00 142.46 37.54 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA ASN D 129 " pdb=" C ASN D 129 " pdb=" N MET D 130 " pdb=" CA MET D 130 " ideal model delta harmonic sigma weight residual 180.00 142.51 37.49 0 5.00e+00 4.00e-02 5.62e+01 ... (remaining 12009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1720 0.049 - 0.097: 880 0.097 - 0.146: 379 0.146 - 0.195: 89 0.195 - 0.243: 24 Chirality restraints: 3092 Sorted by residual: chirality pdb=" CA GLN D 370 " pdb=" N GLN D 370 " pdb=" C GLN D 370 " pdb=" CB GLN D 370 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA GLN C 370 " pdb=" N GLN C 370 " pdb=" C GLN C 370 " pdb=" CB GLN C 370 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLN B 370 " pdb=" N GLN B 370 " pdb=" C GLN B 370 " pdb=" CB GLN B 370 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3089 not shown) Planarity restraints: 3448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 540 " -0.033 2.00e-02 2.50e+03 7.50e-02 5.62e+01 pdb=" C ILE D 540 " 0.129 2.00e-02 2.50e+03 pdb=" O ILE D 540 " -0.057 2.00e-02 2.50e+03 pdb=" N ILE D 541 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 544 " 0.032 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C PRO C 544 " -0.112 2.00e-02 2.50e+03 pdb=" O PRO C 544 " 0.042 2.00e-02 2.50e+03 pdb=" N ALA C 545 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 223 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C ASP C 223 " -0.043 2.00e-02 2.50e+03 pdb=" O ASP C 223 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG C 224 " 0.015 2.00e-02 2.50e+03 ... (remaining 3445 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 225 2.58 - 3.16: 16710 3.16 - 3.74: 32308 3.74 - 4.32: 43338 4.32 - 4.90: 65051 Nonbonded interactions: 157632 Sorted by model distance: nonbonded pdb=" OD1 ASP D 542 " pdb="CA CA A 803 " model vdw 1.997 2.510 nonbonded pdb=" OD1 ASP C 542 " pdb="CA CA A 803 " model vdw 2.030 2.510 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR D 360 " pdb=" OG1 THR D 366 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR C 360 " pdb=" OG1 THR C 366 " model vdw 2.228 3.040 ... (remaining 157627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 28 through 801) 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.700 Find NCS groups from input model: 0.610 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.010 0.396 20108 Z= 0.536 Angle : 1.494 17.542 27268 Z= 0.799 Chirality : 0.068 0.243 3092 Planarity : 0.008 0.075 3448 Dihedral : 14.786 179.729 7396 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.71 % Favored : 88.75 % Rotamer: Outliers : 5.48 % Allowed : 9.12 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -5.38 (0.13), residues: 2436 helix: -3.93 (0.08), residues: 1208 sheet: -6.48 (0.12), residues: 56 loop : -2.92 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG C 153 TYR 0.029 0.004 TYR B 324 PHE 0.028 0.004 PHE C 434 TRP 0.033 0.004 TRP B 613 HIS 0.027 0.004 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.01036 / 0.54 (20104) covalent geometry : angle 1.49354 / 0.80 (27268) hydrogen bonds : bond 0.30578 / 20.25 ( 808) hydrogen bonds : angle 10.42007 / 7.18 ( 2292) Misc. bond : bond 0.00165 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 624 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 VAL cc_start: 0.8814 (t) cc_final: 0.8341 (p) REVERT: A 127 ASN cc_start: 0.8740 (m110) cc_final: 0.8359 (p0) REVERT: A 208 ASN cc_start: 0.9184 (t160) cc_final: 0.8869 (t0) REVERT: A 211 PHE cc_start: 0.8369 (t80) cc_final: 0.7487 (t80) REVERT: A 229 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7797 (mp) REVERT: A 280 LEU cc_start: 0.9115 (tp) cc_final: 0.8766 (tp) REVERT: A 324 TYR cc_start: 0.7964 (p90) cc_final: 0.7137 (p90) REVERT: A 364 ASP cc_start: 0.9212 (m-30) cc_final: 0.8838 (t0) REVERT: A 367 LEU cc_start: 0.8970 (tt) cc_final: 0.7577 (tt) REVERT: A 398 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9221 (tt) REVERT: A 435 MET cc_start: 0.9039 (mmp) cc_final: 0.8750 (mmm) REVERT: A 438 VAL cc_start: 0.9293 (p) cc_final: 0.9063 (m) REVERT: A 442 MET cc_start: 0.8924 (tpp) cc_final: 0.8428 (tpp) REVERT: A 462 TRP cc_start: 0.9423 (m100) cc_final: 0.9108 (m100) REVERT: A 464 ASN cc_start: 0.8908 (t160) cc_final: 0.8539 (t0) REVERT: A 497 MET cc_start: 0.8690 (tmm) cc_final: 0.8483 (tmm) REVERT: A 509 TYR cc_start: 0.9206 (t80) cc_final: 0.8449 (t80) REVERT: A 515 GLU cc_start: 0.8754 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 520 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8098 (tm) REVERT: A 577 MET cc_start: 0.8688 (mmm) cc_final: 0.8340 (mmm) REVERT: B 58 VAL cc_start: 0.8782 (t) cc_final: 0.8288 (p) REVERT: B 127 ASN cc_start: 0.8697 (m110) cc_final: 0.8402 (p0) REVERT: B 208 ASN cc_start: 0.9178 (t160) cc_final: 0.8857 (t0) REVERT: B 211 PHE cc_start: 0.8361 (t80) cc_final: 0.7487 (t80) REVERT: B 229 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7780 (mp) REVERT: B 324 TYR cc_start: 0.7965 (p90) cc_final: 0.7138 (p90) REVERT: B 364 ASP cc_start: 0.9207 (m-30) cc_final: 0.8849 (t0) REVERT: B 398 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9231 (tt) REVERT: B 435 MET cc_start: 0.9039 (mmp) cc_final: 0.8784 (mmm) REVERT: B 438 VAL cc_start: 0.9289 (p) cc_final: 0.9059 (m) REVERT: B 442 MET cc_start: 0.8923 (tpp) cc_final: 0.8432 (tpp) REVERT: B 462 TRP cc_start: 0.9426 (m100) cc_final: 0.9082 (m100) REVERT: B 464 ASN cc_start: 0.8906 (t160) cc_final: 0.8391 (t0) REVERT: B 509 TYR cc_start: 0.9200 (t80) cc_final: 0.8431 (t80) REVERT: B 515 GLU cc_start: 0.8738 (mm-30) cc_final: 0.7897 (mm-30) REVERT: B 528 MET cc_start: 0.8354 (ttm) cc_final: 0.8125 (ttm) REVERT: C 58 VAL cc_start: 0.8846 (t) cc_final: 0.8405 (p) REVERT: C 127 ASN cc_start: 0.8733 (m110) cc_final: 0.8386 (p0) REVERT: C 208 ASN cc_start: 0.9166 (t160) cc_final: 0.8851 (t0) REVERT: C 211 PHE cc_start: 0.8373 (t80) cc_final: 0.7423 (t80) REVERT: C 229 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7776 (mp) REVERT: C 245 LYS cc_start: 0.9272 (ptpp) cc_final: 0.9068 (mttt) REVERT: C 280 LEU cc_start: 0.9118 (tp) cc_final: 0.8729 (tp) REVERT: C 324 TYR cc_start: 0.8043 (p90) cc_final: 0.7269 (p90) REVERT: C 364 ASP cc_start: 0.9207 (m-30) cc_final: 0.8646 (t70) REVERT: C 367 LEU cc_start: 0.8969 (tt) cc_final: 0.7589 (tt) REVERT: C 398 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9230 (tt) REVERT: C 435 MET cc_start: 0.9040 (mmp) cc_final: 0.8736 (mmm) REVERT: C 438 VAL cc_start: 0.9299 (p) cc_final: 0.9083 (m) REVERT: C 442 MET cc_start: 0.8927 (tpp) cc_final: 0.8436 (tpp) REVERT: C 462 TRP cc_start: 0.9392 (m100) cc_final: 0.9128 (m100) REVERT: C 464 ASN cc_start: 0.8924 (t160) cc_final: 0.8564 (t0) REVERT: C 497 MET cc_start: 0.8694 (tmm) cc_final: 0.8319 (tmm) REVERT: C 509 TYR cc_start: 0.9198 (t80) cc_final: 0.8384 (t80) REVERT: C 520 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8093 (tm) REVERT: C 528 MET cc_start: 0.8405 (ttm) cc_final: 0.8182 (ttm) REVERT: C 577 MET cc_start: 0.8720 (mmm) cc_final: 0.8408 (mmm) REVERT: D 58 VAL cc_start: 0.8814 (t) cc_final: 0.8362 (p) REVERT: D 127 ASN cc_start: 0.8704 (m110) cc_final: 0.8408 (p0) REVERT: D 208 ASN cc_start: 0.9166 (t160) cc_final: 0.8843 (t0) REVERT: D 211 PHE cc_start: 0.8358 (t80) cc_final: 0.7475 (t80) REVERT: D 229 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7784 (mp) REVERT: D 245 LYS cc_start: 0.9295 (ptpp) cc_final: 0.9093 (mttt) REVERT: D 280 LEU cc_start: 0.9113 (tp) cc_final: 0.8738 (tp) REVERT: D 324 TYR cc_start: 0.8034 (p90) cc_final: 0.7228 (p90) REVERT: D 364 ASP cc_start: 0.9219 (m-30) cc_final: 0.8639 (t70) REVERT: D 367 LEU cc_start: 0.8959 (tt) cc_final: 0.7619 (tt) REVERT: D 398 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9208 (tt) REVERT: D 435 MET cc_start: 0.9026 (mmp) cc_final: 0.8747 (mmm) REVERT: D 438 VAL cc_start: 0.9280 (p) cc_final: 0.9067 (m) REVERT: D 442 MET cc_start: 0.8951 (tpp) cc_final: 0.8428 (tpp) REVERT: D 462 TRP cc_start: 0.9413 (m100) cc_final: 0.9114 (m100) REVERT: D 464 ASN cc_start: 0.8906 (t160) cc_final: 0.8551 (t0) REVERT: D 485 MET cc_start: 0.8547 (mmt) cc_final: 0.8041 (mmt) REVERT: D 497 MET cc_start: 0.8722 (tmm) cc_final: 0.8405 (tmm) REVERT: D 509 TYR cc_start: 0.9221 (t80) cc_final: 0.8380 (t80) REVERT: D 515 GLU cc_start: 0.8737 (mm-30) cc_final: 0.7926 (mm-30) REVERT: D 520 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8063 (tm) REVERT: D 528 MET cc_start: 0.8389 (ttm) cc_final: 0.8177 (ttm) REVERT: D 542 ASP cc_start: 0.8044 (t70) cc_final: 0.7690 (p0) REVERT: D 577 MET cc_start: 0.8715 (mmm) cc_final: 0.6940 (mmm) outliers start: 116 outliers final: 32 residues processed: 683 average time/residue: 0.1436 time to fit residues: 146.8901 Evaluate side-chains 499 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 456 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.2980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN A 158 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 158 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN B 596 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN C 596 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN D 596 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077627 restraints weight = 56891.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.079894 restraints weight = 35107.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.081543 restraints weight = 25071.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082706 restraints weight = 19389.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083506 restraints weight = 16082.282| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20108 Z= 0.180 Angle : 0.863 12.944 27268 Z= 0.438 Chirality : 0.047 0.172 3092 Planarity : 0.005 0.048 3448 Dihedral : 9.560 173.406 2692 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.72 % Favored : 92.08 % Rotamer: Outliers : 0.61 % Allowed : 7.70 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.93 (0.15), residues: 2436 helix: -2.43 (0.11), residues: 1276 sheet: -6.47 (0.12), residues: 56 loop : -2.51 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 621 TYR 0.019 0.002 TYR C 432 PHE 0.019 0.002 PHE D 504 TRP 0.010 0.001 TRP B 495 HIS 0.007 0.001 HIS D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (20104) covalent geometry : angle 0.86334 / 0.44 (27268) hydrogen bonds : bond 0.05250 / 3.46 ( 808) hydrogen bonds : angle 5.79883 / 3.98 ( 2292) Misc. bond : bond 0.00026 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 599 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 92 LEU cc_start: 0.8798 (pt) cc_final: 0.8561 (tt) REVERT: A 99 MET cc_start: 0.8837 (mmp) cc_final: 0.8612 (mmm) REVERT: A 110 MET cc_start: 0.8647 (mmm) cc_final: 0.7603 (mmm) REVERT: A 127 ASN cc_start: 0.8785 (m110) cc_final: 0.8485 (p0) REVERT: A 204 ILE cc_start: 0.9558 (mm) cc_final: 0.9353 (mm) REVERT: A 209 LYS cc_start: 0.9673 (mtpt) cc_final: 0.8959 (mtpp) REVERT: A 306 GLN cc_start: 0.8918 (mp10) cc_final: 0.8567 (mp10) REVERT: A 318 SER cc_start: 0.9317 (t) cc_final: 0.8962 (p) REVERT: A 364 ASP cc_start: 0.9186 (m-30) cc_final: 0.8532 (t70) REVERT: A 367 LEU cc_start: 0.8622 (tt) cc_final: 0.7440 (tt) REVERT: A 368 LEU cc_start: 0.9368 (pp) cc_final: 0.9113 (pt) REVERT: A 435 MET cc_start: 0.8973 (mmp) cc_final: 0.8706 (mmm) REVERT: A 442 MET cc_start: 0.8669 (tpp) cc_final: 0.8316 (tpp) REVERT: A 497 MET cc_start: 0.8799 (tmm) cc_final: 0.8355 (tmm) REVERT: A 504 PHE cc_start: 0.9223 (m-80) cc_final: 0.8985 (m-80) REVERT: A 509 TYR cc_start: 0.9115 (t80) cc_final: 0.8496 (t80) REVERT: A 515 GLU cc_start: 0.8816 (mm-30) cc_final: 0.7743 (mm-30) REVERT: A 553 PHE cc_start: 0.8032 (t80) cc_final: 0.7671 (t80) REVERT: A 556 SER cc_start: 0.9167 (m) cc_final: 0.8931 (p) REVERT: A 557 ILE cc_start: 0.9176 (pt) cc_final: 0.8772 (tp) REVERT: A 570 MET cc_start: 0.8305 (ppp) cc_final: 0.7972 (tmm) REVERT: A 577 MET cc_start: 0.8624 (mmm) cc_final: 0.8337 (mmm) REVERT: B 35 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 92 LEU cc_start: 0.8768 (pt) cc_final: 0.8514 (tt) REVERT: B 110 MET cc_start: 0.8724 (mmm) cc_final: 0.7671 (mmm) REVERT: B 127 ASN cc_start: 0.8763 (m110) cc_final: 0.8534 (p0) REVERT: B 204 ILE cc_start: 0.9544 (mm) cc_final: 0.9341 (mm) REVERT: B 209 LYS cc_start: 0.9684 (mtpt) cc_final: 0.8998 (mtpp) REVERT: B 306 GLN cc_start: 0.8909 (mp10) cc_final: 0.8577 (mp10) REVERT: B 318 SER cc_start: 0.9304 (t) cc_final: 0.8961 (p) REVERT: B 364 ASP cc_start: 0.9179 (m-30) cc_final: 0.8547 (t70) REVERT: B 367 LEU cc_start: 0.8604 (tt) cc_final: 0.7472 (tt) REVERT: B 368 LEU cc_start: 0.9358 (pp) cc_final: 0.9106 (pt) REVERT: B 398 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9252 (mp) REVERT: B 435 MET cc_start: 0.8959 (mmp) cc_final: 0.8730 (mmm) REVERT: B 442 MET cc_start: 0.8676 (tpp) cc_final: 0.8312 (tpp) REVERT: B 504 PHE cc_start: 0.9211 (m-80) cc_final: 0.8988 (m-80) REVERT: B 509 TYR cc_start: 0.9100 (t80) cc_final: 0.8473 (t80) REVERT: B 515 GLU cc_start: 0.8807 (mm-30) cc_final: 0.7807 (mm-30) REVERT: B 528 MET cc_start: 0.8354 (ttm) cc_final: 0.8044 (ttm) REVERT: B 553 PHE cc_start: 0.8040 (t80) cc_final: 0.7688 (t80) REVERT: B 556 SER cc_start: 0.9181 (m) cc_final: 0.8926 (p) REVERT: B 557 ILE cc_start: 0.9171 (pt) cc_final: 0.8755 (tp) REVERT: C 35 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8099 (mt-10) REVERT: C 92 LEU cc_start: 0.8778 (pt) cc_final: 0.8532 (tt) REVERT: C 110 MET cc_start: 0.8665 (mmm) cc_final: 0.7584 (mmm) REVERT: C 127 ASN cc_start: 0.8779 (m110) cc_final: 0.8507 (p0) REVERT: C 209 LYS cc_start: 0.9690 (mtpt) cc_final: 0.8999 (mtpp) REVERT: C 306 GLN cc_start: 0.8875 (mp10) cc_final: 0.8489 (mp10) REVERT: C 318 SER cc_start: 0.9333 (t) cc_final: 0.8988 (p) REVERT: C 364 ASP cc_start: 0.9182 (m-30) cc_final: 0.8569 (t70) REVERT: C 367 LEU cc_start: 0.8608 (tt) cc_final: 0.7449 (tt) REVERT: C 368 LEU cc_start: 0.9348 (pp) cc_final: 0.9104 (pt) REVERT: C 435 MET cc_start: 0.8961 (mmp) cc_final: 0.8702 (mmm) REVERT: C 442 MET cc_start: 0.8668 (tpp) cc_final: 0.8322 (tpp) REVERT: C 497 MET cc_start: 0.8671 (tmm) cc_final: 0.8278 (tmm) REVERT: C 504 PHE cc_start: 0.9197 (m-80) cc_final: 0.8984 (m-80) REVERT: C 509 TYR cc_start: 0.9098 (t80) cc_final: 0.8455 (t80) REVERT: C 515 GLU cc_start: 0.8813 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 528 MET cc_start: 0.8301 (ttm) cc_final: 0.7953 (ttm) REVERT: C 553 PHE cc_start: 0.8030 (t80) cc_final: 0.7673 (t80) REVERT: C 556 SER cc_start: 0.9160 (m) cc_final: 0.8925 (p) REVERT: C 557 ILE cc_start: 0.9180 (pt) cc_final: 0.8767 (tp) REVERT: D 35 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8142 (mt-10) REVERT: D 92 LEU cc_start: 0.8808 (pt) cc_final: 0.8537 (tt) REVERT: D 110 MET cc_start: 0.8709 (mmm) cc_final: 0.7657 (mmm) REVERT: D 127 ASN cc_start: 0.8784 (m110) cc_final: 0.8508 (p0) REVERT: D 204 ILE cc_start: 0.9552 (mm) cc_final: 0.9352 (mm) REVERT: D 209 LYS cc_start: 0.9684 (mtpt) cc_final: 0.8996 (mtpp) REVERT: D 306 GLN cc_start: 0.8842 (mp10) cc_final: 0.8634 (mp10) REVERT: D 318 SER cc_start: 0.9330 (t) cc_final: 0.8964 (p) REVERT: D 364 ASP cc_start: 0.9206 (m-30) cc_final: 0.8543 (t70) REVERT: D 367 LEU cc_start: 0.8606 (tt) cc_final: 0.7276 (tt) REVERT: D 368 LEU cc_start: 0.9362 (pp) cc_final: 0.9126 (pp) REVERT: D 442 MET cc_start: 0.8649 (tpp) cc_final: 0.8327 (tpp) REVERT: D 497 MET cc_start: 0.8832 (tmm) cc_final: 0.8335 (tmm) REVERT: D 504 PHE cc_start: 0.9145 (m-80) cc_final: 0.8826 (m-80) REVERT: D 509 TYR cc_start: 0.9115 (t80) cc_final: 0.8444 (t80) REVERT: D 515 GLU cc_start: 0.8805 (mm-30) cc_final: 0.7812 (mm-30) REVERT: D 528 MET cc_start: 0.8300 (ttm) cc_final: 0.8038 (ttm) REVERT: D 570 MET cc_start: 0.8332 (ppp) cc_final: 0.8100 (tmm) REVERT: D 573 LEU cc_start: 0.9447 (tp) cc_final: 0.9246 (tt) REVERT: D 577 MET cc_start: 0.8567 (mmm) cc_final: 0.8199 (mmm) outliers start: 13 outliers final: 0 residues processed: 600 average time/residue: 0.1391 time to fit residues: 132.3922 Evaluate side-chains 468 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 467 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 106 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 102 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** 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 = 0.3309 r_free = 0.3309 target = 0.095617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.078370 restraints weight = 57523.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.080720 restraints weight = 35392.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.082425 restraints weight = 25026.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.083560 restraints weight = 19461.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.084448 restraints weight = 16230.927| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20108 Z= 0.158 Angle : 0.812 13.064 27268 Z= 0.404 Chirality : 0.045 0.182 3092 Planarity : 0.004 0.045 3448 Dihedral : 9.012 165.745 2692 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.62 % Favored : 91.30 % Rotamer: Outliers : 0.66 % Allowed : 5.91 % Favored : 93.43 % 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: -3.41 (0.15), residues: 2436 helix: -1.77 (0.13), residues: 1288 sheet: -6.40 (0.12), residues: 56 loop : -2.58 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 589 TYR 0.012 0.001 TYR D 432 PHE 0.017 0.001 PHE B 493 TRP 0.009 0.001 TRP A 583 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (20104) covalent geometry : angle 0.81174 / 0.40 (27268) hydrogen bonds : bond 0.04331 / 2.86 ( 808) hydrogen bonds : angle 5.24660 / 3.61 ( 2292) Misc. bond : bond 0.00036 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 567 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8857 (pt) cc_final: 0.8620 (tt) REVERT: A 110 MET cc_start: 0.8547 (mmm) cc_final: 0.7436 (mmm) REVERT: A 127 ASN cc_start: 0.8662 (m110) cc_final: 0.8421 (p0) REVERT: A 209 LYS cc_start: 0.9655 (mtpt) cc_final: 0.9090 (mttp) REVERT: A 303 GLU cc_start: 0.8432 (tp30) cc_final: 0.8040 (tp30) REVERT: A 306 GLN cc_start: 0.8811 (mp10) cc_final: 0.8320 (mp10) REVERT: A 315 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 316 LEU cc_start: 0.9339 (tt) cc_final: 0.9130 (tt) REVERT: A 318 SER cc_start: 0.9330 (t) cc_final: 0.9079 (p) REVERT: A 364 ASP cc_start: 0.9229 (m-30) cc_final: 0.8533 (t70) REVERT: A 367 LEU cc_start: 0.8605 (tt) cc_final: 0.7024 (tt) REVERT: A 368 LEU cc_start: 0.9344 (pp) cc_final: 0.9117 (pp) REVERT: A 442 MET cc_start: 0.8416 (tpp) cc_final: 0.8206 (tpp) REVERT: A 481 MET cc_start: 0.9037 (mmm) cc_final: 0.8809 (mmm) REVERT: A 497 MET cc_start: 0.8794 (tmm) cc_final: 0.8319 (tmm) REVERT: A 504 PHE cc_start: 0.9204 (m-80) cc_final: 0.8981 (m-80) REVERT: A 509 TYR cc_start: 0.9114 (t80) cc_final: 0.8504 (t80) REVERT: A 515 GLU cc_start: 0.8858 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 556 SER cc_start: 0.9221 (m) cc_final: 0.8898 (p) REVERT: A 573 LEU cc_start: 0.9305 (tt) cc_final: 0.9105 (tt) REVERT: A 584 ARG cc_start: 0.8864 (mmt180) cc_final: 0.8550 (mmt180) REVERT: B 92 LEU cc_start: 0.8834 (pt) cc_final: 0.8601 (tt) REVERT: B 110 MET cc_start: 0.8580 (mmm) cc_final: 0.7369 (mmm) REVERT: B 127 ASN cc_start: 0.8638 (m110) cc_final: 0.8372 (p0) REVERT: B 130 MET cc_start: 0.7768 (mmm) cc_final: 0.7425 (mmm) REVERT: B 209 LYS cc_start: 0.9662 (mtpt) cc_final: 0.9102 (mttp) REVERT: B 245 LYS cc_start: 0.9077 (mttt) cc_final: 0.8724 (mptt) REVERT: B 303 GLU cc_start: 0.8434 (tp30) cc_final: 0.8030 (tp30) REVERT: B 306 GLN cc_start: 0.8823 (mp10) cc_final: 0.8323 (mp10) REVERT: B 318 SER cc_start: 0.9286 (t) cc_final: 0.9027 (p) REVERT: B 364 ASP cc_start: 0.9157 (m-30) cc_final: 0.8505 (t70) REVERT: B 367 LEU cc_start: 0.8685 (tt) cc_final: 0.7227 (tt) REVERT: B 368 LEU cc_start: 0.9332 (pp) cc_final: 0.9096 (pp) REVERT: B 442 MET cc_start: 0.8477 (tpp) cc_final: 0.8268 (tpp) REVERT: B 509 TYR cc_start: 0.9100 (t80) cc_final: 0.8545 (t80) REVERT: B 515 GLU cc_start: 0.8854 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 528 MET cc_start: 0.8227 (ttm) cc_final: 0.7896 (ttm) REVERT: B 557 ILE cc_start: 0.9279 (pt) cc_final: 0.9046 (tp) REVERT: B 584 ARG cc_start: 0.8900 (mmt180) cc_final: 0.8597 (mmt180) REVERT: C 92 LEU cc_start: 0.8731 (pt) cc_final: 0.8482 (tt) REVERT: C 110 MET cc_start: 0.8632 (mmm) cc_final: 0.7471 (mmm) REVERT: C 127 ASN cc_start: 0.8656 (m110) cc_final: 0.8360 (p0) REVERT: C 209 LYS cc_start: 0.9672 (mtpt) cc_final: 0.9104 (mttp) REVERT: C 280 LEU cc_start: 0.8763 (tp) cc_final: 0.8531 (tp) REVERT: C 303 GLU cc_start: 0.8425 (tp30) cc_final: 0.8020 (tp30) REVERT: C 306 GLN cc_start: 0.8794 (mp10) cc_final: 0.8325 (mp10) REVERT: C 315 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8149 (tm-30) REVERT: C 318 SER cc_start: 0.9288 (t) cc_final: 0.9023 (p) REVERT: C 364 ASP cc_start: 0.9216 (m-30) cc_final: 0.8564 (t70) REVERT: C 367 LEU cc_start: 0.8588 (tt) cc_final: 0.7043 (tt) REVERT: C 368 LEU cc_start: 0.9325 (pp) cc_final: 0.9109 (pp) REVERT: C 442 MET cc_start: 0.8479 (tpp) cc_final: 0.8248 (tpp) REVERT: C 485 MET cc_start: 0.9314 (mmt) cc_final: 0.9093 (mmt) REVERT: C 497 MET cc_start: 0.8589 (tmm) cc_final: 0.8309 (tmm) REVERT: C 509 TYR cc_start: 0.9081 (t80) cc_final: 0.8468 (t80) REVERT: C 515 GLU cc_start: 0.8864 (mm-30) cc_final: 0.7926 (mm-30) REVERT: C 528 MET cc_start: 0.8226 (ttm) cc_final: 0.7851 (ttm) REVERT: C 556 SER cc_start: 0.9219 (m) cc_final: 0.8917 (p) REVERT: C 557 ILE cc_start: 0.9256 (pt) cc_final: 0.8873 (tp) REVERT: C 584 ARG cc_start: 0.8838 (mmt180) cc_final: 0.8503 (mmt180) REVERT: D 92 LEU cc_start: 0.8877 (pt) cc_final: 0.8622 (tt) REVERT: D 110 MET cc_start: 0.8638 (mmm) cc_final: 0.7405 (mmm) REVERT: D 127 ASN cc_start: 0.8687 (m110) cc_final: 0.8353 (p0) REVERT: D 209 LYS cc_start: 0.9676 (mtpt) cc_final: 0.9105 (mttp) REVERT: D 280 LEU cc_start: 0.8745 (tp) cc_final: 0.8537 (tp) REVERT: D 303 GLU cc_start: 0.8467 (tp30) cc_final: 0.8088 (tp30) REVERT: D 306 GLN cc_start: 0.8925 (mp10) cc_final: 0.8369 (mp10) REVERT: D 318 SER cc_start: 0.9326 (t) cc_final: 0.9083 (p) REVERT: D 364 ASP cc_start: 0.9223 (m-30) cc_final: 0.8552 (t70) REVERT: D 367 LEU cc_start: 0.8596 (tt) cc_final: 0.6955 (tt) REVERT: D 368 LEU cc_start: 0.9326 (pp) cc_final: 0.9092 (pp) REVERT: D 435 MET cc_start: 0.8849 (mmm) cc_final: 0.8605 (mmm) REVERT: D 442 MET cc_start: 0.8515 (tpp) cc_final: 0.8269 (tpp) REVERT: D 485 MET cc_start: 0.8931 (mmt) cc_final: 0.8548 (mmt) REVERT: D 497 MET cc_start: 0.8777 (tmm) cc_final: 0.8384 (tmm) REVERT: D 504 PHE cc_start: 0.9223 (m-80) cc_final: 0.8979 (m-80) REVERT: D 509 TYR cc_start: 0.9137 (t80) cc_final: 0.8476 (t80) REVERT: D 515 GLU cc_start: 0.8883 (mm-30) cc_final: 0.7918 (mm-30) REVERT: D 528 MET cc_start: 0.8206 (ttm) cc_final: 0.7893 (ttm) REVERT: D 570 MET cc_start: 0.8122 (ppp) cc_final: 0.7905 (tmm) REVERT: D 577 MET cc_start: 0.8195 (mmm) cc_final: 0.6844 (mmm) REVERT: D 584 ARG cc_start: 0.8881 (mmt180) cc_final: 0.8557 (mmt180) outliers start: 14 outliers final: 2 residues processed: 572 average time/residue: 0.1395 time to fit residues: 126.3750 Evaluate side-chains 449 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 447 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 188 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 141 optimal weight: 0.0020 chunk 219 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 211 optimal weight: 0.4980 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.077925 restraints weight = 57123.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.080364 restraints weight = 34900.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.082145 restraints weight = 24648.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.083380 restraints weight = 19113.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.084294 restraints weight = 15931.640| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20108 Z= 0.156 Angle : 0.796 12.803 27268 Z= 0.393 Chirality : 0.045 0.181 3092 Planarity : 0.004 0.050 3448 Dihedral : 8.582 159.140 2692 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.42 % Favored : 91.54 % Rotamer: Outliers : 0.19 % Allowed : 5.10 % Favored : 94.71 % 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: -2.98 (0.16), residues: 2436 helix: -1.36 (0.13), residues: 1300 sheet: -6.45 (0.11), residues: 56 loop : -2.44 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 589 TYR 0.012 0.001 TYR A 555 PHE 0.031 0.002 PHE C 504 TRP 0.015 0.001 TRP D 583 HIS 0.010 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (20104) covalent geometry : angle 0.79591 / 0.39 (27268) hydrogen bonds : bond 0.03901 / 2.60 ( 808) hydrogen bonds : angle 4.96810 / 3.42 ( 2292) Misc. bond : bond 0.00018 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 573 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8955 (pt) cc_final: 0.8542 (tp) REVERT: A 110 MET cc_start: 0.8358 (mmm) cc_final: 0.7472 (mmm) REVERT: A 127 ASN cc_start: 0.8747 (m110) cc_final: 0.8313 (p0) REVERT: A 209 LYS cc_start: 0.9641 (mtpt) cc_final: 0.9082 (mtpp) REVERT: A 211 PHE cc_start: 0.8216 (t80) cc_final: 0.7754 (t80) REVERT: A 245 LYS cc_start: 0.9052 (mttt) cc_final: 0.8658 (mptt) REVERT: A 280 LEU cc_start: 0.8872 (tp) cc_final: 0.8604 (tp) REVERT: A 303 GLU cc_start: 0.8466 (tp30) cc_final: 0.8153 (tp30) REVERT: A 315 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8185 (tm-30) REVERT: A 318 SER cc_start: 0.9318 (t) cc_final: 0.9042 (p) REVERT: A 364 ASP cc_start: 0.9111 (m-30) cc_final: 0.8584 (t70) REVERT: A 367 LEU cc_start: 0.8636 (tt) cc_final: 0.7235 (tt) REVERT: A 485 MET cc_start: 0.9328 (mmt) cc_final: 0.9074 (mmt) REVERT: A 497 MET cc_start: 0.8844 (tmm) cc_final: 0.8414 (tmm) REVERT: A 509 TYR cc_start: 0.9150 (t80) cc_final: 0.8534 (t80) REVERT: A 515 GLU cc_start: 0.8871 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 556 SER cc_start: 0.9301 (m) cc_final: 0.8939 (p) REVERT: A 570 MET cc_start: 0.8329 (ppp) cc_final: 0.7878 (tmm) REVERT: A 584 ARG cc_start: 0.8866 (mmt180) cc_final: 0.8659 (mmt180) REVERT: B 110 MET cc_start: 0.8435 (mmm) cc_final: 0.7630 (mmm) REVERT: B 127 ASN cc_start: 0.8707 (m110) cc_final: 0.8287 (p0) REVERT: B 209 LYS cc_start: 0.9645 (mtpt) cc_final: 0.9087 (mtpp) REVERT: B 211 PHE cc_start: 0.8207 (t80) cc_final: 0.7757 (t80) REVERT: B 245 LYS cc_start: 0.9078 (mttt) cc_final: 0.8622 (mptt) REVERT: B 303 GLU cc_start: 0.8461 (tp30) cc_final: 0.8165 (tp30) REVERT: B 318 SER cc_start: 0.9317 (t) cc_final: 0.9068 (p) REVERT: B 364 ASP cc_start: 0.9086 (m-30) cc_final: 0.8585 (t70) REVERT: B 367 LEU cc_start: 0.8626 (tt) cc_final: 0.7131 (tt) REVERT: B 397 ILE cc_start: 0.9060 (mt) cc_final: 0.8856 (mm) REVERT: B 398 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9064 (mp) REVERT: B 485 MET cc_start: 0.9248 (mmt) cc_final: 0.9031 (mmt) REVERT: B 497 MET cc_start: 0.9244 (tmm) cc_final: 0.8811 (tmm) REVERT: B 509 TYR cc_start: 0.9158 (t80) cc_final: 0.8549 (t80) REVERT: B 515 GLU cc_start: 0.8863 (mm-30) cc_final: 0.7912 (mm-30) REVERT: B 528 MET cc_start: 0.8330 (ttm) cc_final: 0.7919 (ttm) REVERT: B 556 SER cc_start: 0.9322 (m) cc_final: 0.8949 (p) REVERT: B 557 ILE cc_start: 0.9289 (pt) cc_final: 0.8953 (tp) REVERT: B 584 ARG cc_start: 0.8895 (mmt180) cc_final: 0.8688 (mmt180) REVERT: C 92 LEU cc_start: 0.8917 (pt) cc_final: 0.8531 (tp) REVERT: C 110 MET cc_start: 0.8501 (mmm) cc_final: 0.7621 (mmm) REVERT: C 127 ASN cc_start: 0.8774 (m110) cc_final: 0.8382 (p0) REVERT: C 209 LYS cc_start: 0.9644 (mtpt) cc_final: 0.9102 (mttp) REVERT: C 211 PHE cc_start: 0.8199 (t80) cc_final: 0.7736 (t80) REVERT: C 245 LYS cc_start: 0.9037 (mttt) cc_final: 0.8628 (mptt) REVERT: C 280 LEU cc_start: 0.8853 (tp) cc_final: 0.8639 (tp) REVERT: C 303 GLU cc_start: 0.8493 (tp30) cc_final: 0.8183 (tp30) REVERT: C 315 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 318 SER cc_start: 0.9327 (t) cc_final: 0.9062 (p) REVERT: C 364 ASP cc_start: 0.9093 (m-30) cc_final: 0.8611 (t70) REVERT: C 367 LEU cc_start: 0.8656 (tt) cc_final: 0.7223 (tt) REVERT: C 397 ILE cc_start: 0.9099 (mt) cc_final: 0.8896 (mm) REVERT: C 485 MET cc_start: 0.9335 (mmt) cc_final: 0.9033 (mmt) REVERT: C 497 MET cc_start: 0.8577 (tmm) cc_final: 0.8341 (tmm) REVERT: C 509 TYR cc_start: 0.9107 (t80) cc_final: 0.8475 (t80) REVERT: C 515 GLU cc_start: 0.8944 (mm-30) cc_final: 0.7990 (mm-30) REVERT: C 528 MET cc_start: 0.8317 (ttm) cc_final: 0.7927 (ttm) REVERT: C 535 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8708 (tm-30) REVERT: C 556 SER cc_start: 0.9297 (m) cc_final: 0.8973 (p) REVERT: C 557 ILE cc_start: 0.9271 (pt) cc_final: 0.8921 (tp) REVERT: C 584 ARG cc_start: 0.8939 (mmt180) cc_final: 0.8635 (mmt180) REVERT: C 612 LEU cc_start: 0.8781 (tt) cc_final: 0.8376 (mm) REVERT: D 92 LEU cc_start: 0.8945 (pt) cc_final: 0.8541 (tp) REVERT: D 110 MET cc_start: 0.8414 (mmm) cc_final: 0.7134 (mmm) REVERT: D 127 ASN cc_start: 0.8762 (m110) cc_final: 0.8331 (p0) REVERT: D 209 LYS cc_start: 0.9643 (mtpt) cc_final: 0.9108 (mtpp) REVERT: D 211 PHE cc_start: 0.8213 (t80) cc_final: 0.7749 (t80) REVERT: D 245 LYS cc_start: 0.9034 (mttt) cc_final: 0.8730 (mptt) REVERT: D 280 LEU cc_start: 0.8892 (tp) cc_final: 0.8636 (tp) REVERT: D 315 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8191 (tm-30) REVERT: D 318 SER cc_start: 0.9338 (t) cc_final: 0.9054 (p) REVERT: D 364 ASP cc_start: 0.9119 (m-30) cc_final: 0.8601 (t70) REVERT: D 367 LEU cc_start: 0.8645 (tt) cc_final: 0.7112 (tt) REVERT: D 368 LEU cc_start: 0.9273 (pp) cc_final: 0.9013 (pt) REVERT: D 435 MET cc_start: 0.8878 (mmm) cc_final: 0.8621 (mmm) REVERT: D 497 MET cc_start: 0.8784 (tmm) cc_final: 0.8401 (tmm) REVERT: D 504 PHE cc_start: 0.9271 (m-80) cc_final: 0.9054 (m-80) REVERT: D 509 TYR cc_start: 0.9178 (t80) cc_final: 0.8497 (t80) REVERT: D 515 GLU cc_start: 0.8908 (mm-30) cc_final: 0.7915 (mm-30) REVERT: D 528 MET cc_start: 0.8296 (ttm) cc_final: 0.7931 (ttm) REVERT: D 556 SER cc_start: 0.9275 (m) cc_final: 0.8927 (p) REVERT: D 557 ILE cc_start: 0.9242 (pt) cc_final: 0.8897 (tp) REVERT: D 570 MET cc_start: 0.8215 (ppp) cc_final: 0.7962 (tmm) REVERT: D 577 MET cc_start: 0.8221 (mmm) cc_final: 0.7184 (mmm) REVERT: D 584 ARG cc_start: 0.8912 (mmt180) cc_final: 0.8603 (mmt180) REVERT: D 612 LEU cc_start: 0.8754 (tt) cc_final: 0.8378 (mm) outliers start: 4 outliers final: 0 residues processed: 573 average time/residue: 0.1345 time to fit residues: 122.9582 Evaluate side-chains 458 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 457 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.096206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.078837 restraints weight = 56481.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.081258 restraints weight = 34581.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.082999 restraints weight = 24336.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084136 restraints weight = 18782.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.085012 restraints weight = 15623.335| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20108 Z= 0.152 Angle : 0.817 13.352 27268 Z= 0.390 Chirality : 0.044 0.181 3092 Planarity : 0.004 0.061 3448 Dihedral : 8.296 152.812 2692 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.19 % Allowed : 4.77 % Favored : 95.04 % 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: -2.73 (0.16), residues: 2436 helix: -1.04 (0.14), residues: 1272 sheet: -6.45 (0.10), residues: 56 loop : -2.46 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 589 TYR 0.019 0.001 TYR B 67 PHE 0.025 0.002 PHE A 504 TRP 0.015 0.001 TRP A 583 HIS 0.006 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (20104) covalent geometry : angle 0.81746 / 0.39 (27268) hydrogen bonds : bond 0.03780 / 2.54 ( 808) hydrogen bonds : angle 4.94578 / 3.40 ( 2292) Misc. bond : bond 0.00010 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 548 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8970 (pt) cc_final: 0.8627 (tp) REVERT: A 99 MET cc_start: 0.8875 (mmp) cc_final: 0.8584 (mmm) REVERT: A 110 MET cc_start: 0.8473 (mmm) cc_final: 0.7062 (mmm) REVERT: A 127 ASN cc_start: 0.8647 (m110) cc_final: 0.8318 (p0) REVERT: A 209 LYS cc_start: 0.9576 (mtpt) cc_final: 0.9054 (mttp) REVERT: A 211 PHE cc_start: 0.8204 (t80) cc_final: 0.7653 (t80) REVERT: A 245 LYS cc_start: 0.9058 (mttt) cc_final: 0.8673 (mptt) REVERT: A 280 LEU cc_start: 0.8963 (tp) cc_final: 0.8665 (tp) REVERT: A 303 GLU cc_start: 0.8528 (tp30) cc_final: 0.8188 (tp30) REVERT: A 315 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 318 SER cc_start: 0.9357 (t) cc_final: 0.9047 (p) REVERT: A 364 ASP cc_start: 0.9076 (m-30) cc_final: 0.8594 (t70) REVERT: A 367 LEU cc_start: 0.8554 (tt) cc_final: 0.8332 (tt) REVERT: A 442 MET cc_start: 0.8570 (tpp) cc_final: 0.8312 (tpp) REVERT: A 454 MET cc_start: 0.8248 (tpt) cc_final: 0.8047 (tpt) REVERT: A 485 MET cc_start: 0.9297 (mmt) cc_final: 0.8985 (mmt) REVERT: A 497 MET cc_start: 0.8810 (tmm) cc_final: 0.8398 (tmm) REVERT: A 509 TYR cc_start: 0.9144 (t80) cc_final: 0.8461 (t80) REVERT: A 556 SER cc_start: 0.9284 (m) cc_final: 0.8915 (p) REVERT: A 603 MET cc_start: 0.8608 (mtt) cc_final: 0.8356 (mtt) REVERT: A 612 LEU cc_start: 0.8704 (tt) cc_final: 0.8313 (mm) REVERT: B 92 LEU cc_start: 0.8989 (pt) cc_final: 0.8609 (tp) REVERT: B 99 MET cc_start: 0.8831 (mmp) cc_final: 0.8588 (mmm) REVERT: B 110 MET cc_start: 0.8490 (mmm) cc_final: 0.7467 (mmm) REVERT: B 127 ASN cc_start: 0.8698 (m110) cc_final: 0.8232 (p0) REVERT: B 209 LYS cc_start: 0.9578 (mtpt) cc_final: 0.9059 (mttp) REVERT: B 211 PHE cc_start: 0.8191 (t80) cc_final: 0.7670 (t80) REVERT: B 245 LYS cc_start: 0.9084 (mttt) cc_final: 0.8818 (mptt) REVERT: B 280 LEU cc_start: 0.9060 (tp) cc_final: 0.8677 (tp) REVERT: B 303 GLU cc_start: 0.8533 (tp30) cc_final: 0.8205 (tp30) REVERT: B 315 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 318 SER cc_start: 0.9328 (t) cc_final: 0.9042 (p) REVERT: B 364 ASP cc_start: 0.9042 (m-30) cc_final: 0.8575 (t70) REVERT: B 367 LEU cc_start: 0.8680 (tt) cc_final: 0.7077 (tt) REVERT: B 432 TYR cc_start: 0.9042 (t80) cc_final: 0.8813 (t80) REVERT: B 442 MET cc_start: 0.8629 (tpp) cc_final: 0.8390 (tpp) REVERT: B 480 ILE cc_start: 0.9436 (mm) cc_final: 0.9180 (mm) REVERT: B 485 MET cc_start: 0.9316 (mmt) cc_final: 0.8916 (mmt) REVERT: B 497 MET cc_start: 0.9260 (tmm) cc_final: 0.8760 (tmm) REVERT: B 509 TYR cc_start: 0.9125 (t80) cc_final: 0.8449 (t80) REVERT: B 556 SER cc_start: 0.9320 (m) cc_final: 0.8929 (p) REVERT: B 557 ILE cc_start: 0.9293 (pt) cc_final: 0.8948 (tp) REVERT: B 583 TRP cc_start: 0.7744 (m100) cc_final: 0.7479 (m100) REVERT: B 612 LEU cc_start: 0.8669 (tt) cc_final: 0.8303 (mm) REVERT: C 92 LEU cc_start: 0.8983 (pt) cc_final: 0.8609 (tp) REVERT: C 99 MET cc_start: 0.8907 (mmp) cc_final: 0.8550 (mmm) REVERT: C 110 MET cc_start: 0.8475 (mmm) cc_final: 0.7053 (mmm) REVERT: C 127 ASN cc_start: 0.8661 (m110) cc_final: 0.8339 (p0) REVERT: C 209 LYS cc_start: 0.9597 (mtpt) cc_final: 0.9043 (mttm) REVERT: C 211 PHE cc_start: 0.8201 (t80) cc_final: 0.7610 (t80) REVERT: C 245 LYS cc_start: 0.8957 (mttt) cc_final: 0.8543 (mptt) REVERT: C 280 LEU cc_start: 0.8877 (tp) cc_final: 0.8666 (tp) REVERT: C 303 GLU cc_start: 0.8492 (tp30) cc_final: 0.8154 (tp30) REVERT: C 315 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8163 (tm-30) REVERT: C 318 SER cc_start: 0.9298 (t) cc_final: 0.8979 (p) REVERT: C 324 TYR cc_start: 0.7733 (p90) cc_final: 0.7005 (p90) REVERT: C 364 ASP cc_start: 0.9058 (m-30) cc_final: 0.8606 (t70) REVERT: C 424 PRO cc_start: 0.8397 (Cg_endo) cc_final: 0.8192 (Cg_exo) REVERT: C 442 MET cc_start: 0.8595 (tpp) cc_final: 0.8335 (tpp) REVERT: C 485 MET cc_start: 0.9355 (mmt) cc_final: 0.8946 (mmt) REVERT: C 509 TYR cc_start: 0.9103 (t80) cc_final: 0.8414 (t80) REVERT: C 515 GLU cc_start: 0.8916 (mm-30) cc_final: 0.7980 (mm-30) REVERT: C 528 MET cc_start: 0.8290 (ttm) cc_final: 0.7916 (ttm) REVERT: C 556 SER cc_start: 0.9282 (m) cc_final: 0.8960 (p) REVERT: C 557 ILE cc_start: 0.9291 (pt) cc_final: 0.8901 (tp) REVERT: C 603 MET cc_start: 0.8601 (mtt) cc_final: 0.8363 (mtt) REVERT: D 92 LEU cc_start: 0.8992 (pt) cc_final: 0.8597 (tp) REVERT: D 99 MET cc_start: 0.8839 (mmp) cc_final: 0.8590 (mmm) REVERT: D 110 MET cc_start: 0.8384 (mmm) cc_final: 0.7385 (mmm) REVERT: D 127 ASN cc_start: 0.8658 (m110) cc_final: 0.8322 (p0) REVERT: D 209 LYS cc_start: 0.9598 (mtpt) cc_final: 0.9046 (mttm) REVERT: D 211 PHE cc_start: 0.8191 (t80) cc_final: 0.7629 (t80) REVERT: D 245 LYS cc_start: 0.8969 (mttt) cc_final: 0.8558 (mptt) REVERT: D 280 LEU cc_start: 0.8988 (tp) cc_final: 0.8732 (tp) REVERT: D 315 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8243 (tm-30) REVERT: D 318 SER cc_start: 0.9311 (t) cc_final: 0.9014 (p) REVERT: D 324 TYR cc_start: 0.7754 (p90) cc_final: 0.7028 (p90) REVERT: D 364 ASP cc_start: 0.9065 (m-30) cc_final: 0.8607 (t70) REVERT: D 435 MET cc_start: 0.8980 (mmm) cc_final: 0.8700 (mmm) REVERT: D 442 MET cc_start: 0.8521 (tpp) cc_final: 0.8272 (tpp) REVERT: D 497 MET cc_start: 0.8761 (tmm) cc_final: 0.8411 (tmm) REVERT: D 509 TYR cc_start: 0.9118 (t80) cc_final: 0.8473 (t80) REVERT: D 556 SER cc_start: 0.9246 (m) cc_final: 0.8907 (p) REVERT: D 557 ILE cc_start: 0.9252 (pt) cc_final: 0.8899 (tp) REVERT: D 570 MET cc_start: 0.8247 (ppp) cc_final: 0.8012 (tmm) REVERT: D 577 MET cc_start: 0.8132 (mmm) cc_final: 0.7353 (mmm) REVERT: D 603 MET cc_start: 0.8610 (mtt) cc_final: 0.8351 (mtt) REVERT: D 612 LEU cc_start: 0.8792 (tt) cc_final: 0.8459 (mm) outliers start: 4 outliers final: 0 residues processed: 548 average time/residue: 0.1172 time to fit residues: 103.7891 Evaluate side-chains 455 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 93 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 234 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 197 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.080450 restraints weight = 56228.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.082912 restraints weight = 34183.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.084620 restraints weight = 23900.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.085782 restraints weight = 18362.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086687 restraints weight = 15192.050| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20108 Z= 0.137 Angle : 0.805 12.977 27268 Z= 0.384 Chirality : 0.044 0.187 3092 Planarity : 0.004 0.051 3448 Dihedral : 7.621 137.252 2692 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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: -2.52 (0.16), residues: 2436 helix: -0.83 (0.14), residues: 1288 sheet: -6.48 (0.10), residues: 56 loop : -2.41 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 589 TYR 0.019 0.001 TYR D 432 PHE 0.020 0.001 PHE C 343 TRP 0.015 0.001 TRP A 462 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (20104) covalent geometry : angle 0.80492 / 0.38 (27268) hydrogen bonds : bond 0.03748 / 2.49 ( 808) hydrogen bonds : angle 4.77342 / 3.29 ( 2292) Misc. bond : bond 0.00034 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8867 (pt) cc_final: 0.8510 (tp) REVERT: A 110 MET cc_start: 0.8382 (mmm) cc_final: 0.7521 (mmm) REVERT: A 209 LYS cc_start: 0.9551 (mtpt) cc_final: 0.8993 (mttm) REVERT: A 211 PHE cc_start: 0.8247 (t80) cc_final: 0.7734 (t80) REVERT: A 245 LYS cc_start: 0.8980 (mttt) cc_final: 0.8637 (mptt) REVERT: A 280 LEU cc_start: 0.9096 (tp) cc_final: 0.8865 (tp) REVERT: A 298 THR cc_start: 0.8771 (m) cc_final: 0.8514 (p) REVERT: A 303 GLU cc_start: 0.8583 (tp30) cc_final: 0.8233 (tp30) REVERT: A 315 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8104 (tm-30) REVERT: A 324 TYR cc_start: 0.7635 (p90) cc_final: 0.7043 (p90) REVERT: A 364 ASP cc_start: 0.9079 (m-30) cc_final: 0.8726 (t70) REVERT: A 378 MET cc_start: 0.7492 (mmt) cc_final: 0.7270 (mmp) REVERT: A 424 PRO cc_start: 0.8332 (Cg_endo) cc_final: 0.8131 (Cg_exo) REVERT: A 485 MET cc_start: 0.9250 (mmt) cc_final: 0.8883 (mmt) REVERT: A 497 MET cc_start: 0.8781 (tmm) cc_final: 0.8386 (tmm) REVERT: A 509 TYR cc_start: 0.9092 (t80) cc_final: 0.8459 (t80) REVERT: A 556 SER cc_start: 0.9310 (m) cc_final: 0.8971 (p) REVERT: A 557 ILE cc_start: 0.9207 (pt) cc_final: 0.8916 (tp) REVERT: A 603 MET cc_start: 0.8541 (mtt) cc_final: 0.8255 (mtt) REVERT: A 612 LEU cc_start: 0.8832 (tt) cc_final: 0.8529 (mm) REVERT: B 92 LEU cc_start: 0.8820 (pt) cc_final: 0.8469 (tp) REVERT: B 110 MET cc_start: 0.8478 (mmm) cc_final: 0.7182 (mmm) REVERT: B 127 ASN cc_start: 0.8579 (m110) cc_final: 0.8285 (p0) REVERT: B 209 LYS cc_start: 0.9564 (mtpt) cc_final: 0.9005 (mttm) REVERT: B 211 PHE cc_start: 0.8240 (t80) cc_final: 0.7778 (t80) REVERT: B 245 LYS cc_start: 0.9050 (mttt) cc_final: 0.8595 (mptt) REVERT: B 280 LEU cc_start: 0.9083 (tp) cc_final: 0.8761 (tp) REVERT: B 298 THR cc_start: 0.8761 (m) cc_final: 0.8555 (p) REVERT: B 303 GLU cc_start: 0.8542 (tp30) cc_final: 0.8176 (tp30) REVERT: B 315 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8146 (tm-30) REVERT: B 318 SER cc_start: 0.9301 (t) cc_final: 0.9019 (p) REVERT: B 324 TYR cc_start: 0.7705 (p90) cc_final: 0.7146 (p90) REVERT: B 364 ASP cc_start: 0.9068 (m-30) cc_final: 0.8715 (t70) REVERT: B 378 MET cc_start: 0.7522 (mmt) cc_final: 0.7286 (mmp) REVERT: B 424 PRO cc_start: 0.7797 (Cg_endo) cc_final: 0.7594 (Cg_exo) REVERT: B 432 TYR cc_start: 0.9045 (t80) cc_final: 0.8785 (t80) REVERT: B 485 MET cc_start: 0.9200 (mmt) cc_final: 0.8842 (mmt) REVERT: B 497 MET cc_start: 0.8682 (tmm) cc_final: 0.8461 (ttp) REVERT: B 509 TYR cc_start: 0.9149 (t80) cc_final: 0.8464 (t80) REVERT: B 556 SER cc_start: 0.9255 (m) cc_final: 0.8890 (p) REVERT: B 557 ILE cc_start: 0.9268 (pt) cc_final: 0.8936 (tp) REVERT: B 583 TRP cc_start: 0.7735 (m100) cc_final: 0.7497 (m100) REVERT: B 603 MET cc_start: 0.8550 (mtt) cc_final: 0.8258 (mtt) REVERT: B 612 LEU cc_start: 0.8800 (tt) cc_final: 0.8511 (mm) REVERT: C 92 LEU cc_start: 0.8811 (pt) cc_final: 0.8469 (tp) REVERT: C 110 MET cc_start: 0.8428 (mmm) cc_final: 0.7750 (mmm) REVERT: C 211 PHE cc_start: 0.8218 (t80) cc_final: 0.7737 (t80) REVERT: C 245 LYS cc_start: 0.8976 (mttt) cc_final: 0.8593 (mptt) REVERT: C 280 LEU cc_start: 0.9049 (tp) cc_final: 0.8847 (tp) REVERT: C 303 GLU cc_start: 0.8551 (tp30) cc_final: 0.8195 (tp30) REVERT: C 315 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8146 (tm-30) REVERT: C 318 SER cc_start: 0.9313 (t) cc_final: 0.9066 (p) REVERT: C 324 TYR cc_start: 0.7664 (p90) cc_final: 0.6962 (p90) REVERT: C 364 ASP cc_start: 0.9056 (m-30) cc_final: 0.8745 (t70) REVERT: C 424 PRO cc_start: 0.8399 (Cg_endo) cc_final: 0.8152 (Cg_exo) REVERT: C 485 MET cc_start: 0.9221 (mmt) cc_final: 0.8699 (mmt) REVERT: C 497 MET cc_start: 0.9033 (tmm) cc_final: 0.8624 (tmm) REVERT: C 509 TYR cc_start: 0.9098 (t80) cc_final: 0.8422 (t80) REVERT: C 556 SER cc_start: 0.9296 (m) cc_final: 0.8943 (p) REVERT: C 557 ILE cc_start: 0.9249 (pt) cc_final: 0.8870 (tp) REVERT: C 603 MET cc_start: 0.8576 (mtt) cc_final: 0.8277 (mtt) REVERT: C 612 LEU cc_start: 0.8629 (tt) cc_final: 0.8407 (mm) REVERT: D 92 LEU cc_start: 0.8857 (pt) cc_final: 0.8511 (tp) REVERT: D 110 MET cc_start: 0.8311 (mmm) cc_final: 0.7414 (mmm) REVERT: D 209 LYS cc_start: 0.9557 (mtpt) cc_final: 0.9003 (mttm) REVERT: D 211 PHE cc_start: 0.8214 (t80) cc_final: 0.7729 (t80) REVERT: D 245 LYS cc_start: 0.8987 (mttt) cc_final: 0.8623 (mptt) REVERT: D 298 THR cc_start: 0.8786 (m) cc_final: 0.8540 (p) REVERT: D 315 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8220 (tm-30) REVERT: D 318 SER cc_start: 0.9355 (t) cc_final: 0.9089 (p) REVERT: D 324 TYR cc_start: 0.7737 (p90) cc_final: 0.6995 (p90) REVERT: D 364 ASP cc_start: 0.9079 (m-30) cc_final: 0.8735 (t70) REVERT: D 378 MET cc_start: 0.7468 (mmt) cc_final: 0.7252 (mmp) REVERT: D 432 TYR cc_start: 0.9056 (t80) cc_final: 0.8758 (t80) REVERT: D 435 MET cc_start: 0.9041 (mmm) cc_final: 0.8744 (mmm) REVERT: D 509 TYR cc_start: 0.9112 (t80) cc_final: 0.8379 (t80) REVERT: D 556 SER cc_start: 0.9219 (m) cc_final: 0.8920 (p) REVERT: D 577 MET cc_start: 0.7939 (mmm) cc_final: 0.7367 (mmm) REVERT: D 603 MET cc_start: 0.8548 (mtt) cc_final: 0.8283 (mtt) REVERT: D 612 LEU cc_start: 0.8765 (tt) cc_final: 0.8471 (mm) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.1167 time to fit residues: 106.9524 Evaluate side-chains 462 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 202 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 203 optimal weight: 0.0060 chunk 243 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 221 optimal weight: 0.0770 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.080624 restraints weight = 56766.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.083088 restraints weight = 35150.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.084801 restraints weight = 24878.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085857 restraints weight = 19314.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.086775 restraints weight = 16214.124| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20108 Z= 0.136 Angle : 0.807 15.153 27268 Z= 0.381 Chirality : 0.044 0.177 3092 Planarity : 0.004 0.031 3448 Dihedral : 6.921 115.598 2692 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.02 % 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: -2.35 (0.17), residues: 2436 helix: -0.67 (0.14), residues: 1288 sheet: -6.47 (0.10), residues: 56 loop : -2.36 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 589 TYR 0.012 0.001 TYR D 432 PHE 0.033 0.002 PHE C 504 TRP 0.018 0.001 TRP B 462 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (20104) covalent geometry : angle 0.80709 / 0.38 (27268) hydrogen bonds : bond 0.03596 / 2.40 ( 808) hydrogen bonds : angle 4.69048 / 3.23 ( 2292) Misc. bond : bond 0.00057 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 556 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8796 (mmp) cc_final: 0.8273 (mmp) REVERT: A 110 MET cc_start: 0.8302 (mmm) cc_final: 0.7195 (mmm) REVERT: A 127 ASN cc_start: 0.8137 (p0) cc_final: 0.7153 (p0) REVERT: A 209 LYS cc_start: 0.9513 (mtpt) cc_final: 0.9081 (mttt) REVERT: A 211 PHE cc_start: 0.8159 (t80) cc_final: 0.7751 (t80) REVERT: A 245 LYS cc_start: 0.8931 (mttt) cc_final: 0.8589 (mptt) REVERT: A 280 LEU cc_start: 0.9029 (tp) cc_final: 0.8749 (tp) REVERT: A 303 GLU cc_start: 0.8592 (tp30) cc_final: 0.8205 (tp30) REVERT: A 315 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 324 TYR cc_start: 0.7583 (p90) cc_final: 0.7052 (p90) REVERT: A 364 ASP cc_start: 0.9003 (m-30) cc_final: 0.8715 (t70) REVERT: A 368 LEU cc_start: 0.9369 (pt) cc_final: 0.9086 (mp) REVERT: A 378 MET cc_start: 0.7434 (mmt) cc_final: 0.7220 (mmp) REVERT: A 424 PRO cc_start: 0.8417 (Cg_endo) cc_final: 0.8194 (Cg_exo) REVERT: A 485 MET cc_start: 0.9151 (mmt) cc_final: 0.8586 (mmt) REVERT: A 509 TYR cc_start: 0.9060 (t80) cc_final: 0.8334 (t80) REVERT: A 556 SER cc_start: 0.9307 (m) cc_final: 0.8897 (p) REVERT: A 603 MET cc_start: 0.8484 (mtt) cc_final: 0.8203 (mtt) REVERT: A 612 LEU cc_start: 0.8767 (tt) cc_final: 0.8530 (mm) REVERT: B 92 LEU cc_start: 0.8684 (pt) cc_final: 0.8362 (tp) REVERT: B 99 MET cc_start: 0.8768 (mmp) cc_final: 0.8306 (mmp) REVERT: B 110 MET cc_start: 0.8411 (mmm) cc_final: 0.7414 (mmm) REVERT: B 209 LYS cc_start: 0.9520 (mtpt) cc_final: 0.9082 (mttt) REVERT: B 211 PHE cc_start: 0.8172 (t80) cc_final: 0.7781 (t80) REVERT: B 280 LEU cc_start: 0.9101 (tp) cc_final: 0.8773 (tp) REVERT: B 298 THR cc_start: 0.8779 (m) cc_final: 0.8558 (p) REVERT: B 303 GLU cc_start: 0.8593 (tp30) cc_final: 0.8215 (tp30) REVERT: B 315 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 318 SER cc_start: 0.9298 (t) cc_final: 0.9030 (p) REVERT: B 324 TYR cc_start: 0.7525 (p90) cc_final: 0.7046 (p90) REVERT: B 364 ASP cc_start: 0.9010 (m-30) cc_final: 0.8721 (t70) REVERT: B 368 LEU cc_start: 0.9401 (pt) cc_final: 0.9107 (mp) REVERT: B 378 MET cc_start: 0.7439 (mmt) cc_final: 0.7234 (mmp) REVERT: B 454 MET cc_start: 0.8041 (tpp) cc_final: 0.7619 (tpp) REVERT: B 485 MET cc_start: 0.9216 (mmt) cc_final: 0.8809 (mmt) REVERT: B 509 TYR cc_start: 0.9077 (t80) cc_final: 0.8381 (t80) REVERT: B 556 SER cc_start: 0.9271 (m) cc_final: 0.8890 (p) REVERT: B 584 ARG cc_start: 0.8734 (mmt180) cc_final: 0.8346 (mmp-170) REVERT: B 603 MET cc_start: 0.8466 (mtt) cc_final: 0.8145 (mtt) REVERT: B 612 LEU cc_start: 0.8729 (tt) cc_final: 0.8514 (mm) REVERT: C 99 MET cc_start: 0.8846 (mmp) cc_final: 0.8471 (mmp) REVERT: C 110 MET cc_start: 0.8343 (mmm) cc_final: 0.6980 (tpp) REVERT: C 127 ASN cc_start: 0.8186 (p0) cc_final: 0.7250 (p0) REVERT: C 209 LYS cc_start: 0.9525 (mtpt) cc_final: 0.9077 (mttt) REVERT: C 211 PHE cc_start: 0.8151 (t80) cc_final: 0.7698 (t80) REVERT: C 245 LYS cc_start: 0.8927 (mttt) cc_final: 0.8506 (mptt) REVERT: C 280 LEU cc_start: 0.9041 (tp) cc_final: 0.8824 (tp) REVERT: C 303 GLU cc_start: 0.8614 (tp30) cc_final: 0.8213 (tp30) REVERT: C 315 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7992 (tm-30) REVERT: C 324 TYR cc_start: 0.7631 (p90) cc_final: 0.6848 (p90) REVERT: C 364 ASP cc_start: 0.9004 (m-30) cc_final: 0.8739 (t70) REVERT: C 378 MET cc_start: 0.7428 (mmt) cc_final: 0.7213 (mmp) REVERT: C 424 PRO cc_start: 0.8435 (Cg_endo) cc_final: 0.8201 (Cg_exo) REVERT: C 485 MET cc_start: 0.9162 (mmt) cc_final: 0.8666 (mmt) REVERT: C 497 MET cc_start: 0.9033 (tmm) cc_final: 0.8606 (tmm) REVERT: C 509 TYR cc_start: 0.9088 (t80) cc_final: 0.8362 (t80) REVERT: C 556 SER cc_start: 0.9275 (m) cc_final: 0.8916 (p) REVERT: C 557 ILE cc_start: 0.9273 (pt) cc_final: 0.8919 (tp) REVERT: C 572 ASN cc_start: 0.9201 (OUTLIER) cc_final: 0.8830 (t0) REVERT: C 583 TRP cc_start: 0.7408 (t-100) cc_final: 0.7081 (t-100) REVERT: C 603 MET cc_start: 0.8518 (mtt) cc_final: 0.8253 (mtt) REVERT: C 612 LEU cc_start: 0.8675 (tt) cc_final: 0.8456 (mm) REVERT: D 99 MET cc_start: 0.8801 (mmp) cc_final: 0.8289 (mmp) REVERT: D 110 MET cc_start: 0.8365 (mmm) cc_final: 0.7507 (mmm) REVERT: D 127 ASN cc_start: 0.8175 (p0) cc_final: 0.7180 (p0) REVERT: D 209 LYS cc_start: 0.9521 (mtpt) cc_final: 0.9092 (mttt) REVERT: D 211 PHE cc_start: 0.8152 (t80) cc_final: 0.7739 (t80) REVERT: D 245 LYS cc_start: 0.8947 (mttt) cc_final: 0.8528 (mptt) REVERT: D 280 LEU cc_start: 0.9023 (tp) cc_final: 0.8665 (tp) REVERT: D 298 THR cc_start: 0.8776 (m) cc_final: 0.8570 (p) REVERT: D 315 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8142 (tm-30) REVERT: D 324 TYR cc_start: 0.7681 (p90) cc_final: 0.6882 (p90) REVERT: D 364 ASP cc_start: 0.9024 (m-30) cc_final: 0.8759 (t70) REVERT: D 378 MET cc_start: 0.7431 (mmt) cc_final: 0.7221 (mmp) REVERT: D 435 MET cc_start: 0.8972 (mmm) cc_final: 0.8696 (mmm) REVERT: D 509 TYR cc_start: 0.9118 (t80) cc_final: 0.8360 (t80) REVERT: D 556 SER cc_start: 0.9235 (m) cc_final: 0.8862 (p) REVERT: D 570 MET cc_start: 0.8018 (ppp) cc_final: 0.7801 (tmm) REVERT: D 573 LEU cc_start: 0.9176 (tt) cc_final: 0.8278 (tt) REVERT: D 574 LEU cc_start: 0.9058 (tp) cc_final: 0.8818 (tt) REVERT: D 583 TRP cc_start: 0.7482 (t-100) cc_final: 0.7041 (t-100) REVERT: D 603 MET cc_start: 0.8538 (mtt) cc_final: 0.8248 (mtt) REVERT: D 612 LEU cc_start: 0.8812 (tt) cc_final: 0.8524 (mm) outliers start: 2 outliers final: 0 residues processed: 558 average time/residue: 0.1201 time to fit residues: 107.8339 Evaluate side-chains 457 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 456 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 112 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 222 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 146 optimal weight: 0.0270 chunk 37 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.098757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.081428 restraints weight = 56155.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.083917 restraints weight = 34899.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085605 restraints weight = 24638.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086885 restraints weight = 19169.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.087725 restraints weight = 15735.593| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20108 Z= 0.135 Angle : 0.819 13.767 27268 Z= 0.385 Chirality : 0.044 0.162 3092 Planarity : 0.004 0.037 3448 Dihedral : 6.039 76.298 2692 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.05 % Allowed : 1.65 % Favored : 98.30 % 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: -2.20 (0.17), residues: 2436 helix: -0.58 (0.14), residues: 1300 sheet: -6.47 (0.10), residues: 56 loop : -2.26 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 589 TYR 0.013 0.001 TYR A 555 PHE 0.044 0.001 PHE C 504 TRP 0.011 0.001 TRP C 583 HIS 0.003 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (20104) covalent geometry : angle 0.81945 / 0.38 (27268) hydrogen bonds : bond 0.03663 / 2.44 ( 808) hydrogen bonds : angle 4.69536 / 3.22 ( 2292) Misc. bond : bond 0.00028 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 570 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8293 (mmm) cc_final: 0.7741 (mmm) REVERT: A 127 ASN cc_start: 0.7901 (p0) cc_final: 0.7127 (p0) REVERT: A 209 LYS cc_start: 0.9582 (mtmt) cc_final: 0.9215 (mttt) REVERT: A 211 PHE cc_start: 0.8156 (t80) cc_final: 0.7703 (t80) REVERT: A 245 LYS cc_start: 0.8905 (mttt) cc_final: 0.8565 (mptt) REVERT: A 255 MET cc_start: 0.8947 (tpt) cc_final: 0.8660 (tpp) REVERT: A 280 LEU cc_start: 0.9096 (tp) cc_final: 0.8881 (tp) REVERT: A 298 THR cc_start: 0.8855 (m) cc_final: 0.8559 (p) REVERT: A 303 GLU cc_start: 0.8604 (tp30) cc_final: 0.8206 (tp30) REVERT: A 315 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8152 (tm-30) REVERT: A 324 TYR cc_start: 0.7622 (p90) cc_final: 0.7038 (p90) REVERT: A 364 ASP cc_start: 0.8985 (m-30) cc_final: 0.8741 (t70) REVERT: A 368 LEU cc_start: 0.9412 (pt) cc_final: 0.9091 (mp) REVERT: A 424 PRO cc_start: 0.8348 (Cg_endo) cc_final: 0.8110 (Cg_exo) REVERT: A 485 MET cc_start: 0.9119 (mmt) cc_final: 0.8455 (mmt) REVERT: A 509 TYR cc_start: 0.9044 (t80) cc_final: 0.8474 (t80) REVERT: A 515 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8095 (mm-30) REVERT: A 556 SER cc_start: 0.9283 (m) cc_final: 0.8919 (p) REVERT: A 603 MET cc_start: 0.8414 (mtt) cc_final: 0.8120 (mtt) REVERT: B 110 MET cc_start: 0.8192 (mmm) cc_final: 0.7654 (mmm) REVERT: B 127 ASN cc_start: 0.8141 (p0) cc_final: 0.7216 (p0) REVERT: B 209 LYS cc_start: 0.9585 (mtmt) cc_final: 0.9198 (mttt) REVERT: B 211 PHE cc_start: 0.8135 (t80) cc_final: 0.7704 (t80) REVERT: B 255 MET cc_start: 0.8945 (tpt) cc_final: 0.8637 (tpp) REVERT: B 260 MET cc_start: 0.9079 (mmm) cc_final: 0.8814 (tpt) REVERT: B 280 LEU cc_start: 0.9001 (tp) cc_final: 0.8739 (tp) REVERT: B 298 THR cc_start: 0.8732 (m) cc_final: 0.8505 (p) REVERT: B 303 GLU cc_start: 0.8589 (tp30) cc_final: 0.8204 (tp30) REVERT: B 315 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8131 (tm-30) REVERT: B 324 TYR cc_start: 0.7530 (p90) cc_final: 0.7064 (p90) REVERT: B 364 ASP cc_start: 0.9005 (m-30) cc_final: 0.8756 (t70) REVERT: B 368 LEU cc_start: 0.9405 (pt) cc_final: 0.9099 (mp) REVERT: B 378 MET cc_start: 0.7366 (mmt) cc_final: 0.7156 (mmp) REVERT: B 485 MET cc_start: 0.9104 (mmt) cc_final: 0.8578 (mmt) REVERT: B 509 TYR cc_start: 0.9065 (t80) cc_final: 0.8335 (t80) REVERT: B 556 SER cc_start: 0.9211 (m) cc_final: 0.8828 (p) REVERT: B 584 ARG cc_start: 0.8794 (mmt180) cc_final: 0.8377 (mmp-170) REVERT: B 603 MET cc_start: 0.8435 (mtt) cc_final: 0.8119 (mtt) REVERT: C 110 MET cc_start: 0.8280 (mmm) cc_final: 0.7497 (mmm) REVERT: C 209 LYS cc_start: 0.9592 (mtmt) cc_final: 0.9194 (mttt) REVERT: C 211 PHE cc_start: 0.8163 (t80) cc_final: 0.7725 (t80) REVERT: C 245 LYS cc_start: 0.8907 (mttt) cc_final: 0.8473 (mptt) REVERT: C 255 MET cc_start: 0.8931 (tpt) cc_final: 0.8602 (tpp) REVERT: C 303 GLU cc_start: 0.8640 (tp30) cc_final: 0.8262 (tp30) REVERT: C 315 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 324 TYR cc_start: 0.7780 (p90) cc_final: 0.6940 (p90) REVERT: C 367 LEU cc_start: 0.8482 (tt) cc_final: 0.6525 (tt) REVERT: C 378 MET cc_start: 0.7197 (mmt) cc_final: 0.6975 (mmp) REVERT: C 424 PRO cc_start: 0.8388 (Cg_endo) cc_final: 0.8110 (Cg_exo) REVERT: C 485 MET cc_start: 0.9105 (mmt) cc_final: 0.8147 (mmt) REVERT: C 497 MET cc_start: 0.9019 (tmm) cc_final: 0.8595 (tmm) REVERT: C 509 TYR cc_start: 0.9095 (t80) cc_final: 0.8474 (t80) REVERT: C 554 MET cc_start: 0.7960 (mtm) cc_final: 0.7740 (mtm) REVERT: C 556 SER cc_start: 0.9314 (m) cc_final: 0.8974 (p) REVERT: C 577 MET cc_start: 0.8723 (mmm) cc_final: 0.6825 (mmm) REVERT: C 603 MET cc_start: 0.8433 (mtt) cc_final: 0.8167 (mtt) REVERT: D 110 MET cc_start: 0.8252 (mmm) cc_final: 0.7186 (mmm) REVERT: D 209 LYS cc_start: 0.9584 (mtmt) cc_final: 0.9200 (mttt) REVERT: D 211 PHE cc_start: 0.8129 (t80) cc_final: 0.7670 (t80) REVERT: D 245 LYS cc_start: 0.8919 (mttt) cc_final: 0.8495 (mptt) REVERT: D 250 GLU cc_start: 0.8552 (tp30) cc_final: 0.8299 (mm-30) REVERT: D 255 MET cc_start: 0.8917 (tpt) cc_final: 0.8606 (tpp) REVERT: D 280 LEU cc_start: 0.8966 (tp) cc_final: 0.8725 (tp) REVERT: D 298 THR cc_start: 0.8784 (m) cc_final: 0.8504 (p) REVERT: D 315 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8206 (tm-30) REVERT: D 324 TYR cc_start: 0.7841 (p90) cc_final: 0.6975 (p90) REVERT: D 435 MET cc_start: 0.9031 (mmm) cc_final: 0.8716 (mmm) REVERT: D 491 MET cc_start: 0.8099 (tpp) cc_final: 0.7777 (mmp) REVERT: D 509 TYR cc_start: 0.9092 (t80) cc_final: 0.8342 (t80) REVERT: D 515 GLU cc_start: 0.8847 (mm-30) cc_final: 0.7907 (mm-30) REVERT: D 556 SER cc_start: 0.9172 (m) cc_final: 0.8852 (p) REVERT: D 557 ILE cc_start: 0.9229 (pt) cc_final: 0.8914 (tp) REVERT: D 577 MET cc_start: 0.8177 (mmt) cc_final: 0.7707 (mmm) REVERT: D 583 TRP cc_start: 0.7573 (t-100) cc_final: 0.7187 (t-100) REVERT: D 584 ARG cc_start: 0.8748 (mmt180) cc_final: 0.8489 (mmt180) REVERT: D 603 MET cc_start: 0.8432 (mtt) cc_final: 0.8140 (mtt) REVERT: D 612 LEU cc_start: 0.8824 (tt) cc_final: 0.8611 (mm) outliers start: 1 outliers final: 1 residues processed: 571 average time/residue: 0.1186 time to fit residues: 109.4104 Evaluate side-chains 464 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 463 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 82 optimal weight: 0.6980 chunk 202 optimal weight: 10.0000 chunk 95 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 138 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.099256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082063 restraints weight = 55580.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084542 restraints weight = 34459.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.086304 restraints weight = 24305.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.087497 restraints weight = 18748.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.088439 restraints weight = 15516.741| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20108 Z= 0.139 Angle : 0.840 13.707 27268 Z= 0.394 Chirality : 0.045 0.191 3092 Planarity : 0.004 0.058 3448 Dihedral : 5.674 49.225 2692 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -2.05 (0.17), residues: 2436 helix: -0.42 (0.14), residues: 1300 sheet: -6.48 (0.10), residues: 56 loop : -2.23 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 589 TYR 0.013 0.001 TYR A 555 PHE 0.039 0.002 PHE A 504 TRP 0.039 0.001 TRP C 583 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (20104) covalent geometry : angle 0.83995 / 0.39 (27268) hydrogen bonds : bond 0.03647 / 2.43 ( 808) hydrogen bonds : angle 4.62100 / 3.18 ( 2292) Misc. bond : bond 0.00024 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8160 (mmm) cc_final: 0.7631 (mmm) REVERT: A 127 ASN cc_start: 0.7732 (p0) cc_final: 0.7412 (p0) REVERT: A 209 LYS cc_start: 0.9557 (mtmt) cc_final: 0.9207 (mttm) REVERT: A 211 PHE cc_start: 0.8077 (t80) cc_final: 0.7668 (t80) REVERT: A 245 LYS cc_start: 0.8823 (mttt) cc_final: 0.8448 (mptt) REVERT: A 260 MET cc_start: 0.9063 (mmm) cc_final: 0.8783 (tpt) REVERT: A 280 LEU cc_start: 0.9035 (tp) cc_final: 0.8767 (tp) REVERT: A 303 GLU cc_start: 0.8621 (tp30) cc_final: 0.8236 (tp30) REVERT: A 315 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8169 (tm-30) REVERT: A 324 TYR cc_start: 0.7644 (p90) cc_final: 0.6930 (p90) REVERT: A 368 LEU cc_start: 0.9379 (pt) cc_final: 0.9091 (mp) REVERT: A 424 PRO cc_start: 0.8320 (Cg_endo) cc_final: 0.8109 (Cg_exo) REVERT: A 485 MET cc_start: 0.9054 (mmt) cc_final: 0.8425 (mmt) REVERT: A 509 TYR cc_start: 0.9056 (t80) cc_final: 0.8422 (t80) REVERT: A 515 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8128 (mm-30) REVERT: A 554 MET cc_start: 0.8323 (mtm) cc_final: 0.8111 (mtm) REVERT: A 556 SER cc_start: 0.9254 (m) cc_final: 0.8893 (p) REVERT: A 603 MET cc_start: 0.8375 (mtt) cc_final: 0.8155 (mtt) REVERT: A 613 TRP cc_start: 0.8345 (t60) cc_final: 0.7732 (t60) REVERT: B 64 LEU cc_start: 0.8630 (tp) cc_final: 0.8341 (tp) REVERT: B 110 MET cc_start: 0.8255 (mmm) cc_final: 0.7568 (mmm) REVERT: B 209 LYS cc_start: 0.9556 (mtmt) cc_final: 0.9212 (mttm) REVERT: B 211 PHE cc_start: 0.8080 (t80) cc_final: 0.7696 (t80) REVERT: B 260 MET cc_start: 0.9110 (mmm) cc_final: 0.8839 (tpt) REVERT: B 280 LEU cc_start: 0.9172 (tp) cc_final: 0.8889 (tp) REVERT: B 298 THR cc_start: 0.8739 (m) cc_final: 0.8466 (p) REVERT: B 303 GLU cc_start: 0.8624 (tp30) cc_final: 0.8232 (tp30) REVERT: B 315 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 324 TYR cc_start: 0.7583 (p90) cc_final: 0.6958 (p90) REVERT: B 368 LEU cc_start: 0.9381 (pt) cc_final: 0.9096 (mp) REVERT: B 509 TYR cc_start: 0.9019 (t80) cc_final: 0.8383 (t80) REVERT: B 556 SER cc_start: 0.9157 (m) cc_final: 0.8790 (p) REVERT: B 557 ILE cc_start: 0.9310 (pt) cc_final: 0.8916 (tp) REVERT: B 584 ARG cc_start: 0.8751 (mmt180) cc_final: 0.8453 (mmp-170) REVERT: B 603 MET cc_start: 0.8414 (mtt) cc_final: 0.8110 (mtt) REVERT: B 613 TRP cc_start: 0.8314 (t60) cc_final: 0.7625 (t60) REVERT: C 110 MET cc_start: 0.8254 (mmm) cc_final: 0.7587 (mmm) REVERT: C 209 LYS cc_start: 0.9567 (mtmt) cc_final: 0.9205 (mttm) REVERT: C 211 PHE cc_start: 0.8120 (t80) cc_final: 0.7699 (t80) REVERT: C 245 LYS cc_start: 0.8846 (mttt) cc_final: 0.8570 (mptt) REVERT: C 280 LEU cc_start: 0.9029 (tp) cc_final: 0.8681 (tp) REVERT: C 303 GLU cc_start: 0.8644 (tp30) cc_final: 0.8247 (tp30) REVERT: C 315 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8119 (tm-30) REVERT: C 324 TYR cc_start: 0.7793 (p90) cc_final: 0.6946 (p90) REVERT: C 367 LEU cc_start: 0.8446 (tt) cc_final: 0.6447 (tt) REVERT: C 485 MET cc_start: 0.9118 (mmt) cc_final: 0.8100 (mmt) REVERT: C 491 MET cc_start: 0.8025 (tpp) cc_final: 0.7753 (mmp) REVERT: C 497 MET cc_start: 0.9036 (tmm) cc_final: 0.8578 (tmm) REVERT: C 509 TYR cc_start: 0.9112 (t80) cc_final: 0.8416 (t80) REVERT: C 556 SER cc_start: 0.9224 (m) cc_final: 0.8866 (p) REVERT: C 577 MET cc_start: 0.8787 (mmm) cc_final: 0.6932 (mmm) REVERT: C 583 TRP cc_start: 0.7589 (m-90) cc_final: 0.7271 (m-90) REVERT: C 584 ARG cc_start: 0.8521 (mmt180) cc_final: 0.8129 (mmt180) REVERT: C 603 MET cc_start: 0.8424 (mtt) cc_final: 0.8160 (mtt) REVERT: D 78 MET cc_start: 0.6525 (pmm) cc_final: 0.5132 (tmm) REVERT: D 81 THR cc_start: 0.9152 (p) cc_final: 0.8876 (p) REVERT: D 110 MET cc_start: 0.8195 (mmm) cc_final: 0.6934 (mmm) REVERT: D 209 LYS cc_start: 0.9558 (mtmt) cc_final: 0.9210 (mttm) REVERT: D 211 PHE cc_start: 0.8073 (t80) cc_final: 0.7663 (t80) REVERT: D 245 LYS cc_start: 0.8910 (mttt) cc_final: 0.8506 (mptt) REVERT: D 280 LEU cc_start: 0.8966 (tp) cc_final: 0.8720 (tp) REVERT: D 298 THR cc_start: 0.8733 (m) cc_final: 0.8497 (p) REVERT: D 315 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 324 TYR cc_start: 0.7869 (p90) cc_final: 0.6958 (p90) REVERT: D 435 MET cc_start: 0.8981 (mmm) cc_final: 0.8672 (mmm) REVERT: D 491 MET cc_start: 0.8106 (tpp) cc_final: 0.7823 (mmp) REVERT: D 509 TYR cc_start: 0.9088 (t80) cc_final: 0.8421 (t80) REVERT: D 515 GLU cc_start: 0.8900 (mm-30) cc_final: 0.7963 (mm-30) REVERT: D 556 SER cc_start: 0.9200 (m) cc_final: 0.8843 (p) REVERT: D 573 LEU cc_start: 0.9091 (tt) cc_final: 0.8830 (tt) REVERT: D 577 MET cc_start: 0.8166 (mmt) cc_final: 0.7838 (mmm) REVERT: D 583 TRP cc_start: 0.7532 (t-100) cc_final: 0.7153 (t-100) REVERT: D 589 ARG cc_start: 0.6930 (ptt-90) cc_final: 0.6657 (ptt-90) REVERT: D 603 MET cc_start: 0.8377 (mtt) cc_final: 0.8158 (mtt) outliers start: 0 outliers final: 0 residues processed: 563 average time/residue: 0.1302 time to fit residues: 117.3119 Evaluate side-chains 460 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 149 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 210 optimal weight: 0.0970 chunk 128 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081817 restraints weight = 55999.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.084299 restraints weight = 34792.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.086067 restraints weight = 24572.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087249 restraints weight = 18933.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.088160 restraints weight = 15662.997| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 20108 Z= 0.144 Angle : 0.845 13.506 27268 Z= 0.395 Chirality : 0.045 0.171 3092 Planarity : 0.004 0.056 3448 Dihedral : 5.605 46.707 2692 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.05 % Allowed : 0.38 % Favored : 99.57 % 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: -1.97 (0.17), residues: 2436 helix: -0.33 (0.14), residues: 1300 sheet: -6.40 (0.12), residues: 64 loop : -2.19 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 589 TYR 0.012 0.001 TYR A 555 PHE 0.049 0.002 PHE B 504 TRP 0.038 0.002 TRP A 583 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (20104) covalent geometry : angle 0.84450 / 0.40 (27268) hydrogen bonds : bond 0.03711 / 2.49 ( 808) hydrogen bonds : angle 4.65325 / 3.19 ( 2292) Misc. bond : bond 0.00003 / 0.00 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 552 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8044 (mmm) cc_final: 0.7562 (mmm) REVERT: A 127 ASN cc_start: 0.7562 (p0) cc_final: 0.7189 (p0) REVERT: A 211 PHE cc_start: 0.8074 (t80) cc_final: 0.7686 (t80) REVERT: A 260 MET cc_start: 0.9093 (mmm) cc_final: 0.8808 (tpt) REVERT: A 280 LEU cc_start: 0.9102 (tp) cc_final: 0.8887 (tp) REVERT: A 303 GLU cc_start: 0.8635 (tp30) cc_final: 0.8245 (tp30) REVERT: A 315 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8187 (tm-30) REVERT: A 324 TYR cc_start: 0.7709 (p90) cc_final: 0.6943 (p90) REVERT: A 367 LEU cc_start: 0.8468 (tt) cc_final: 0.8210 (tt) REVERT: A 368 LEU cc_start: 0.9372 (pt) cc_final: 0.9097 (mp) REVERT: A 485 MET cc_start: 0.9064 (mmt) cc_final: 0.8451 (mmt) REVERT: A 497 MET cc_start: 0.8828 (tmm) cc_final: 0.8546 (tmm) REVERT: A 509 TYR cc_start: 0.9016 (t80) cc_final: 0.8417 (t80) REVERT: A 515 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8105 (mm-30) REVERT: A 556 SER cc_start: 0.9280 (m) cc_final: 0.8870 (p) REVERT: A 583 TRP cc_start: 0.7592 (m-90) cc_final: 0.7189 (m-90) REVERT: A 613 TRP cc_start: 0.8373 (t60) cc_final: 0.7676 (t60) REVERT: B 110 MET cc_start: 0.8248 (mmm) cc_final: 0.7845 (mmm) REVERT: B 180 ARG cc_start: 0.8952 (mtt90) cc_final: 0.8525 (ttm-80) REVERT: B 209 LYS cc_start: 0.9536 (mtmt) cc_final: 0.9180 (mttm) REVERT: B 211 PHE cc_start: 0.8095 (t80) cc_final: 0.7692 (t80) REVERT: B 260 MET cc_start: 0.9092 (mmm) cc_final: 0.8837 (tpt) REVERT: B 280 LEU cc_start: 0.9233 (tp) cc_final: 0.8944 (tp) REVERT: B 298 THR cc_start: 0.8725 (m) cc_final: 0.8504 (p) REVERT: B 303 GLU cc_start: 0.8643 (tp30) cc_final: 0.8254 (tp30) REVERT: B 315 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8201 (tm-30) REVERT: B 324 TYR cc_start: 0.7713 (p90) cc_final: 0.7009 (p90) REVERT: B 367 LEU cc_start: 0.8472 (tt) cc_final: 0.8115 (tt) REVERT: B 368 LEU cc_start: 0.9366 (pt) cc_final: 0.9094 (mp) REVERT: B 485 MET cc_start: 0.8926 (mmt) cc_final: 0.8274 (mmt) REVERT: B 509 TYR cc_start: 0.9063 (t80) cc_final: 0.8406 (t80) REVERT: B 556 SER cc_start: 0.9190 (m) cc_final: 0.8847 (p) REVERT: B 583 TRP cc_start: 0.7479 (m-90) cc_final: 0.7270 (m-90) REVERT: B 603 MET cc_start: 0.8374 (mtt) cc_final: 0.8116 (mtt) REVERT: B 613 TRP cc_start: 0.8348 (t60) cc_final: 0.7620 (t60) REVERT: C 110 MET cc_start: 0.8058 (mmm) cc_final: 0.7362 (mmm) REVERT: C 211 PHE cc_start: 0.8075 (t80) cc_final: 0.7665 (t80) REVERT: C 245 LYS cc_start: 0.8843 (mttt) cc_final: 0.8451 (mptt) REVERT: C 280 LEU cc_start: 0.9047 (tp) cc_final: 0.8716 (tp) REVERT: C 303 GLU cc_start: 0.8630 (tp30) cc_final: 0.8244 (tp30) REVERT: C 315 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8184 (tm-30) REVERT: C 324 TYR cc_start: 0.7836 (p90) cc_final: 0.6934 (p90) REVERT: C 367 LEU cc_start: 0.8510 (tt) cc_final: 0.8102 (tt) REVERT: C 368 LEU cc_start: 0.9377 (pt) cc_final: 0.9074 (mp) REVERT: C 485 MET cc_start: 0.9103 (mmt) cc_final: 0.8095 (mmt) REVERT: C 491 MET cc_start: 0.7969 (tpp) cc_final: 0.7620 (mmp) REVERT: C 497 MET cc_start: 0.8979 (tmm) cc_final: 0.8592 (tmm) REVERT: C 509 TYR cc_start: 0.9074 (t80) cc_final: 0.8431 (t80) REVERT: C 556 SER cc_start: 0.9187 (m) cc_final: 0.8893 (p) REVERT: C 557 ILE cc_start: 0.9303 (pt) cc_final: 0.8933 (tp) REVERT: C 577 MET cc_start: 0.8729 (mmm) cc_final: 0.6833 (mmm) REVERT: C 583 TRP cc_start: 0.7588 (m-90) cc_final: 0.7300 (m-90) REVERT: C 584 ARG cc_start: 0.8636 (mmt180) cc_final: 0.8053 (mmt180) REVERT: D 78 MET cc_start: 0.6412 (pmm) cc_final: 0.5250 (tmm) REVERT: D 110 MET cc_start: 0.8328 (mmm) cc_final: 0.7079 (mmm) REVERT: D 211 PHE cc_start: 0.8063 (t80) cc_final: 0.7678 (t80) REVERT: D 245 LYS cc_start: 0.8882 (mttt) cc_final: 0.8475 (mptt) REVERT: D 280 LEU cc_start: 0.8998 (tp) cc_final: 0.8774 (tp) REVERT: D 298 THR cc_start: 0.8687 (m) cc_final: 0.8447 (p) REVERT: D 315 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8221 (tm-30) REVERT: D 324 TYR cc_start: 0.7821 (p90) cc_final: 0.6811 (p90) REVERT: D 435 MET cc_start: 0.8990 (mmm) cc_final: 0.8681 (mmm) REVERT: D 485 MET cc_start: 0.8775 (mmt) cc_final: 0.8530 (mmt) REVERT: D 491 MET cc_start: 0.8036 (tpp) cc_final: 0.7782 (mmp) REVERT: D 497 MET cc_start: 0.8773 (tmm) cc_final: 0.8527 (tmm) REVERT: D 509 TYR cc_start: 0.9029 (t80) cc_final: 0.8406 (t80) REVERT: D 556 SER cc_start: 0.9219 (m) cc_final: 0.8867 (p) REVERT: D 577 MET cc_start: 0.8119 (mmt) cc_final: 0.7550 (mmt) REVERT: D 583 TRP cc_start: 0.7484 (t-100) cc_final: 0.7152 (t-100) REVERT: D 613 TRP cc_start: 0.8432 (t60) cc_final: 0.7677 (t60) outliers start: 1 outliers final: 0 residues processed: 553 average time/residue: 0.1289 time to fit residues: 114.7870 Evaluate side-chains 461 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 62 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 209 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.082237 restraints weight = 55794.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.084730 restraints weight = 34829.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.086494 restraints weight = 24682.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.087693 restraints weight = 19142.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.088632 restraints weight = 15861.898| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20108 Z= 0.142 Angle : 0.847 13.441 27268 Z= 0.393 Chirality : 0.045 0.165 3092 Planarity : 0.004 0.072 3448 Dihedral : 5.545 44.792 2692 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % 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: -1.92 (0.17), residues: 2436 helix: -0.27 (0.14), residues: 1292 sheet: -6.38 (0.12), residues: 64 loop : -2.18 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 589 TYR 0.010 0.001 TYR A 555 PHE 0.047 0.002 PHE B 504 TRP 0.032 0.001 TRP A 462 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (20104) covalent geometry : angle 0.84736 / 0.39 (27268) hydrogen bonds : bond 0.03679 / 2.46 ( 808) hydrogen bonds : angle 4.67523 / 3.21 ( 2292) Misc. bond : bond 0.00009 / 0.00 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3298.62 seconds wall clock time: 57 minutes 52.12 seconds (3472.12 seconds total)