Starting phenix.real_space_refine on Wed Nov 19 02:18:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d7t_7825/11_2025/6d7t_7825.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d7t_7825/11_2025/6d7t_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_7825/11_2025/6d7t_7825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d7t_7825/11_2025/6d7t_7825.map" model { file = "/net/cci-nas-00/data/ceres_data/6d7t_7825/11_2025/6d7t_7825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d7t_7825/11_2025/6d7t_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 4.58, per 1000 atoms: 0.23 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: 1.88 Conformation dependent library (CDL) restraints added in 873.8 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: 0.65 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: 3.21 Time building geometry restraints manager: 2.46 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: 11744 35.95 - 71.89: 268 71.89 - 107.84: 4 107.84 - 143.78: 0 143.78 - 179.73: 4 Dihedral angle restraints: 12020 sinusoidal: 4876 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 12017 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.530 Find NCS groups from input model: 0.420 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 14.784 179.729 7404 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 covalent geometry : bond 0.01036 (20104) covalent geometry : angle 1.49354 (27268) hydrogen bonds : bond 0.30578 ( 808) hydrogen bonds : angle 10.42007 ( 2292) Misc. bond : bond 0.00165 ( 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 : 0.711 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: A 58 VAL cc_start: 0.8814 (t) cc_final: 0.8339 (p) REVERT: A 63 LYS cc_start: 0.8929 (mmpt) cc_final: 0.8728 (mmmm) 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: 0.7486 (t80) REVERT: A 229 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7773 (mp) REVERT: A 280 LEU cc_start: 0.9115 (tp) cc_final: 0.8767 (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: 0.9062 (m) REVERT: A 442 MET cc_start: 0.8924 (tpp) cc_final: 0.8427 (tpp) REVERT: A 462 TRP cc_start: 0.9423 (m100) cc_final: 0.9108 (m100) REVERT: A 464 ASN cc_start: 0.8909 (t160) cc_final: 0.8542 (t0) REVERT: A 497 MET cc_start: 0.8689 (tmm) cc_final: 0.8482 (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: 0.8097 (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: 0.8287 (p) REVERT: B 63 LYS cc_start: 0.8922 (mmpt) cc_final: 0.8722 (mmmm) REVERT: B 127 ASN cc_start: 0.8698 (m110) cc_final: 0.8402 (p0) REVERT: B 208 ASN cc_start: 0.9178 (t160) cc_final: 0.8858 (t0) REVERT: B 211 PHE cc_start: 0.8361 (t80) cc_final: 0.7486 (t80) REVERT: B 229 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7756 (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: 0.9230 (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: 0.9058 (m) REVERT: B 442 MET cc_start: 0.8924 (tpp) cc_final: 0.8431 (tpp) REVERT: B 462 TRP cc_start: 0.9426 (m100) cc_final: 0.9081 (m100) REVERT: B 464 ASN cc_start: 0.8906 (t160) cc_final: 0.8394 (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: 0.8353 (ttm) cc_final: 0.8124 (ttm) REVERT: C 58 VAL cc_start: 0.8846 (t) cc_final: 0.8404 (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: 0.8852 (t0) REVERT: C 211 PHE cc_start: 0.8373 (t80) cc_final: 0.7422 (t80) REVERT: C 229 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7751 (mp) REVERT: C 245 LYS cc_start: 0.9272 (ptpp) cc_final: 0.9071 (mttt) REVERT: C 280 LEU cc_start: 0.9117 (tp) cc_final: 0.8730 (tp) REVERT: C 324 TYR cc_start: 0.8043 (p90) cc_final: 0.7270 (p90) REVERT: C 364 ASP cc_start: 0.9207 (m-30) cc_final: 0.8645 (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: 0.9229 (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: 0.9082 (m) REVERT: C 442 MET cc_start: 0.8928 (tpp) cc_final: 0.8435 (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: 0.8567 (t0) REVERT: C 497 MET cc_start: 0.8694 (tmm) cc_final: 0.8318 (tmm) REVERT: C 509 TYR cc_start: 0.9199 (t80) cc_final: 0.8384 (t80) REVERT: C 520 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8092 (tm) REVERT: C 528 MET cc_start: 0.8405 (ttm) cc_final: 0.8181 (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: 0.8361 (p) REVERT: D 127 ASN cc_start: 0.8705 (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: 0.7474 (t80) REVERT: D 229 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7761 (mp) 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: 0.9066 (m) REVERT: D 442 MET cc_start: 0.8950 (tpp) cc_final: 0.8427 (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: 0.8554 (t0) REVERT: D 485 MET cc_start: 0.8547 (mmt) cc_final: 0.8042 (mmt) REVERT: D 497 MET cc_start: 0.8721 (tmm) cc_final: 0.8404 (tmm) REVERT: D 509 TYR cc_start: 0.9221 (t80) cc_final: 0.8380 (t80) REVERT: D 515 GLU cc_start: 0.8738 (mm-30) cc_final: 0.7926 (mm-30) REVERT: D 520 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8062 (tm) REVERT: D 528 MET cc_start: 0.8389 (ttm) cc_final: 0.8176 (ttm) REVERT: D 542 ASP cc_start: 0.8044 (t70) cc_final: 0.7691 (p0) REVERT: D 577 MET cc_start: 0.8716 (mmm) cc_final: 0.6939 (mmm) outliers start: 116 outliers final: 28 residues processed: 683 average time/residue: 0.1654 time to fit residues: 167.0083 Evaluate side-chains 499 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 460 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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 = 0.3302 r_free = 0.3302 target = 0.094802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.077892 restraints weight = 56901.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.080219 restraints weight = 35375.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.081805 restraints weight = 25090.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.082870 restraints weight = 19558.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.083767 restraints weight = 16365.398| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20108 Z= 0.181 Angle : 0.864 12.857 27268 Z= 0.439 Chirality : 0.047 0.171 3092 Planarity : 0.005 0.048 3448 Dihedral : 9.556 172.774 2700 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.68 % Favored : 92.12 % Rotamer: Outliers : 0.61 % Allowed : 7.94 % Favored : 91.45 % 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: -3.94 (0.15), residues: 2436 helix: -2.42 (0.12), residues: 1280 sheet: -6.47 (0.12), residues: 56 loop : -2.54 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 621 TYR 0.018 0.002 TYR C 432 PHE 0.019 0.002 PHE D 504 TRP 0.010 0.002 TRP A 583 HIS 0.006 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00399 (20104) covalent geometry : angle 0.86423 (27268) hydrogen bonds : bond 0.05164 ( 808) hydrogen bonds : angle 5.79215 ( 2292) Misc. bond : bond 0.00016 ( 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 613 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 600 time to evaluate : 0.774 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: 0.8426 (mt-10) cc_final: 0.8157 (mt-10) REVERT: A 92 LEU cc_start: 0.8769 (pt) cc_final: 0.8542 (tt) REVERT: A 99 MET cc_start: 0.8794 (mmp) cc_final: 0.8589 (mmm) REVERT: A 110 MET cc_start: 0.8729 (mmm) cc_final: 0.7695 (mmm) REVERT: A 127 ASN cc_start: 0.8772 (m110) cc_final: 0.8484 (p0) REVERT: A 204 ILE cc_start: 0.9555 (mm) cc_final: 0.9350 (mm) REVERT: A 209 LYS cc_start: 0.9667 (mtpt) cc_final: 0.8953 (mtpp) REVERT: A 306 GLN cc_start: 0.8927 (mp10) cc_final: 0.8578 (mp10) REVERT: A 318 SER cc_start: 0.9316 (t) cc_final: 0.8964 (t) REVERT: A 364 ASP cc_start: 0.9173 (m-30) cc_final: 0.8521 (t70) REVERT: A 367 LEU cc_start: 0.8622 (tt) cc_final: 0.7434 (tt) REVERT: A 368 LEU cc_start: 0.9367 (pp) cc_final: 0.9108 (pt) REVERT: A 435 MET cc_start: 0.8948 (mmp) cc_final: 0.8709 (mmm) REVERT: A 442 MET cc_start: 0.8655 (tpp) cc_final: 0.8320 (tpp) REVERT: A 462 TRP cc_start: 0.9344 (m100) cc_final: 0.9125 (m100) REVERT: A 497 MET cc_start: 0.8790 (tmm) cc_final: 0.8350 (tmm) REVERT: A 504 PHE cc_start: 0.9214 (m-80) cc_final: 0.8979 (m-80) REVERT: A 509 TYR cc_start: 0.9103 (t80) cc_final: 0.8496 (t80) REVERT: A 515 GLU cc_start: 0.8810 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 553 PHE cc_start: 0.8018 (t80) cc_final: 0.7669 (t80) REVERT: A 556 SER cc_start: 0.9162 (m) cc_final: 0.8924 (p) REVERT: A 557 ILE cc_start: 0.9179 (pt) cc_final: 0.8770 (tp) REVERT: A 570 MET cc_start: 0.8285 (ppp) cc_final: 0.7943 (tmm) REVERT: A 573 LEU cc_start: 0.9479 (tp) cc_final: 0.9276 (tt) REVERT: A 577 MET cc_start: 0.8618 (mmm) cc_final: 0.8317 (mmm) REVERT: B 35 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8167 (mt-10) REVERT: B 58 VAL cc_start: 0.8732 (t) cc_final: 0.8532 (p) REVERT: B 92 LEU cc_start: 0.8745 (pt) cc_final: 0.8508 (tt) REVERT: B 110 MET cc_start: 0.8699 (mmm) cc_final: 0.7720 (mmm) REVERT: B 127 ASN cc_start: 0.8750 (m110) cc_final: 0.8535 (p0) REVERT: B 204 ILE cc_start: 0.9539 (mm) cc_final: 0.9337 (mm) REVERT: B 209 LYS cc_start: 0.9678 (mtpt) cc_final: 0.8957 (mtpp) REVERT: B 306 GLN cc_start: 0.8918 (mp10) cc_final: 0.8593 (mp10) REVERT: B 318 SER cc_start: 0.9306 (t) cc_final: 0.8967 (p) REVERT: B 364 ASP cc_start: 0.9169 (m-30) cc_final: 0.8532 (t70) REVERT: B 367 LEU cc_start: 0.8603 (tt) cc_final: 0.7462 (tt) REVERT: B 368 LEU cc_start: 0.9358 (pp) cc_final: 0.9105 (pt) REVERT: B 398 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9256 (mp) REVERT: B 435 MET cc_start: 0.8935 (mmp) cc_final: 0.8709 (mmm) REVERT: B 442 MET cc_start: 0.8655 (tpp) cc_final: 0.8319 (tpp) REVERT: B 485 MET cc_start: 0.9219 (mmt) cc_final: 0.8984 (mmt) REVERT: B 502 LEU cc_start: 0.9669 (mt) cc_final: 0.9449 (mm) REVERT: B 504 PHE cc_start: 0.9194 (m-80) cc_final: 0.8959 (m-80) REVERT: B 509 TYR cc_start: 0.9088 (t80) cc_final: 0.8467 (t80) REVERT: B 515 GLU cc_start: 0.8797 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 528 MET cc_start: 0.8337 (ttm) cc_final: 0.8037 (ttm) REVERT: B 553 PHE cc_start: 0.8026 (t80) cc_final: 0.7668 (t80) REVERT: B 556 SER cc_start: 0.9171 (m) cc_final: 0.8923 (p) REVERT: B 557 ILE cc_start: 0.9172 (pt) cc_final: 0.8755 (tp) REVERT: C 35 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8099 (mt-10) REVERT: C 58 VAL cc_start: 0.8717 (t) cc_final: 0.8515 (p) REVERT: C 92 LEU cc_start: 0.8752 (pt) cc_final: 0.8512 (tt) REVERT: C 110 MET cc_start: 0.8741 (mmm) cc_final: 0.7670 (mmm) REVERT: C 127 ASN cc_start: 0.8761 (m110) cc_final: 0.8497 (p0) REVERT: C 209 LYS cc_start: 0.9683 (mtpt) cc_final: 0.8993 (mtpp) REVERT: C 306 GLN cc_start: 0.8886 (mp10) cc_final: 0.8512 (mp10) REVERT: C 318 SER cc_start: 0.9332 (t) cc_final: 0.8992 (t) REVERT: C 364 ASP cc_start: 0.9167 (m-30) cc_final: 0.8551 (t70) REVERT: C 367 LEU cc_start: 0.8612 (tt) cc_final: 0.7442 (tt) REVERT: C 368 LEU cc_start: 0.9348 (pp) cc_final: 0.9107 (pt) REVERT: C 435 MET cc_start: 0.8944 (mmp) cc_final: 0.8689 (mmm) REVERT: C 442 MET cc_start: 0.8656 (tpp) cc_final: 0.8326 (tpp) REVERT: C 497 MET cc_start: 0.8655 (tmm) cc_final: 0.8269 (tmm) REVERT: C 504 PHE cc_start: 0.9192 (m-80) cc_final: 0.8982 (m-80) REVERT: C 509 TYR cc_start: 0.9087 (t80) cc_final: 0.8442 (t80) REVERT: C 515 GLU cc_start: 0.8808 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 528 MET cc_start: 0.8283 (ttm) cc_final: 0.7942 (ttm) REVERT: C 553 PHE cc_start: 0.8009 (t80) cc_final: 0.7670 (t80) REVERT: C 556 SER cc_start: 0.9146 (m) cc_final: 0.8913 (p) REVERT: C 557 ILE cc_start: 0.9181 (pt) cc_final: 0.8768 (tp) REVERT: C 577 MET cc_start: 0.8671 (mmm) cc_final: 0.8399 (mmm) REVERT: D 35 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8146 (mt-10) REVERT: D 92 LEU cc_start: 0.8780 (pt) cc_final: 0.8517 (tt) REVERT: D 110 MET cc_start: 0.8702 (mmm) cc_final: 0.7666 (mmm) REVERT: D 127 ASN cc_start: 0.8767 (m110) cc_final: 0.8502 (p0) REVERT: D 204 ILE cc_start: 0.9548 (mm) cc_final: 0.9340 (mm) REVERT: D 209 LYS cc_start: 0.9675 (mtpt) cc_final: 0.8988 (mtpp) REVERT: D 306 GLN cc_start: 0.8852 (mp10) cc_final: 0.8647 (mp10) REVERT: D 318 SER cc_start: 0.9333 (t) cc_final: 0.8998 (t) REVERT: D 364 ASP cc_start: 0.9193 (m-30) cc_final: 0.8527 (t70) REVERT: D 367 LEU cc_start: 0.8605 (tt) cc_final: 0.7263 (tt) REVERT: D 368 LEU cc_start: 0.9361 (pp) cc_final: 0.9127 (pp) REVERT: D 442 MET cc_start: 0.8640 (tpp) cc_final: 0.8331 (tpp) REVERT: D 497 MET cc_start: 0.8824 (tmm) cc_final: 0.8319 (tmm) REVERT: D 504 PHE cc_start: 0.9136 (m-80) cc_final: 0.8820 (m-80) REVERT: D 509 TYR cc_start: 0.9102 (t80) cc_final: 0.8438 (t80) REVERT: D 515 GLU cc_start: 0.8800 (mm-30) cc_final: 0.7810 (mm-30) REVERT: D 528 MET cc_start: 0.8283 (ttm) cc_final: 0.8035 (ttm) REVERT: D 570 MET cc_start: 0.8321 (ppp) cc_final: 0.8077 (tmm) REVERT: D 573 LEU cc_start: 0.9465 (tp) cc_final: 0.9262 (tt) REVERT: D 577 MET cc_start: 0.8472 (mmm) cc_final: 0.8156 (mmm) outliers start: 13 outliers final: 0 residues processed: 601 average time/residue: 0.1290 time to fit residues: 122.3840 Evaluate side-chains 470 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 469 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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: 3.9990 chunk 223 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 102 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 197 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** 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** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** 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 = 0.3281 r_free = 0.3281 target = 0.093957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.076236 restraints weight = 58436.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.078616 restraints weight = 35128.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.080163 restraints weight = 24591.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.081457 restraints weight = 19437.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082228 restraints weight = 15987.406| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20108 Z= 0.188 Angle : 0.815 13.028 27268 Z= 0.412 Chirality : 0.046 0.187 3092 Planarity : 0.004 0.042 3448 Dihedral : 9.106 168.636 2700 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.95 % Favored : 90.85 % Rotamer: Outliers : 0.66 % Allowed : 6.19 % Favored : 93.15 % 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: -3.35 (0.16), residues: 2436 helix: -1.70 (0.13), residues: 1292 sheet: -6.42 (0.12), residues: 56 loop : -2.57 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 589 TYR 0.012 0.002 TYR D 432 PHE 0.018 0.002 PHE B 493 TRP 0.009 0.001 TRP A 583 HIS 0.005 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00427 (20104) covalent geometry : angle 0.81483 (27268) hydrogen bonds : bond 0.04395 ( 808) hydrogen bonds : angle 5.30543 ( 2292) Misc. bond : bond 0.00063 ( 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 574 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 560 time to evaluate : 0.716 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: A 63 LYS cc_start: 0.8457 (mmpt) cc_final: 0.8047 (mmmm) REVERT: A 92 LEU cc_start: 0.8853 (pt) cc_final: 0.8513 (tt) REVERT: A 110 MET cc_start: 0.8596 (mmm) cc_final: 0.7239 (mmm) REVERT: A 127 ASN cc_start: 0.8781 (m110) cc_final: 0.8411 (p0) REVERT: A 209 LYS cc_start: 0.9678 (mtpt) cc_final: 0.9096 (mttp) REVERT: A 245 LYS cc_start: 0.9119 (mttt) cc_final: 0.8806 (mptt) REVERT: A 303 GLU cc_start: 0.8520 (tp30) cc_final: 0.8090 (tp30) REVERT: A 306 GLN cc_start: 0.8820 (mp10) cc_final: 0.8301 (mp10) REVERT: A 364 ASP cc_start: 0.9238 (m-30) cc_final: 0.8556 (t70) REVERT: A 368 LEU cc_start: 0.9344 (pp) cc_final: 0.9103 (pp) REVERT: A 442 MET cc_start: 0.8568 (tpp) cc_final: 0.8205 (tpp) REVERT: A 497 MET cc_start: 0.8971 (tmm) cc_final: 0.8423 (tmm) REVERT: A 504 PHE cc_start: 0.9255 (m-80) cc_final: 0.9037 (m-80) REVERT: A 509 TYR cc_start: 0.9174 (t80) cc_final: 0.8540 (t80) REVERT: A 515 GLU cc_start: 0.8945 (mm-30) cc_final: 0.7966 (mm-30) REVERT: A 556 SER cc_start: 0.9281 (m) cc_final: 0.8964 (p) REVERT: A 557 ILE cc_start: 0.9272 (pt) cc_final: 0.8887 (tp) REVERT: A 584 ARG cc_start: 0.8876 (mmt180) cc_final: 0.8559 (mmt180) REVERT: B 63 LYS cc_start: 0.8443 (mmpt) cc_final: 0.8225 (mmmm) REVERT: B 92 LEU cc_start: 0.8834 (pt) cc_final: 0.8605 (tt) REVERT: B 99 MET cc_start: 0.8960 (mmp) cc_final: 0.8687 (mmm) REVERT: B 110 MET cc_start: 0.8658 (mmm) cc_final: 0.7381 (mmm) REVERT: B 127 ASN cc_start: 0.8735 (m110) cc_final: 0.8332 (p0) REVERT: B 209 LYS cc_start: 0.9672 (mtpt) cc_final: 0.9098 (mttp) REVERT: B 245 LYS cc_start: 0.9085 (mttt) cc_final: 0.8758 (mptt) REVERT: B 280 LEU cc_start: 0.8904 (tp) cc_final: 0.8653 (tp) REVERT: B 303 GLU cc_start: 0.8476 (tp30) cc_final: 0.8055 (tp30) REVERT: B 306 GLN cc_start: 0.8822 (mp10) cc_final: 0.8309 (mp10) REVERT: B 315 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8253 (tm-30) REVERT: B 318 SER cc_start: 0.9316 (t) cc_final: 0.9094 (p) REVERT: B 364 ASP cc_start: 0.9227 (m-30) cc_final: 0.8569 (t70) REVERT: B 367 LEU cc_start: 0.8665 (tt) cc_final: 0.7233 (tt) REVERT: B 368 LEU cc_start: 0.9339 (pp) cc_final: 0.9086 (pp) REVERT: B 398 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9198 (mp) REVERT: B 442 MET cc_start: 0.8600 (tpp) cc_final: 0.8260 (tpp) REVERT: B 481 MET cc_start: 0.9015 (mmm) cc_final: 0.8755 (mmm) REVERT: B 504 PHE cc_start: 0.9250 (m-80) cc_final: 0.9025 (m-80) REVERT: B 509 TYR cc_start: 0.9171 (t80) cc_final: 0.8563 (t80) REVERT: B 515 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8015 (mm-30) REVERT: B 528 MET cc_start: 0.8271 (ttm) cc_final: 0.7993 (ttm) REVERT: B 556 SER cc_start: 0.9287 (m) cc_final: 0.8972 (p) REVERT: B 557 ILE cc_start: 0.9295 (pt) cc_final: 0.8914 (tp) REVERT: B 584 ARG cc_start: 0.8939 (mmt180) cc_final: 0.8613 (mmt180) REVERT: C 92 LEU cc_start: 0.8896 (pt) cc_final: 0.8617 (tt) REVERT: C 99 MET cc_start: 0.8933 (mmp) cc_final: 0.8682 (mmm) REVERT: C 110 MET cc_start: 0.8687 (mmm) cc_final: 0.7340 (mmm) REVERT: C 127 ASN cc_start: 0.8809 (m110) cc_final: 0.8452 (p0) REVERT: C 209 LYS cc_start: 0.9692 (mtpt) cc_final: 0.9115 (mtpp) REVERT: C 303 GLU cc_start: 0.8493 (tp30) cc_final: 0.8078 (tp30) REVERT: C 306 GLN cc_start: 0.8806 (mp10) cc_final: 0.8314 (mp10) REVERT: C 318 SER cc_start: 0.9363 (t) cc_final: 0.8883 (p) REVERT: C 364 ASP cc_start: 0.9266 (m-30) cc_final: 0.8628 (t70) REVERT: C 368 LEU cc_start: 0.9339 (pp) cc_final: 0.9101 (pp) REVERT: C 442 MET cc_start: 0.8609 (tpp) cc_final: 0.8282 (tpp) REVERT: C 497 MET cc_start: 0.8724 (tmm) cc_final: 0.8383 (tmm) REVERT: C 509 TYR cc_start: 0.9154 (t80) cc_final: 0.8539 (t80) REVERT: C 515 GLU cc_start: 0.8958 (mm-30) cc_final: 0.7946 (mm-30) REVERT: C 528 MET cc_start: 0.8276 (ttm) cc_final: 0.7901 (ttm) REVERT: C 556 SER cc_start: 0.9287 (m) cc_final: 0.8985 (p) REVERT: C 557 ILE cc_start: 0.9308 (pt) cc_final: 0.8906 (tp) REVERT: C 577 MET cc_start: 0.8903 (mmm) cc_final: 0.8618 (mmm) REVERT: C 584 ARG cc_start: 0.8851 (mmt180) cc_final: 0.8517 (mmt180) REVERT: D 92 LEU cc_start: 0.8859 (pt) cc_final: 0.8500 (tt) REVERT: D 110 MET cc_start: 0.8722 (mmm) cc_final: 0.7354 (mmm) REVERT: D 127 ASN cc_start: 0.8778 (m110) cc_final: 0.8402 (p0) REVERT: D 209 LYS cc_start: 0.9693 (mtpt) cc_final: 0.9094 (mttp) REVERT: D 318 SER cc_start: 0.9361 (t) cc_final: 0.8870 (p) REVERT: D 364 ASP cc_start: 0.9271 (m-30) cc_final: 0.8617 (t70) REVERT: D 367 LEU cc_start: 0.8623 (tt) cc_final: 0.7079 (tt) REVERT: D 368 LEU cc_start: 0.9340 (pp) cc_final: 0.9099 (pp) REVERT: D 435 MET cc_start: 0.8926 (mmm) cc_final: 0.8679 (mmm) REVERT: D 442 MET cc_start: 0.8653 (tpp) cc_final: 0.8292 (tpp) REVERT: D 485 MET cc_start: 0.8945 (mmt) cc_final: 0.8451 (mmt) REVERT: D 497 MET cc_start: 0.8833 (tmm) cc_final: 0.8439 (tmm) REVERT: D 509 TYR cc_start: 0.9179 (t80) cc_final: 0.8508 (t80) REVERT: D 515 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8005 (mm-30) REVERT: D 528 MET cc_start: 0.8293 (ttm) cc_final: 0.8017 (ttm) REVERT: D 557 ILE cc_start: 0.9270 (pt) cc_final: 0.8975 (tp) REVERT: D 577 MET cc_start: 0.8292 (mmm) cc_final: 0.6799 (mmm) REVERT: D 584 ARG cc_start: 0.8869 (mmt180) cc_final: 0.8641 (mmt180) outliers start: 14 outliers final: 2 residues processed: 564 average time/residue: 0.1336 time to fit residues: 118.4345 Evaluate side-chains 450 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 447 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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: 5.9990 chunk 216 optimal weight: 0.0470 chunk 238 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 203 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.078678 restraints weight = 56849.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.081146 restraints weight = 34675.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.082938 restraints weight = 24464.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.084143 restraints weight = 18979.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.085115 restraints weight = 15831.716| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4043 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= 0.148 Angle : 0.808 14.487 27268 Z= 0.394 Chirality : 0.045 0.184 3092 Planarity : 0.004 0.038 3448 Dihedral : 8.763 165.411 2700 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.09 % Favored : 91.79 % Rotamer: Outliers : 0.28 % Allowed : 4.96 % Favored : 94.75 % 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: -2.86 (0.16), residues: 2436 helix: -1.27 (0.13), residues: 1264 sheet: -6.43 (0.11), residues: 56 loop : -2.35 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 589 TYR 0.012 0.001 TYR C 526 PHE 0.032 0.002 PHE C 504 TRP 0.015 0.001 TRP C 583 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00339 (20104) covalent geometry : angle 0.80791 (27268) hydrogen bonds : bond 0.03891 ( 808) hydrogen bonds : angle 4.96952 ( 2292) Misc. bond : bond 0.00023 ( 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 583 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 577 time to evaluate : 1.081 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 63 LYS cc_start: 0.8536 (mmpt) cc_final: 0.8127 (mmmm) REVERT: A 92 LEU cc_start: 0.8954 (pt) cc_final: 0.8548 (tp) REVERT: A 99 MET cc_start: 0.8891 (mmp) cc_final: 0.8608 (mmm) REVERT: A 110 MET cc_start: 0.8405 (mmm) cc_final: 0.7076 (mmm) REVERT: A 127 ASN cc_start: 0.8748 (m110) cc_final: 0.8416 (p0) REVERT: A 209 LYS cc_start: 0.9644 (mtpt) cc_final: 0.9073 (mttp) REVERT: A 211 PHE cc_start: 0.8226 (t80) cc_final: 0.7729 (t80) REVERT: A 245 LYS cc_start: 0.9082 (mttt) cc_final: 0.8636 (mptt) REVERT: A 280 LEU cc_start: 0.8791 (tp) cc_final: 0.8560 (tp) REVERT: A 303 GLU cc_start: 0.8459 (tp30) cc_final: 0.8174 (tp30) REVERT: A 318 SER cc_start: 0.9344 (t) cc_final: 0.8838 (p) REVERT: A 364 ASP cc_start: 0.9092 (m-30) cc_final: 0.8564 (t70) REVERT: A 485 MET cc_start: 0.9251 (mmt) cc_final: 0.8931 (mmt) REVERT: A 497 MET cc_start: 0.8850 (tmm) cc_final: 0.8406 (tmm) REVERT: A 504 PHE cc_start: 0.9239 (m-80) cc_final: 0.9033 (m-80) REVERT: A 509 TYR cc_start: 0.9109 (t80) cc_final: 0.8482 (t80) REVERT: A 515 GLU cc_start: 0.8869 (mm-30) cc_final: 0.7813 (mm-30) REVERT: A 556 SER cc_start: 0.9292 (m) cc_final: 0.8928 (p) REVERT: A 570 MET cc_start: 0.8280 (ppp) cc_final: 0.7853 (tmm) REVERT: B 44 ILE cc_start: 0.9273 (pt) cc_final: 0.9039 (pt) REVERT: B 63 LYS cc_start: 0.8446 (mmpt) cc_final: 0.8054 (mmmm) REVERT: B 92 LEU cc_start: 0.8835 (pt) cc_final: 0.8592 (tt) REVERT: B 110 MET cc_start: 0.8462 (mmm) cc_final: 0.7629 (mmm) REVERT: B 127 ASN cc_start: 0.8732 (m110) cc_final: 0.8245 (p0) REVERT: B 209 LYS cc_start: 0.9641 (mtpt) cc_final: 0.9082 (mttp) REVERT: B 211 PHE cc_start: 0.8181 (t80) cc_final: 0.7728 (t80) REVERT: B 245 LYS cc_start: 0.9087 (mttt) cc_final: 0.8640 (mptt) REVERT: B 280 LEU cc_start: 0.8909 (tp) cc_final: 0.8641 (tp) REVERT: B 303 GLU cc_start: 0.8447 (tp30) cc_final: 0.8163 (tp30) REVERT: B 318 SER cc_start: 0.9314 (t) cc_final: 0.9070 (p) REVERT: B 364 ASP cc_start: 0.9087 (m-30) cc_final: 0.8577 (t70) REVERT: B 367 LEU cc_start: 0.8603 (tt) cc_final: 0.7018 (tt) REVERT: B 368 LEU cc_start: 0.9271 (pp) cc_final: 0.9021 (pt) REVERT: B 397 ILE cc_start: 0.9084 (mt) cc_final: 0.8866 (mm) REVERT: B 398 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9091 (mp) REVERT: B 485 MET cc_start: 0.9229 (mmt) cc_final: 0.9018 (mmt) REVERT: B 497 MET cc_start: 0.9257 (tmm) cc_final: 0.8828 (tmm) REVERT: B 509 TYR cc_start: 0.9142 (t80) cc_final: 0.8516 (t80) REVERT: B 515 GLU cc_start: 0.8885 (mm-30) cc_final: 0.7968 (mm-30) REVERT: B 556 SER cc_start: 0.9305 (m) cc_final: 0.8918 (p) REVERT: B 557 ILE cc_start: 0.9275 (pt) cc_final: 0.8917 (tp) REVERT: B 584 ARG cc_start: 0.8936 (mmt180) cc_final: 0.8658 (mmt180) REVERT: C 99 MET cc_start: 0.8849 (mmp) cc_final: 0.8610 (mmm) REVERT: C 110 MET cc_start: 0.8563 (mmm) cc_final: 0.7701 (mmm) REVERT: C 127 ASN cc_start: 0.8749 (m110) cc_final: 0.8381 (p0) REVERT: C 209 LYS cc_start: 0.9647 (mtpt) cc_final: 0.9159 (mttt) REVERT: C 211 PHE cc_start: 0.8201 (t80) cc_final: 0.7759 (t80) REVERT: C 245 LYS cc_start: 0.9032 (mttt) cc_final: 0.8601 (mptt) REVERT: C 280 LEU cc_start: 0.8840 (tp) cc_final: 0.8529 (tp) REVERT: C 303 GLU cc_start: 0.8481 (tp30) cc_final: 0.8184 (tp30) REVERT: C 318 SER cc_start: 0.9378 (t) cc_final: 0.8901 (p) REVERT: C 364 ASP cc_start: 0.9074 (m-30) cc_final: 0.8588 (t70) REVERT: C 368 LEU cc_start: 0.9275 (pp) cc_final: 0.9048 (pt) REVERT: C 485 MET cc_start: 0.9249 (mmt) cc_final: 0.8553 (mmt) REVERT: C 497 MET cc_start: 0.8597 (tmm) cc_final: 0.8323 (tmm) REVERT: C 509 TYR cc_start: 0.9126 (t80) cc_final: 0.8471 (t80) REVERT: C 515 GLU cc_start: 0.8940 (mm-30) cc_final: 0.7967 (mm-30) REVERT: C 528 MET cc_start: 0.8283 (ttm) cc_final: 0.7925 (ttm) REVERT: C 535 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8656 (tm-30) REVERT: C 556 SER cc_start: 0.9295 (m) cc_final: 0.8964 (p) REVERT: C 557 ILE cc_start: 0.9279 (pt) cc_final: 0.8901 (tp) REVERT: C 577 MET cc_start: 0.8792 (mmm) cc_final: 0.7001 (mmm) REVERT: D 92 LEU cc_start: 0.8928 (pt) cc_final: 0.8436 (tp) REVERT: D 110 MET cc_start: 0.8590 (mmm) cc_final: 0.7543 (mmm) REVERT: D 127 ASN cc_start: 0.8777 (m110) cc_final: 0.8432 (p0) REVERT: D 209 LYS cc_start: 0.9648 (mtpt) cc_final: 0.9094 (mtpp) REVERT: D 211 PHE cc_start: 0.8219 (t80) cc_final: 0.7762 (t80) REVERT: D 280 LEU cc_start: 0.8864 (tp) cc_final: 0.8597 (tp) REVERT: D 318 SER cc_start: 0.9364 (t) cc_final: 0.8877 (p) REVERT: D 364 ASP cc_start: 0.9105 (m-30) cc_final: 0.8590 (t70) REVERT: D 367 LEU cc_start: 0.8637 (tt) cc_final: 0.7113 (tt) REVERT: D 368 LEU cc_start: 0.9269 (pp) cc_final: 0.9008 (pt) REVERT: D 435 MET cc_start: 0.8886 (mmm) cc_final: 0.8602 (mmm) REVERT: D 462 TRP cc_start: 0.9388 (m100) cc_final: 0.9062 (m100) REVERT: D 485 MET cc_start: 0.8997 (mmt) cc_final: 0.8764 (mmt) REVERT: D 497 MET cc_start: 0.8789 (tmm) cc_final: 0.8394 (tmm) REVERT: D 509 TYR cc_start: 0.9166 (t80) cc_final: 0.8488 (t80) REVERT: D 515 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8111 (mm-30) REVERT: D 528 MET cc_start: 0.8270 (ttm) cc_final: 0.7918 (ttm) REVERT: D 556 SER cc_start: 0.9272 (m) cc_final: 0.8918 (p) REVERT: D 557 ILE cc_start: 0.9250 (pt) cc_final: 0.8906 (tp) REVERT: D 570 MET cc_start: 0.8211 (ppp) cc_final: 0.7933 (tmm) REVERT: D 577 MET cc_start: 0.8184 (mmm) cc_final: 0.7216 (mmm) outliers start: 6 outliers final: 0 residues processed: 579 average time/residue: 0.1408 time to fit residues: 128.9776 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 : 0.808 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 239 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.079462 restraints weight = 56230.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.081908 restraints weight = 34360.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.083533 restraints weight = 24131.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084758 restraints weight = 18875.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.085647 restraints weight = 15604.071| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4281 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= 0.146 Angle : 0.816 14.904 27268 Z= 0.388 Chirality : 0.044 0.187 3092 Planarity : 0.004 0.063 3448 Dihedral : 8.568 162.238 2700 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % 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: -2.72 (0.16), residues: 2436 helix: -1.06 (0.14), residues: 1288 sheet: -6.46 (0.10), residues: 56 loop : -2.42 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 589 TYR 0.022 0.001 TYR C 67 PHE 0.027 0.002 PHE C 244 TRP 0.017 0.001 TRP C 583 HIS 0.003 0.001 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00334 (20104) covalent geometry : angle 0.81599 (27268) hydrogen bonds : bond 0.03786 ( 808) hydrogen bonds : angle 4.90693 ( 2292) Misc. bond : bond 0.00017 ( 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 558 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 557 time to evaluate : 0.771 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: A 92 LEU cc_start: 0.8963 (pt) cc_final: 0.8595 (tp) REVERT: A 110 MET cc_start: 0.8414 (mmm) cc_final: 0.7452 (mmm) REVERT: A 127 ASN cc_start: 0.8659 (m110) cc_final: 0.8389 (p0) REVERT: A 209 LYS cc_start: 0.9571 (mtpt) cc_final: 0.9051 (mttp) REVERT: A 211 PHE cc_start: 0.8273 (t80) cc_final: 0.7635 (t80) REVERT: A 245 LYS cc_start: 0.9067 (mttt) cc_final: 0.8683 (mptt) REVERT: A 280 LEU cc_start: 0.8863 (tp) cc_final: 0.8648 (tp) REVERT: A 298 THR cc_start: 0.8853 (m) cc_final: 0.8600 (p) REVERT: A 303 GLU cc_start: 0.8569 (tp30) cc_final: 0.8230 (tp30) REVERT: A 364 ASP cc_start: 0.9049 (m-30) cc_final: 0.8560 (t70) REVERT: A 367 LEU cc_start: 0.8597 (tt) cc_final: 0.6982 (tt) REVERT: A 424 PRO cc_start: 0.8394 (Cg_endo) cc_final: 0.8183 (Cg_exo) REVERT: A 442 MET cc_start: 0.8500 (tpp) cc_final: 0.8285 (tpp) REVERT: A 485 MET cc_start: 0.9222 (mmt) cc_final: 0.8854 (mmt) REVERT: A 497 MET cc_start: 0.8808 (tmm) cc_final: 0.8416 (tmm) REVERT: A 509 TYR cc_start: 0.9133 (t80) cc_final: 0.8458 (t80) REVERT: A 556 SER cc_start: 0.9253 (m) cc_final: 0.8916 (p) REVERT: A 612 LEU cc_start: 0.8662 (tt) cc_final: 0.8294 (mm) REVERT: B 92 LEU cc_start: 0.8834 (pt) cc_final: 0.8417 (tp) REVERT: B 99 MET cc_start: 0.8858 (mmp) cc_final: 0.8571 (mmm) REVERT: B 110 MET cc_start: 0.8484 (mmm) cc_final: 0.7110 (mmm) REVERT: B 127 ASN cc_start: 0.8624 (m110) cc_final: 0.8286 (p0) REVERT: B 209 LYS cc_start: 0.9589 (mtpt) cc_final: 0.9061 (mttp) REVERT: B 211 PHE cc_start: 0.8201 (t80) cc_final: 0.7658 (t80) REVERT: B 245 LYS cc_start: 0.9069 (mttt) cc_final: 0.8656 (mptt) REVERT: B 280 LEU cc_start: 0.9059 (tp) cc_final: 0.8770 (tp) REVERT: B 303 GLU cc_start: 0.8558 (tp30) cc_final: 0.8216 (tp30) REVERT: B 318 SER cc_start: 0.9320 (t) cc_final: 0.9072 (p) REVERT: B 364 ASP cc_start: 0.9036 (m-30) cc_final: 0.8555 (t70) REVERT: B 367 LEU cc_start: 0.8669 (tt) cc_final: 0.7080 (tt) REVERT: B 368 LEU cc_start: 0.9251 (pp) cc_final: 0.8965 (pt) REVERT: B 442 MET cc_start: 0.8563 (tpp) cc_final: 0.8319 (tpp) REVERT: B 454 MET cc_start: 0.8326 (tpt) cc_final: 0.8007 (tpp) REVERT: B 480 ILE cc_start: 0.9430 (mm) cc_final: 0.9176 (mm) REVERT: B 485 MET cc_start: 0.9293 (mmt) cc_final: 0.8897 (mmt) REVERT: B 497 MET cc_start: 0.9232 (tmm) cc_final: 0.8780 (tmm) REVERT: B 509 TYR cc_start: 0.9141 (t80) cc_final: 0.8465 (t80) REVERT: B 515 GLU cc_start: 0.8914 (mm-30) cc_final: 0.7984 (mm-30) REVERT: B 556 SER cc_start: 0.9295 (m) cc_final: 0.8929 (p) REVERT: B 557 ILE cc_start: 0.9287 (pt) cc_final: 0.8951 (tp) REVERT: C 99 MET cc_start: 0.8874 (mmp) cc_final: 0.8596 (mmm) REVERT: C 110 MET cc_start: 0.8597 (mmm) cc_final: 0.7242 (mmm) REVERT: C 127 ASN cc_start: 0.8670 (m110) cc_final: 0.8334 (p0) REVERT: C 139 ARG cc_start: 0.9139 (mmm160) cc_final: 0.8926 (mmm-85) REVERT: C 211 PHE cc_start: 0.8191 (t80) cc_final: 0.7620 (t80) REVERT: C 245 LYS cc_start: 0.8949 (mttt) cc_final: 0.8534 (mptt) REVERT: C 303 GLU cc_start: 0.8539 (tp30) cc_final: 0.8227 (tp30) REVERT: C 318 SER cc_start: 0.9369 (t) cc_final: 0.8989 (p) REVERT: C 364 ASP cc_start: 0.9047 (m-30) cc_final: 0.8597 (t70) REVERT: C 424 PRO cc_start: 0.8404 (Cg_endo) cc_final: 0.8189 (Cg_exo) REVERT: C 442 MET cc_start: 0.8506 (tpp) cc_final: 0.8295 (tpp) REVERT: C 485 MET cc_start: 0.9164 (mmt) cc_final: 0.8543 (mmt) REVERT: C 509 TYR cc_start: 0.9076 (t80) cc_final: 0.8405 (t80) REVERT: C 515 GLU cc_start: 0.8956 (mm-30) cc_final: 0.7977 (mm-30) REVERT: C 556 SER cc_start: 0.9283 (m) cc_final: 0.8920 (p) REVERT: C 557 ILE cc_start: 0.9247 (pt) cc_final: 0.8897 (tp) REVERT: C 577 MET cc_start: 0.8569 (mmm) cc_final: 0.6698 (mmm) REVERT: D 92 LEU cc_start: 0.8877 (pt) cc_final: 0.8591 (tp) REVERT: D 99 MET cc_start: 0.8806 (mmp) cc_final: 0.8567 (mmm) REVERT: D 110 MET cc_start: 0.8531 (mmm) cc_final: 0.7761 (mmm) REVERT: D 127 ASN cc_start: 0.8757 (m110) cc_final: 0.8474 (p0) REVERT: D 209 LYS cc_start: 0.9594 (mtpt) cc_final: 0.9044 (mttp) REVERT: D 211 PHE cc_start: 0.8175 (t80) cc_final: 0.7600 (t80) REVERT: D 280 LEU cc_start: 0.8934 (tp) cc_final: 0.8715 (tp) REVERT: D 364 ASP cc_start: 0.9048 (m-30) cc_final: 0.8600 (t70) REVERT: D 435 MET cc_start: 0.8967 (mmm) cc_final: 0.8674 (mmm) REVERT: D 442 MET cc_start: 0.8472 (tpp) cc_final: 0.8247 (tpp) REVERT: D 462 TRP cc_start: 0.9318 (m100) cc_final: 0.9035 (m100) REVERT: D 497 MET cc_start: 0.8768 (tmm) cc_final: 0.8394 (tmm) REVERT: D 509 TYR cc_start: 0.9115 (t80) cc_final: 0.8425 (t80) REVERT: D 515 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8157 (mm-30) REVERT: D 556 SER cc_start: 0.9247 (m) cc_final: 0.8891 (p) REVERT: D 557 ILE cc_start: 0.9261 (pt) cc_final: 0.8892 (tp) REVERT: D 577 MET cc_start: 0.8153 (mmm) cc_final: 0.7403 (mmm) REVERT: D 612 LEU cc_start: 0.8657 (tt) cc_final: 0.8294 (mm) outliers start: 1 outliers final: 0 residues processed: 557 average time/residue: 0.1342 time to fit residues: 119.3504 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 : 0.800 ------------------------------------------------------------------------------- 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: 0.0770 chunk 186 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 197 optimal weight: 0.3980 chunk 174 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 56 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.081747 restraints weight = 55616.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.084183 restraints weight = 34178.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085811 restraints weight = 24104.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087040 restraints weight = 18847.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087837 restraints weight = 15586.228| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 20108 Z= 0.137 Angle : 0.812 13.071 27268 Z= 0.385 Chirality : 0.044 0.188 3092 Planarity : 0.004 0.047 3448 Dihedral : 8.070 151.046 2700 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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: -2.54 (0.16), residues: 2436 helix: -0.86 (0.14), residues: 1292 sheet: -6.47 (0.10), residues: 56 loop : -2.42 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 589 TYR 0.017 0.001 TYR D 432 PHE 0.028 0.001 PHE A 504 TRP 0.029 0.001 TRP B 583 HIS 0.003 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00314 (20104) covalent geometry : angle 0.81174 (27268) hydrogen bonds : bond 0.03720 ( 808) hydrogen bonds : angle 4.75779 ( 2292) Misc. bond : bond 0.00006 ( 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 556 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 0.813 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: A 92 LEU cc_start: 0.8801 (pt) cc_final: 0.8457 (tp) REVERT: A 99 MET cc_start: 0.8829 (mmp) cc_final: 0.8450 (mmm) REVERT: A 110 MET cc_start: 0.8274 (mmm) cc_final: 0.7455 (mmm) REVERT: A 211 PHE cc_start: 0.8302 (t80) cc_final: 0.7755 (t80) REVERT: A 215 MET cc_start: 0.8528 (mtp) cc_final: 0.8274 (mtp) REVERT: A 245 LYS cc_start: 0.9037 (mttt) cc_final: 0.8816 (mptt) REVERT: A 280 LEU cc_start: 0.9059 (tp) cc_final: 0.8766 (tp) REVERT: A 303 GLU cc_start: 0.8563 (tp30) cc_final: 0.8210 (tp30) REVERT: A 324 TYR cc_start: 0.7657 (p90) cc_final: 0.7149 (p90) REVERT: A 364 ASP cc_start: 0.9044 (m-30) cc_final: 0.8693 (t70) REVERT: A 424 PRO cc_start: 0.8388 (Cg_endo) cc_final: 0.8166 (Cg_exo) REVERT: A 432 TYR cc_start: 0.9159 (t80) cc_final: 0.8882 (t80) REVERT: A 485 MET cc_start: 0.9189 (mmt) cc_final: 0.8723 (mmt) REVERT: A 509 TYR cc_start: 0.9095 (t80) cc_final: 0.8482 (t80) REVERT: A 528 MET cc_start: 0.8311 (ttm) cc_final: 0.7903 (tmm) REVERT: A 556 SER cc_start: 0.9280 (m) cc_final: 0.8917 (p) REVERT: A 603 MET cc_start: 0.8503 (mtt) cc_final: 0.8147 (mtt) REVERT: B 92 LEU cc_start: 0.8922 (pt) cc_final: 0.8571 (tp) REVERT: B 110 MET cc_start: 0.8372 (mmm) cc_final: 0.7428 (mmm) REVERT: B 211 PHE cc_start: 0.8229 (t80) cc_final: 0.7748 (t80) REVERT: B 245 LYS cc_start: 0.9028 (mttt) cc_final: 0.8806 (mptt) REVERT: B 280 LEU cc_start: 0.9087 (tp) cc_final: 0.8806 (tp) REVERT: B 303 GLU cc_start: 0.8571 (tp30) cc_final: 0.8229 (tp30) REVERT: B 315 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8044 (tm-30) REVERT: B 318 SER cc_start: 0.9325 (t) cc_final: 0.9042 (p) REVERT: B 324 TYR cc_start: 0.7639 (p90) cc_final: 0.7112 (p90) REVERT: B 364 ASP cc_start: 0.9036 (m-30) cc_final: 0.8693 (t70) REVERT: B 454 MET cc_start: 0.8352 (tpt) cc_final: 0.8073 (tpp) REVERT: B 485 MET cc_start: 0.9231 (mmt) cc_final: 0.8876 (mmt) REVERT: B 509 TYR cc_start: 0.9112 (t80) cc_final: 0.8455 (t80) REVERT: B 556 SER cc_start: 0.9250 (m) cc_final: 0.8917 (p) REVERT: B 603 MET cc_start: 0.8541 (mtt) cc_final: 0.8252 (mtt) REVERT: C 99 MET cc_start: 0.8794 (mmp) cc_final: 0.8466 (mmm) REVERT: C 110 MET cc_start: 0.8439 (mmm) cc_final: 0.7529 (mmm) REVERT: C 211 PHE cc_start: 0.8228 (t80) cc_final: 0.7719 (t80) REVERT: C 245 LYS cc_start: 0.8928 (mttt) cc_final: 0.8569 (mptt) REVERT: C 280 LEU cc_start: 0.8959 (tp) cc_final: 0.8616 (tp) REVERT: C 303 GLU cc_start: 0.8542 (tp30) cc_final: 0.8199 (tp30) REVERT: C 364 ASP cc_start: 0.9023 (m-30) cc_final: 0.8704 (t70) REVERT: C 378 MET cc_start: 0.7487 (mmt) cc_final: 0.7266 (mmp) REVERT: C 424 PRO cc_start: 0.8412 (Cg_endo) cc_final: 0.8182 (Cg_exo) REVERT: C 497 MET cc_start: 0.9002 (tmm) cc_final: 0.8628 (tmm) REVERT: C 509 TYR cc_start: 0.9046 (t80) cc_final: 0.8392 (t80) REVERT: C 556 SER cc_start: 0.9274 (m) cc_final: 0.8908 (p) REVERT: C 577 MET cc_start: 0.8325 (mmm) cc_final: 0.7990 (mmm) REVERT: C 603 MET cc_start: 0.8558 (mtt) cc_final: 0.8276 (mtt) REVERT: C 612 LEU cc_start: 0.8623 (tt) cc_final: 0.8371 (mm) REVERT: D 110 MET cc_start: 0.8441 (mmm) cc_final: 0.7426 (mmm) REVERT: D 127 ASN cc_start: 0.8661 (m110) cc_final: 0.8408 (p0) REVERT: D 211 PHE cc_start: 0.8233 (t80) cc_final: 0.7735 (t80) REVERT: D 280 LEU cc_start: 0.9046 (tp) cc_final: 0.8742 (tp) REVERT: D 298 THR cc_start: 0.8790 (m) cc_final: 0.8535 (p) REVERT: D 364 ASP cc_start: 0.9028 (m-30) cc_final: 0.8703 (t70) REVERT: D 432 TYR cc_start: 0.9055 (t80) cc_final: 0.8799 (t80) REVERT: D 435 MET cc_start: 0.9021 (mmm) cc_final: 0.8721 (mmm) REVERT: D 462 TRP cc_start: 0.9243 (m100) cc_final: 0.8953 (m100) REVERT: D 509 TYR cc_start: 0.9096 (t80) cc_final: 0.8383 (t80) REVERT: D 556 SER cc_start: 0.9242 (m) cc_final: 0.8874 (p) REVERT: D 570 MET cc_start: 0.8168 (ppp) cc_final: 0.7965 (tmm) REVERT: D 577 MET cc_start: 0.7976 (mmm) cc_final: 0.7089 (mmm) REVERT: D 603 MET cc_start: 0.8534 (mtt) cc_final: 0.8214 (mtt) REVERT: D 612 LEU cc_start: 0.8607 (tt) cc_final: 0.8397 (mm) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 0.1333 time to fit residues: 119.2126 Evaluate side-chains 441 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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: 9.9990 chunk 61 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 572 ASN C 158 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.078301 restraints weight = 56800.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.080706 restraints weight = 34730.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.082365 restraints weight = 24407.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083495 restraints weight = 18938.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084368 restraints weight = 15770.236| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20108 Z= 0.173 Angle : 0.811 15.221 27268 Z= 0.392 Chirality : 0.045 0.182 3092 Planarity : 0.004 0.042 3448 Dihedral : 7.964 152.220 2700 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: -2.37 (0.17), residues: 2436 helix: -0.72 (0.14), residues: 1292 sheet: -6.49 (0.10), residues: 56 loop : -2.33 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 589 TYR 0.017 0.001 TYR B 432 PHE 0.022 0.002 PHE C 493 TRP 0.011 0.001 TRP A 462 HIS 0.003 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00398 (20104) covalent geometry : angle 0.81068 (27268) hydrogen bonds : bond 0.03736 ( 808) hydrogen bonds : angle 4.83417 ( 2292) Misc. bond : bond 0.00023 ( 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 538 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 0.765 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: A 78 MET cc_start: 0.7174 (pmm) cc_final: 0.5980 (tmm) REVERT: A 110 MET cc_start: 0.8367 (mmm) cc_final: 0.7413 (mmm) REVERT: A 127 ASN cc_start: 0.8078 (p0) cc_final: 0.7266 (p0) REVERT: A 209 LYS cc_start: 0.9534 (mtpt) cc_final: 0.8966 (mtpp) REVERT: A 211 PHE cc_start: 0.8217 (t80) cc_final: 0.7766 (t80) REVERT: A 215 MET cc_start: 0.8489 (mtp) cc_final: 0.8223 (mtp) REVERT: A 245 LYS cc_start: 0.9077 (mttt) cc_final: 0.8844 (mptt) REVERT: A 280 LEU cc_start: 0.9117 (tp) cc_final: 0.8887 (tp) REVERT: A 298 THR cc_start: 0.8816 (m) cc_final: 0.8566 (p) REVERT: A 303 GLU cc_start: 0.8636 (tp30) cc_final: 0.8277 (tp30) REVERT: A 324 TYR cc_start: 0.7852 (p90) cc_final: 0.7238 (p90) REVERT: A 364 ASP cc_start: 0.9020 (m-30) cc_final: 0.8735 (t70) REVERT: A 410 MET cc_start: 0.4757 (tmm) cc_final: 0.4553 (ttp) REVERT: A 424 PRO cc_start: 0.8389 (Cg_endo) cc_final: 0.8155 (Cg_exo) REVERT: A 485 MET cc_start: 0.9061 (mmt) cc_final: 0.8550 (mmt) REVERT: A 509 TYR cc_start: 0.9170 (t80) cc_final: 0.8459 (t80) REVERT: A 554 MET cc_start: 0.8266 (mtt) cc_final: 0.8056 (mtp) REVERT: A 556 SER cc_start: 0.9373 (m) cc_final: 0.8999 (p) REVERT: A 557 ILE cc_start: 0.9315 (pt) cc_final: 0.8982 (tp) REVERT: A 603 MET cc_start: 0.8514 (mtt) cc_final: 0.8219 (mtt) REVERT: A 612 LEU cc_start: 0.8757 (tt) cc_final: 0.8483 (mm) REVERT: B 99 MET cc_start: 0.8743 (mmp) cc_final: 0.8397 (mmm) REVERT: B 110 MET cc_start: 0.8446 (mmm) cc_final: 0.7553 (mmm) REVERT: B 127 ASN cc_start: 0.8189 (p0) cc_final: 0.7222 (p0) REVERT: B 209 LYS cc_start: 0.9543 (mtpt) cc_final: 0.8986 (mtpp) REVERT: B 211 PHE cc_start: 0.8170 (t80) cc_final: 0.7749 (t80) REVERT: B 280 LEU cc_start: 0.9153 (tp) cc_final: 0.8947 (tp) REVERT: B 303 GLU cc_start: 0.8641 (tp30) cc_final: 0.8278 (tp30) REVERT: B 315 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 318 SER cc_start: 0.9312 (t) cc_final: 0.9050 (p) REVERT: B 324 TYR cc_start: 0.7801 (p90) cc_final: 0.7183 (p90) REVERT: B 364 ASP cc_start: 0.9030 (m-30) cc_final: 0.8743 (t70) REVERT: B 432 TYR cc_start: 0.9155 (t80) cc_final: 0.8939 (t80) REVERT: B 454 MET cc_start: 0.8414 (tpt) cc_final: 0.8150 (tpp) REVERT: B 485 MET cc_start: 0.9187 (mmt) cc_final: 0.8870 (mmt) REVERT: B 509 TYR cc_start: 0.9127 (t80) cc_final: 0.8475 (t80) REVERT: B 556 SER cc_start: 0.9337 (m) cc_final: 0.8965 (p) REVERT: B 557 ILE cc_start: 0.9361 (pt) cc_final: 0.8981 (tp) REVERT: B 603 MET cc_start: 0.8482 (mtt) cc_final: 0.8199 (mtt) REVERT: B 612 LEU cc_start: 0.8730 (tt) cc_final: 0.8476 (mm) REVERT: C 110 MET cc_start: 0.8483 (mmm) cc_final: 0.7556 (mmm) REVERT: C 209 LYS cc_start: 0.9557 (mtpt) cc_final: 0.8991 (mtpp) REVERT: C 211 PHE cc_start: 0.8189 (t80) cc_final: 0.7751 (t80) REVERT: C 245 LYS cc_start: 0.8990 (mttt) cc_final: 0.8598 (mptt) REVERT: C 280 LEU cc_start: 0.9005 (tp) cc_final: 0.8765 (tp) REVERT: C 298 THR cc_start: 0.8897 (m) cc_final: 0.8575 (p) REVERT: C 303 GLU cc_start: 0.8658 (tp30) cc_final: 0.8280 (tp30) REVERT: C 324 TYR cc_start: 0.7764 (p90) cc_final: 0.7168 (p90) REVERT: C 364 ASP cc_start: 0.9023 (m-30) cc_final: 0.8756 (t70) REVERT: C 378 MET cc_start: 0.7503 (mmt) cc_final: 0.7302 (mmp) REVERT: C 424 PRO cc_start: 0.8403 (Cg_endo) cc_final: 0.8169 (Cg_exo) REVERT: C 485 MET cc_start: 0.9198 (mmt) cc_final: 0.8461 (mmt) REVERT: C 497 MET cc_start: 0.9041 (tmm) cc_final: 0.8600 (tmm) REVERT: C 509 TYR cc_start: 0.9141 (t80) cc_final: 0.8448 (t80) REVERT: C 556 SER cc_start: 0.9343 (m) cc_final: 0.8942 (p) REVERT: C 557 ILE cc_start: 0.9333 (pt) cc_final: 0.8901 (tp) REVERT: C 577 MET cc_start: 0.8632 (mmm) cc_final: 0.6617 (mmm) REVERT: C 589 ARG cc_start: 0.7202 (ptt-90) cc_final: 0.6705 (ptt-90) REVERT: C 603 MET cc_start: 0.8512 (mtt) cc_final: 0.8250 (mtt) REVERT: C 612 LEU cc_start: 0.8775 (tt) cc_final: 0.8537 (mm) REVERT: D 99 MET cc_start: 0.8790 (mmp) cc_final: 0.8276 (mmm) REVERT: D 110 MET cc_start: 0.8403 (mmm) cc_final: 0.7197 (mmm) REVERT: D 127 ASN cc_start: 0.8684 (m110) cc_final: 0.8374 (p0) REVERT: D 209 LYS cc_start: 0.9556 (mtpt) cc_final: 0.9001 (mtpp) REVERT: D 211 PHE cc_start: 0.8190 (t80) cc_final: 0.7750 (t80) REVERT: D 280 LEU cc_start: 0.9108 (tp) cc_final: 0.8832 (tp) REVERT: D 324 TYR cc_start: 0.7824 (p90) cc_final: 0.7213 (p90) REVERT: D 364 ASP cc_start: 0.9017 (m-30) cc_final: 0.8751 (t70) REVERT: D 435 MET cc_start: 0.9008 (mmm) cc_final: 0.8738 (mmm) REVERT: D 497 MET cc_start: 0.9048 (tmm) cc_final: 0.8637 (tmm) REVERT: D 509 TYR cc_start: 0.9159 (t80) cc_final: 0.8445 (t80) REVERT: D 556 SER cc_start: 0.9338 (m) cc_final: 0.8956 (p) REVERT: D 557 ILE cc_start: 0.9288 (pt) cc_final: 0.8915 (tp) REVERT: D 577 MET cc_start: 0.8075 (mmm) cc_final: 0.7316 (mmm) REVERT: D 603 MET cc_start: 0.8491 (mtt) cc_final: 0.8235 (mtt) REVERT: D 612 LEU cc_start: 0.8815 (tt) cc_final: 0.8567 (mm) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.1265 time to fit residues: 109.6337 Evaluate side-chains 449 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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: 0.9990 chunk 150 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 206 optimal weight: 0.0060 chunk 34 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 572 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** 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 = 0.3356 r_free = 0.3356 target = 0.097973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.080829 restraints weight = 55687.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.083238 restraints weight = 33843.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.084653 restraints weight = 23768.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086007 restraints weight = 19004.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.086890 restraints weight = 15528.741| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20108 Z= 0.137 Angle : 0.828 13.505 27268 Z= 0.389 Chirality : 0.045 0.175 3092 Planarity : 0.004 0.042 3448 Dihedral : 7.480 137.394 2700 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.09 % Allowed : 1.61 % 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: -2.24 (0.17), residues: 2436 helix: -0.56 (0.14), residues: 1288 sheet: -6.49 (0.10), residues: 56 loop : -2.34 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 589 TYR 0.015 0.001 TYR B 432 PHE 0.023 0.001 PHE B 493 TRP 0.017 0.001 TRP A 462 HIS 0.005 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00318 (20104) covalent geometry : angle 0.82825 (27268) hydrogen bonds : bond 0.03667 ( 808) hydrogen bonds : angle 4.71529 ( 2292) Misc. bond : bond 0.00026 ( 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 550 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 548 time to evaluate : 0.898 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 78 MET cc_start: 0.7093 (pmm) cc_final: 0.5626 (tmm) REVERT: A 110 MET cc_start: 0.8244 (mmm) cc_final: 0.7299 (mmm) REVERT: A 127 ASN cc_start: 0.7964 (p0) cc_final: 0.7535 (p0) REVERT: A 209 LYS cc_start: 0.9530 (mtpt) cc_final: 0.9042 (mttm) REVERT: A 211 PHE cc_start: 0.8215 (t80) cc_final: 0.7761 (t80) REVERT: A 280 LEU cc_start: 0.9150 (tp) cc_final: 0.8888 (tp) REVERT: A 298 THR cc_start: 0.8767 (m) cc_final: 0.8518 (p) REVERT: A 303 GLU cc_start: 0.8602 (tp30) cc_final: 0.8199 (tp30) REVERT: A 324 TYR cc_start: 0.7778 (p90) cc_final: 0.7152 (p90) REVERT: A 364 ASP cc_start: 0.9015 (m-30) cc_final: 0.8735 (t70) REVERT: A 410 MET cc_start: 0.5160 (tmm) cc_final: 0.4660 (ttp) REVERT: A 485 MET cc_start: 0.9068 (mmt) cc_final: 0.8409 (mmt) REVERT: A 509 TYR cc_start: 0.9081 (t80) cc_final: 0.8319 (t80) REVERT: A 554 MET cc_start: 0.8252 (mtt) cc_final: 0.7985 (mtt) REVERT: A 556 SER cc_start: 0.9356 (m) cc_final: 0.8977 (p) REVERT: A 603 MET cc_start: 0.8469 (mtt) cc_final: 0.8180 (mtt) REVERT: B 110 MET cc_start: 0.8316 (mmm) cc_final: 0.7096 (tpp) REVERT: B 209 LYS cc_start: 0.9606 (mtmt) cc_final: 0.9182 (mttt) REVERT: B 211 PHE cc_start: 0.8172 (t80) cc_final: 0.7770 (t80) REVERT: B 255 MET cc_start: 0.8947 (tpt) cc_final: 0.8679 (tpp) REVERT: B 260 MET cc_start: 0.9076 (mmm) cc_final: 0.8860 (tpt) REVERT: B 280 LEU cc_start: 0.9142 (tp) cc_final: 0.8875 (tp) REVERT: B 298 THR cc_start: 0.8802 (m) cc_final: 0.8541 (p) REVERT: B 303 GLU cc_start: 0.8614 (tp30) cc_final: 0.8228 (tp30) REVERT: B 315 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 318 SER cc_start: 0.9322 (t) cc_final: 0.9065 (p) REVERT: B 324 TYR cc_start: 0.7668 (p90) cc_final: 0.7060 (p90) REVERT: B 364 ASP cc_start: 0.8997 (m-30) cc_final: 0.8735 (t70) REVERT: B 368 LEU cc_start: 0.9370 (pt) cc_final: 0.9097 (mp) REVERT: B 485 MET cc_start: 0.9222 (mmt) cc_final: 0.8794 (mmt) REVERT: B 509 TYR cc_start: 0.9117 (t80) cc_final: 0.8363 (t80) REVERT: B 556 SER cc_start: 0.9328 (m) cc_final: 0.9018 (p) REVERT: B 603 MET cc_start: 0.8434 (mtt) cc_final: 0.8127 (mtt) REVERT: C 99 MET cc_start: 0.8803 (mmp) cc_final: 0.8427 (mmp) REVERT: C 110 MET cc_start: 0.8395 (mmm) cc_final: 0.7108 (tpp) REVERT: C 209 LYS cc_start: 0.9617 (mtmt) cc_final: 0.9194 (mttt) REVERT: C 211 PHE cc_start: 0.8165 (t80) cc_final: 0.7752 (t80) REVERT: C 245 LYS cc_start: 0.8949 (mttt) cc_final: 0.8591 (mptt) REVERT: C 280 LEU cc_start: 0.8944 (tp) cc_final: 0.8681 (tp) REVERT: C 298 THR cc_start: 0.8836 (m) cc_final: 0.8559 (p) REVERT: C 303 GLU cc_start: 0.8602 (tp30) cc_final: 0.8227 (tp30) REVERT: C 324 TYR cc_start: 0.7681 (p90) cc_final: 0.7040 (p90) REVERT: C 364 ASP cc_start: 0.9010 (m-30) cc_final: 0.8751 (t70) REVERT: C 424 PRO cc_start: 0.8417 (Cg_endo) cc_final: 0.8142 (Cg_exo) REVERT: C 497 MET cc_start: 0.9005 (tmm) cc_final: 0.8597 (tmm) REVERT: C 509 TYR cc_start: 0.9070 (t80) cc_final: 0.8390 (t80) REVERT: C 556 SER cc_start: 0.9306 (m) cc_final: 0.8943 (p) REVERT: C 557 ILE cc_start: 0.9282 (pt) cc_final: 0.8931 (tp) REVERT: C 572 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8792 (t0) REVERT: C 577 MET cc_start: 0.8464 (mmm) cc_final: 0.8157 (mmm) REVERT: C 603 MET cc_start: 0.8483 (mtt) cc_final: 0.8220 (mtt) REVERT: D 64 LEU cc_start: 0.8715 (tp) cc_final: 0.8507 (tp) REVERT: D 110 MET cc_start: 0.8306 (mmm) cc_final: 0.7284 (mmm) REVERT: D 127 ASN cc_start: 0.8619 (m110) cc_final: 0.8280 (p0) REVERT: D 209 LYS cc_start: 0.9605 (mtmt) cc_final: 0.9170 (mttt) REVERT: D 211 PHE cc_start: 0.8187 (t80) cc_final: 0.7766 (t80) REVERT: D 280 LEU cc_start: 0.9086 (tp) cc_final: 0.8817 (tp) REVERT: D 324 TYR cc_start: 0.7685 (p90) cc_final: 0.7040 (p90) REVERT: D 364 ASP cc_start: 0.8983 (m-30) cc_final: 0.8737 (t70) REVERT: D 367 LEU cc_start: 0.8407 (tt) cc_final: 0.8191 (tt) REVERT: D 435 MET cc_start: 0.9027 (mmm) cc_final: 0.8727 (mmm) REVERT: D 497 MET cc_start: 0.9002 (tmm) cc_final: 0.8569 (tmm) REVERT: D 509 TYR cc_start: 0.9126 (t80) cc_final: 0.8345 (t80) REVERT: D 556 SER cc_start: 0.9262 (m) cc_final: 0.8883 (p) REVERT: D 557 ILE cc_start: 0.9260 (pt) cc_final: 0.8937 (tp) REVERT: D 570 MET cc_start: 0.7982 (ppp) cc_final: 0.7686 (tmm) REVERT: D 577 MET cc_start: 0.7998 (mmm) cc_final: 0.7207 (mmm) REVERT: D 603 MET cc_start: 0.8461 (mtt) cc_final: 0.8181 (mtt) outliers start: 2 outliers final: 0 residues processed: 550 average time/residue: 0.1275 time to fit residues: 113.0585 Evaluate side-chains 456 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 455 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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: 0.0870 chunk 202 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 572 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** 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 = 0.3333 r_free = 0.3333 target = 0.096473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079442 restraints weight = 55937.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081873 restraints weight = 34107.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.083359 restraints weight = 23861.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.084664 restraints weight = 18884.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085512 restraints weight = 15452.617| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 20108 Z= 0.160 Angle : 0.840 14.083 27268 Z= 0.400 Chirality : 0.046 0.186 3092 Planarity : 0.004 0.042 3448 Dihedral : 7.118 128.287 2700 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.05 % Allowed : 1.37 % Favored : 98.58 % 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: -2.10 (0.17), residues: 2436 helix: -0.46 (0.14), residues: 1300 sheet: -6.36 (0.14), residues: 64 loop : -2.23 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 589 TYR 0.015 0.001 TYR A 555 PHE 0.032 0.002 PHE C 562 TRP 0.035 0.001 TRP C 583 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00377 (20104) covalent geometry : angle 0.83955 (27268) hydrogen bonds : bond 0.03700 ( 808) hydrogen bonds : angle 4.75979 ( 2292) Misc. bond : bond 0.00028 ( 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 544 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 543 time to evaluate : 0.687 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: A 78 MET cc_start: 0.7271 (pmm) cc_final: 0.5851 (tmm) REVERT: A 110 MET cc_start: 0.8420 (mmm) cc_final: 0.7469 (mmm) REVERT: A 209 LYS cc_start: 0.9593 (mtmt) cc_final: 0.9230 (mttp) REVERT: A 211 PHE cc_start: 0.8228 (t80) cc_final: 0.7835 (t80) REVERT: A 280 LEU cc_start: 0.9227 (tp) cc_final: 0.9002 (tp) REVERT: A 298 THR cc_start: 0.8804 (m) cc_final: 0.8549 (p) REVERT: A 324 TYR cc_start: 0.7895 (p90) cc_final: 0.7128 (p90) REVERT: A 364 ASP cc_start: 0.9026 (m-30) cc_final: 0.8770 (t70) REVERT: A 367 LEU cc_start: 0.8538 (tt) cc_final: 0.8326 (tt) REVERT: A 368 LEU cc_start: 0.9326 (pt) cc_final: 0.9049 (mp) REVERT: A 485 MET cc_start: 0.9061 (mmt) cc_final: 0.8451 (mmt) REVERT: A 509 TYR cc_start: 0.9116 (t80) cc_final: 0.8384 (t80) REVERT: A 515 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 556 SER cc_start: 0.9409 (m) cc_final: 0.9027 (p) REVERT: A 557 ILE cc_start: 0.9366 (pt) cc_final: 0.9026 (tp) REVERT: A 584 ARG cc_start: 0.8751 (mmt180) cc_final: 0.8460 (mmt180) REVERT: A 603 MET cc_start: 0.8448 (mtt) cc_final: 0.8166 (mtt) REVERT: B 110 MET cc_start: 0.8303 (mmm) cc_final: 0.7492 (mmm) REVERT: B 209 LYS cc_start: 0.9596 (mtmt) cc_final: 0.9209 (mttp) REVERT: B 211 PHE cc_start: 0.8136 (t80) cc_final: 0.7765 (t80) REVERT: B 280 LEU cc_start: 0.9223 (tp) cc_final: 0.9003 (tp) REVERT: B 298 THR cc_start: 0.8793 (m) cc_final: 0.8572 (p) REVERT: B 315 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 318 SER cc_start: 0.9297 (t) cc_final: 0.9060 (p) REVERT: B 324 TYR cc_start: 0.7847 (p90) cc_final: 0.7054 (p90) REVERT: B 364 ASP cc_start: 0.9015 (m-30) cc_final: 0.8778 (t70) REVERT: B 368 LEU cc_start: 0.9351 (pt) cc_final: 0.9052 (mp) REVERT: B 509 TYR cc_start: 0.9086 (t80) cc_final: 0.8372 (t80) REVERT: B 554 MET cc_start: 0.8353 (mtm) cc_final: 0.8124 (mtm) REVERT: B 556 SER cc_start: 0.9362 (m) cc_final: 0.9037 (p) REVERT: B 557 ILE cc_start: 0.9350 (pt) cc_final: 0.8902 (tp) REVERT: B 603 MET cc_start: 0.8418 (mtt) cc_final: 0.8132 (mtt) REVERT: C 110 MET cc_start: 0.8362 (mmm) cc_final: 0.7835 (mmm) REVERT: C 209 LYS cc_start: 0.9606 (mtmt) cc_final: 0.9216 (mttp) REVERT: C 211 PHE cc_start: 0.8178 (t80) cc_final: 0.7785 (t80) REVERT: C 245 LYS cc_start: 0.8967 (mttt) cc_final: 0.8598 (mptt) REVERT: C 260 MET cc_start: 0.9072 (mmm) cc_final: 0.8869 (tpt) REVERT: C 280 LEU cc_start: 0.9018 (tp) cc_final: 0.8809 (tp) REVERT: C 298 THR cc_start: 0.8890 (m) cc_final: 0.8562 (p) REVERT: C 303 GLU cc_start: 0.8658 (tp30) cc_final: 0.8270 (tp30) REVERT: C 324 TYR cc_start: 0.7813 (p90) cc_final: 0.7175 (p90) REVERT: C 364 ASP cc_start: 0.9014 (m-30) cc_final: 0.8780 (t70) REVERT: C 424 PRO cc_start: 0.8389 (Cg_endo) cc_final: 0.8144 (Cg_exo) REVERT: C 485 MET cc_start: 0.9282 (mmt) cc_final: 0.8521 (mmt) REVERT: C 497 MET cc_start: 0.9016 (tmm) cc_final: 0.8610 (tmm) REVERT: C 509 TYR cc_start: 0.9096 (t80) cc_final: 0.8364 (t80) REVERT: C 554 MET cc_start: 0.8174 (mtm) cc_final: 0.7905 (mtm) REVERT: C 556 SER cc_start: 0.9360 (m) cc_final: 0.8985 (p) REVERT: C 557 ILE cc_start: 0.9352 (pt) cc_final: 0.8935 (tp) REVERT: C 577 MET cc_start: 0.8704 (mmm) cc_final: 0.6738 (mmm) REVERT: C 583 TRP cc_start: 0.7645 (m-90) cc_final: 0.7349 (m-90) REVERT: C 584 ARG cc_start: 0.8580 (mmt180) cc_final: 0.8204 (mmt180) REVERT: C 603 MET cc_start: 0.8454 (mtt) cc_final: 0.8191 (mtt) REVERT: D 110 MET cc_start: 0.8326 (mmm) cc_final: 0.7185 (mmm) REVERT: D 127 ASN cc_start: 0.8647 (m110) cc_final: 0.8292 (p0) REVERT: D 209 LYS cc_start: 0.9587 (mtmt) cc_final: 0.9204 (mttp) REVERT: D 211 PHE cc_start: 0.8187 (t80) cc_final: 0.7794 (t80) REVERT: D 280 LEU cc_start: 0.9175 (tp) cc_final: 0.8934 (tp) REVERT: D 324 TYR cc_start: 0.7844 (p90) cc_final: 0.7169 (p90) REVERT: D 435 MET cc_start: 0.9042 (mmm) cc_final: 0.8749 (mmm) REVERT: D 497 MET cc_start: 0.8997 (tmm) cc_final: 0.8560 (tmm) REVERT: D 509 TYR cc_start: 0.9132 (t80) cc_final: 0.8408 (t80) REVERT: D 556 SER cc_start: 0.9259 (m) cc_final: 0.8898 (p) REVERT: D 557 ILE cc_start: 0.9308 (pt) cc_final: 0.8936 (tp) REVERT: D 577 MET cc_start: 0.8099 (mmm) cc_final: 0.7726 (mmm) REVERT: D 584 ARG cc_start: 0.8765 (mmt180) cc_final: 0.8540 (mmt180) REVERT: D 603 MET cc_start: 0.8458 (mtt) cc_final: 0.8183 (mtt) outliers start: 1 outliers final: 0 residues processed: 544 average time/residue: 0.1284 time to fit residues: 111.7165 Evaluate side-chains 447 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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: 3.9990 chunk 233 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 0.0060 chunk 178 optimal weight: 0.8980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 572 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** 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 = 0.3342 r_free = 0.3342 target = 0.096948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.079811 restraints weight = 56122.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.082306 restraints weight = 34146.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.083774 restraints weight = 23781.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.085187 restraints weight = 18830.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.086052 restraints weight = 15279.739| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20108 Z= 0.157 Angle : 0.858 14.131 27268 Z= 0.407 Chirality : 0.046 0.176 3092 Planarity : 0.004 0.066 3448 Dihedral : 6.631 115.309 2700 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.09 % Allowed : 0.76 % Favored : 99.15 % 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: -2.01 (0.17), residues: 2436 helix: -0.37 (0.14), residues: 1296 sheet: -6.35 (0.14), residues: 64 loop : -2.20 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 589 TYR 0.023 0.001 TYR B 432 PHE 0.045 0.002 PHE C 504 TRP 0.035 0.002 TRP A 583 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00373 (20104) covalent geometry : angle 0.85837 (27268) hydrogen bonds : bond 0.03723 ( 808) hydrogen bonds : angle 4.75842 ( 2292) Misc. bond : bond 0.00038 ( 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 546 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 544 time to evaluate : 0.745 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: A 78 MET cc_start: 0.7367 (pmm) cc_final: 0.5956 (tmm) REVERT: A 99 MET cc_start: 0.8764 (mmp) cc_final: 0.8527 (mmp) REVERT: A 110 MET cc_start: 0.8537 (mmm) cc_final: 0.7438 (mmm) REVERT: A 127 ASN cc_start: 0.8084 (p0) cc_final: 0.7179 (p0) REVERT: A 209 LYS cc_start: 0.9582 (mtmt) cc_final: 0.9216 (mttp) REVERT: A 211 PHE cc_start: 0.8256 (t80) cc_final: 0.7696 (t80) REVERT: A 280 LEU cc_start: 0.9114 (tp) cc_final: 0.8876 (tp) REVERT: A 298 THR cc_start: 0.8792 (m) cc_final: 0.8555 (p) REVERT: A 324 TYR cc_start: 0.7854 (p90) cc_final: 0.7022 (p90) REVERT: A 364 ASP cc_start: 0.9024 (m-30) cc_final: 0.8792 (t70) REVERT: A 368 LEU cc_start: 0.9355 (pt) cc_final: 0.9069 (mp) REVERT: A 485 MET cc_start: 0.9032 (mmt) cc_final: 0.8452 (mmt) REVERT: A 509 TYR cc_start: 0.9088 (t80) cc_final: 0.8346 (t80) REVERT: A 515 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 556 SER cc_start: 0.9428 (m) cc_final: 0.9037 (p) REVERT: A 557 ILE cc_start: 0.9410 (pt) cc_final: 0.9033 (tp) REVERT: A 583 TRP cc_start: 0.7700 (m-90) cc_final: 0.7321 (m-90) REVERT: A 603 MET cc_start: 0.8384 (mtt) cc_final: 0.8129 (mtt) REVERT: B 51 LEU cc_start: 0.8900 (mt) cc_final: 0.8633 (tt) REVERT: B 110 MET cc_start: 0.8248 (mmm) cc_final: 0.7254 (mmm) REVERT: B 180 ARG cc_start: 0.8974 (mtt90) cc_final: 0.8533 (ttm-80) REVERT: B 209 LYS cc_start: 0.9583 (mtmt) cc_final: 0.9204 (mttp) REVERT: B 211 PHE cc_start: 0.8139 (t80) cc_final: 0.7802 (t80) REVERT: B 280 LEU cc_start: 0.9184 (tp) cc_final: 0.8922 (tp) REVERT: B 298 THR cc_start: 0.8814 (m) cc_final: 0.8548 (p) REVERT: B 303 GLU cc_start: 0.8676 (tp30) cc_final: 0.8276 (tp30) REVERT: B 315 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 324 TYR cc_start: 0.7905 (p90) cc_final: 0.7044 (p90) REVERT: B 364 ASP cc_start: 0.8997 (m-30) cc_final: 0.8787 (t70) REVERT: B 368 LEU cc_start: 0.9348 (pt) cc_final: 0.9066 (mp) REVERT: B 485 MET cc_start: 0.9136 (mmt) cc_final: 0.8633 (mmt) REVERT: B 509 TYR cc_start: 0.9109 (t80) cc_final: 0.8399 (t80) REVERT: B 556 SER cc_start: 0.9361 (m) cc_final: 0.9027 (p) REVERT: B 557 ILE cc_start: 0.9347 (pt) cc_final: 0.8935 (tp) REVERT: B 584 ARG cc_start: 0.8519 (mmt180) cc_final: 0.8185 (mmt180) REVERT: B 603 MET cc_start: 0.8351 (mtt) cc_final: 0.8074 (mtt) REVERT: C 51 LEU cc_start: 0.8883 (mt) cc_final: 0.8611 (tt) REVERT: C 110 MET cc_start: 0.8425 (mmm) cc_final: 0.6932 (mmm) REVERT: C 209 LYS cc_start: 0.9606 (mtmt) cc_final: 0.9202 (mttt) REVERT: C 211 PHE cc_start: 0.8171 (t80) cc_final: 0.7811 (t80) REVERT: C 245 LYS cc_start: 0.8954 (mttt) cc_final: 0.8721 (mptt) REVERT: C 280 LEU cc_start: 0.9044 (tp) cc_final: 0.8783 (tp) REVERT: C 298 THR cc_start: 0.8833 (m) cc_final: 0.8545 (p) REVERT: C 303 GLU cc_start: 0.8681 (tp30) cc_final: 0.8308 (tp30) REVERT: C 364 ASP cc_start: 0.9009 (m-30) cc_final: 0.8791 (t70) REVERT: C 424 PRO cc_start: 0.8368 (Cg_endo) cc_final: 0.8110 (Cg_exo) REVERT: C 485 MET cc_start: 0.9289 (mmt) cc_final: 0.8575 (mmt) REVERT: C 497 MET cc_start: 0.9012 (tmm) cc_final: 0.8599 (tmm) REVERT: C 509 TYR cc_start: 0.9095 (t80) cc_final: 0.8366 (t80) REVERT: C 556 SER cc_start: 0.9363 (m) cc_final: 0.8993 (p) REVERT: C 577 MET cc_start: 0.8612 (mmm) cc_final: 0.6584 (mmm) REVERT: C 583 TRP cc_start: 0.7719 (m-90) cc_final: 0.7408 (m-90) REVERT: C 584 ARG cc_start: 0.8634 (mmt180) cc_final: 0.8030 (mmt180) REVERT: C 603 MET cc_start: 0.8399 (mtt) cc_final: 0.8175 (mtt) REVERT: C 613 TRP cc_start: 0.8437 (t60) cc_final: 0.8105 (t60) REVERT: D 78 MET cc_start: 0.6871 (pmm) cc_final: 0.5268 (tmm) REVERT: D 110 MET cc_start: 0.8234 (mmm) cc_final: 0.7070 (mmm) REVERT: D 127 ASN cc_start: 0.8609 (m110) cc_final: 0.8281 (p0) REVERT: D 209 LYS cc_start: 0.9574 (mtmt) cc_final: 0.9199 (mttt) REVERT: D 211 PHE cc_start: 0.8149 (t80) cc_final: 0.7814 (t80) REVERT: D 280 LEU cc_start: 0.9110 (tp) cc_final: 0.8849 (tp) REVERT: D 435 MET cc_start: 0.9037 (mmm) cc_final: 0.8739 (mmm) REVERT: D 497 MET cc_start: 0.8989 (tmm) cc_final: 0.8574 (tmm) REVERT: D 509 TYR cc_start: 0.9106 (t80) cc_final: 0.8349 (t80) REVERT: D 556 SER cc_start: 0.9306 (m) cc_final: 0.8940 (p) REVERT: D 557 ILE cc_start: 0.9330 (pt) cc_final: 0.8972 (tp) REVERT: D 570 MET cc_start: 0.7966 (ppp) cc_final: 0.7599 (tmm) REVERT: D 577 MET cc_start: 0.8031 (mmm) cc_final: 0.7543 (mmm) REVERT: D 583 TRP cc_start: 0.7903 (m-90) cc_final: 0.7374 (m-90) REVERT: D 603 MET cc_start: 0.8397 (mtt) cc_final: 0.8170 (mtt) REVERT: D 613 TRP cc_start: 0.8403 (t60) cc_final: 0.8066 (t60) outliers start: 2 outliers final: 0 residues processed: 546 average time/residue: 0.1315 time to fit residues: 114.5372 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 : 0.749 ------------------------------------------------------------------------------- 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: 7.9990 chunk 53 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 209 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 211 optimal weight: 0.4980 chunk 228 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 197 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 572 ASN ** C 36 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081445 restraints weight = 55660.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.083969 restraints weight = 34118.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085745 restraints weight = 23917.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087024 restraints weight = 18408.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.087890 restraints weight = 15122.619| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5220 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= 0.143 Angle : 0.855 14.503 27268 Z= 0.400 Chirality : 0.045 0.188 3092 Planarity : 0.004 0.072 3448 Dihedral : 5.992 76.077 2700 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.05 % Allowed : 0.19 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.98 (0.17), residues: 2436 helix: -0.32 (0.14), residues: 1292 sheet: -6.40 (0.13), residues: 64 loop : -2.21 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 589 TYR 0.014 0.001 TYR A 555 PHE 0.047 0.002 PHE B 504 TRP 0.025 0.001 TRP D 583 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00336 (20104) covalent geometry : angle 0.85526 (27268) hydrogen bonds : bond 0.03683 ( 808) hydrogen bonds : angle 4.68145 ( 2292) Misc. bond : bond 0.00039 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3426.39 seconds wall clock time: 60 minutes 2.54 seconds (3602.54 seconds total)