Starting phenix.real_space_refine on Fri Jul 3 09:20:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i6v_35208/07_2026/8i6v_35208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6v_35208/07_2026/8i6v_35208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i6v_35208/07_2026/8i6v_35208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6v_35208/07_2026/8i6v_35208.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i6v_35208/07_2026/8i6v_35208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6v_35208/07_2026/8i6v_35208.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8i6v_35208/07_2026/8i6v_35208.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i6v_35208/07_2026/8i6v_35208.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Mn 1 7.51 5 P 7 5.49 5 S 36 5.16 5 C 8515 2.51 5 N 2219 2.21 5 O 2394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13172 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 811 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "B" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 804 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "D" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5640 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 31, 'TRANS': 646} Chain breaks: 4 Chain: "E" Number of atoms: 5022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 5022 Classifications: {'peptide': 611} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 584} Chain breaks: 3 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' MN': 1, '3PO': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 3.08, per 1000 atoms: 0.23 Number of scatterers: 13172 At special positions: 0 Unit cell: (149.776, 117.438, 154.031, 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) Mn 1 24.99 S 36 16.00 P 7 15.00 O 2394 8.00 N 2219 7.00 C 8515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 742.2 milliseconds 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 62.7% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 22 through 53 removed outlier: 4.244A pdb=" N PHE A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 40 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 84 removed outlier: 4.048A pdb=" N GLY A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 removed outlier: 3.910A pdb=" N PHE A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 52 Processing helix chain 'B' and resid 55 through 87 Processing helix chain 'B' and resid 99 through 122 removed outlier: 3.867A pdb=" N TYR B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 53 removed outlier: 4.120A pdb=" N PHE C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 89 Processing helix chain 'C' and resid 98 through 121 removed outlier: 3.772A pdb=" N THR C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 11 through 16 Proline residue: D 14 - end of helix No H-bonds generated for 'chain 'D' and resid 11 through 16' Processing helix chain 'D' and resid 21 through 29 Processing helix chain 'D' and resid 30 through 36 removed outlier: 3.509A pdb=" N ILE D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 87 removed outlier: 3.511A pdb=" N ARG D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 134 removed outlier: 3.797A pdb=" N PHE D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 151 removed outlier: 4.025A pdb=" N LEU D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 177 removed outlier: 3.574A pdb=" N TYR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 177 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 removed outlier: 4.024A pdb=" N LYS D 193 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 226 Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 329 through 333 removed outlier: 3.600A pdb=" N ASP D 332 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS D 333 " --> pdb=" O LEU D 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 333' Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 375 through 389 removed outlier: 3.559A pdb=" N ASN D 379 " --> pdb=" O PRO D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 413 removed outlier: 3.527A pdb=" N LEU D 395 " --> pdb=" O GLN D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 479 removed outlier: 3.648A pdb=" N ARG D 477 " --> pdb=" O ASN D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 515 Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 550 through 554 Processing helix chain 'D' and resid 560 through 587 removed outlier: 3.835A pdb=" N ARG D 587 " --> pdb=" O ASP D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 726 removed outlier: 4.064A pdb=" N TRP D 700 " --> pdb=" O GLU D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 731 Processing helix chain 'D' and resid 733 through 767 removed outlier: 3.787A pdb=" N ASP D 738 " --> pdb=" O PRO D 734 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU D 739 " --> pdb=" O GLN D 735 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 740 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 741 " --> pdb=" O ALA D 737 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR D 742 " --> pdb=" O ASP D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 805 removed outlier: 3.715A pdb=" N ALA D 784 " --> pdb=" O PRO D 780 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D 803 " --> pdb=" O PHE D 799 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG D 804 " --> pdb=" O LYS D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 834 removed outlier: 3.662A pdb=" N GLN D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP D 827 " --> pdb=" O LYS D 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 removed outlier: 3.754A pdb=" N LYS E 9 " --> pdb=" O GLU E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 21 through 37 Processing helix chain 'E' and resid 41 through 87 Processing helix chain 'E' and resid 97 through 138 Processing helix chain 'E' and resid 142 through 153 removed outlier: 3.831A pdb=" N VAL E 148 " --> pdb=" O PRO E 144 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG E 149 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 178 Processing helix chain 'E' and resid 207 through 217 removed outlier: 3.660A pdb=" N LYS E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 255 Processing helix chain 'E' and resid 303 through 309 Processing helix chain 'E' and resid 313 through 318 removed outlier: 3.575A pdb=" N PHE E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 325 Processing helix chain 'E' and resid 328 through 350 Processing helix chain 'E' and resid 413 through 415 No H-bonds generated for 'chain 'E' and resid 413 through 415' Processing helix chain 'E' and resid 438 through 446 Processing helix chain 'E' and resid 457 through 467 Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.585A pdb=" N ASP E 482 " --> pdb=" O PRO E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 524 Processing helix chain 'E' and resid 623 through 648 removed outlier: 4.079A pdb=" N GLU E 628 " --> pdb=" O TYR E 624 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE E 637 " --> pdb=" O SER E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 655 No H-bonds generated for 'chain 'E' and resid 653 through 655' Processing helix chain 'E' and resid 656 through 687 removed outlier: 3.769A pdb=" N SER E 660 " --> pdb=" O ALA E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 718 Processing sheet with id=AA1, first strand: chain 'D' and resid 353 through 361 removed outlier: 4.383A pdb=" N ILE D 336 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU D 322 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 418 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP D 302 " --> pdb=" O PRO D 416 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL D 417 " --> pdb=" O ARG D 447 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG D 447 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG D 419 " --> pdb=" O TYR D 445 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR D 445 " --> pdb=" O ARG D 419 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR D 421 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE D 443 " --> pdb=" O THR D 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 353 through 361 removed outlier: 4.383A pdb=" N ILE D 336 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU D 322 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 418 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP D 302 " --> pdb=" O PRO D 416 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL D 417 " --> pdb=" O ARG D 447 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG D 447 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG D 419 " --> pdb=" O TYR D 445 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR D 445 " --> pdb=" O ARG D 419 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR D 421 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE D 443 " --> pdb=" O THR D 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'D' and resid 246 through 247 removed outlier: 3.528A pdb=" N ASN D 246 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR E 275 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TYR E 268 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA E 260 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N HIS E 263 " --> pdb=" O PHE E 242 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE E 237 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE E 358 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER E 239 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG E 356 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR E 241 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL E 354 " --> pdb=" O ARG E 384 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG E 384 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG E 356 " --> pdb=" O MET E 382 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET E 382 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE E 358 " --> pdb=" O LEU E 380 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU E 380 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU E 366 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL E 372 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 246 through 247 removed outlier: 3.528A pdb=" N ASN D 246 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR E 275 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TYR E 268 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA E 260 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N HIS E 263 " --> pdb=" O PHE E 242 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE E 237 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE E 358 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER E 239 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG E 356 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR E 241 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL E 354 " --> pdb=" O ARG E 384 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG E 384 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG E 356 " --> pdb=" O MET E 382 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET E 382 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE E 358 " --> pdb=" O LEU E 380 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU E 380 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU E 366 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL E 372 " --> pdb=" O LEU E 366 " (cutoff:3.500A) removed outlier: 15.661A pdb=" N ASP E 369 " --> pdb=" O GLN E 432 " (cutoff:3.500A) removed outlier: 12.059A pdb=" N GLN E 432 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG E 371 " --> pdb=" O GLN E 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 893 hydrogen bonds defined for protein. 2604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2184 1.32 - 1.45: 3611 1.45 - 1.57: 7598 1.57 - 1.69: 5 1.69 - 1.82: 64 Bond restraints: 13462 Sorted by residual: bond pdb=" O12 POV C 201 " pdb=" P POV C 201 " ideal model delta sigma weight residual 1.657 1.739 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" N VAL D 74 " pdb=" CA VAL D 74 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.19e-02 7.06e+03 1.22e+01 bond pdb=" C PRO D 456 " pdb=" O PRO D 456 " ideal model delta sigma weight residual 1.233 1.197 0.036 1.16e-02 7.43e+03 9.43e+00 bond pdb=" N SER D 43 " pdb=" CA SER D 43 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.14e-02 7.69e+03 9.35e+00 bond pdb=" O3 PO4 D 901 " pdb=" P PO4 D 901 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.07e+00 ... (remaining 13457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 17997 2.54 - 5.07: 174 5.07 - 7.61: 22 7.61 - 10.15: 4 10.15 - 12.68: 1 Bond angle restraints: 18198 Sorted by residual: angle pdb=" C ARG C 90 " pdb=" CA ARG C 90 " pdb=" CB ARG C 90 " ideal model delta sigma weight residual 116.54 110.06 6.48 1.15e+00 7.56e-01 3.18e+01 angle pdb=" C ASN D 454 " pdb=" N ARG D 455 " pdb=" CA ARG D 455 " ideal model delta sigma weight residual 123.15 117.28 5.87 1.21e+00 6.83e-01 2.35e+01 angle pdb=" N LEU D 81 " pdb=" CA LEU D 81 " pdb=" C LEU D 81 " ideal model delta sigma weight residual 112.34 106.65 5.69 1.30e+00 5.92e-01 1.92e+01 angle pdb=" PA 3PO E 801 " pdb=" O3A 3PO E 801 " pdb=" PB 3PO E 801 " ideal model delta sigma weight residual 136.78 124.10 12.68 3.00e+00 1.11e-01 1.79e+01 angle pdb=" CA PRO D 456 " pdb=" C PRO D 456 " pdb=" O PRO D 456 " ideal model delta sigma weight residual 121.34 116.82 4.52 1.14e+00 7.69e-01 1.57e+01 ... (remaining 18193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.12: 7618 27.12 - 54.23: 426 54.23 - 81.35: 22 81.35 - 108.46: 13 108.46 - 135.58: 1 Dihedral angle restraints: 8080 sinusoidal: 3398 harmonic: 4682 Sorted by residual: dihedral pdb=" CA TYR D 507 " pdb=" C TYR D 507 " pdb=" N GLU D 508 " pdb=" CA GLU D 508 " ideal model delta harmonic sigma weight residual 180.00 -155.57 -24.43 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" C37 POV C 201 " pdb=" C38 POV C 201 " pdb=" C39 POV C 201 " pdb="C310 POV C 201 " ideal model delta sinusoidal sigma weight residual -179.61 -44.03 -135.58 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" C27 POV C 201 " pdb=" C28 POV C 201 " pdb=" C29 POV C 201 " pdb="C210 POV C 201 " ideal model delta sinusoidal sigma weight residual 127.48 -131.63 -100.89 1 3.00e+01 1.11e-03 1.27e+01 ... (remaining 8077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1460 0.039 - 0.079: 417 0.079 - 0.118: 101 0.118 - 0.158: 22 0.158 - 0.197: 5 Chirality restraints: 2005 Sorted by residual: chirality pdb=" CA LYS D 86 " pdb=" N LYS D 86 " pdb=" C LYS D 86 " pdb=" CB LYS D 86 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA LEU D 75 " pdb=" N LEU D 75 " pdb=" C LEU D 75 " pdb=" CB LEU D 75 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA THR D 85 " pdb=" N THR D 85 " pdb=" C THR D 85 " pdb=" CB THR D 85 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 2002 not shown) Planarity restraints: 2299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 100 " -0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO A 101 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 34 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C ILE D 34 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE D 34 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS D 35 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 779 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO D 780 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 780 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 780 " 0.028 5.00e-02 4.00e+02 ... (remaining 2296 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 135 2.67 - 3.23: 12014 3.23 - 3.79: 19537 3.79 - 4.34: 25695 4.34 - 4.90: 43822 Nonbonded interactions: 101203 Sorted by model distance: nonbonded pdb=" O3A 3PO E 801 " pdb="MN MN E 802 " model vdw 2.114 2.320 nonbonded pdb=" O ALA D 189 " pdb=" OG SER D 192 " model vdw 2.242 3.040 nonbonded pdb=" O1G 3PO E 801 " pdb=" O HOH E 901 " model vdw 2.259 3.040 nonbonded pdb=" O PRO D 780 " pdb=" OH TYR E 631 " model vdw 2.274 3.040 nonbonded pdb=" O4 PO4 D 901 " pdb=" O HOH D1001 " model vdw 2.302 3.040 ... (remaining 101198 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 22 through 121) selection = (chain 'B' and resid 22 through 121) selection = (chain 'C' and resid 22 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.004 0.082 13462 Z= 0.207 Angle : 0.602 12.684 18198 Z= 0.328 Chirality : 0.041 0.197 2005 Planarity : 0.004 0.085 2299 Dihedral : 15.377 135.580 5044 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.25 % Favored : 96.56 % Rotamer: Outliers : 0.28 % Allowed : 0.76 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.38 (0.22), residues: 1570 helix: 2.69 (0.17), residues: 924 sheet: 1.38 (0.39), residues: 176 loop : -0.71 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 196 TYR 0.027 0.001 TYR D 169 PHE 0.017 0.001 PHE C 39 TRP 0.013 0.001 TRP E 267 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.21 (13462) covalent geometry : angle 0.60243 / 0.33 (18198) hydrogen bonds : bond 0.12946 / 8.15 ( 832) hydrogen bonds : angle 4.78932 / 3.53 ( 2604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: B 64 LEU cc_start: 0.5598 (tp) cc_final: 0.5394 (tp) REVERT: D 141 VAL cc_start: 0.8887 (m) cc_final: 0.8594 (p) REVERT: D 343 PHE cc_start: 0.7503 (m-80) cc_final: 0.7303 (m-80) REVERT: E 323 LYS cc_start: 0.7648 (ttmm) cc_final: 0.7316 (ptmt) outliers start: 4 outliers final: 3 residues processed: 174 average time/residue: 0.1104 time to fit residues: 28.8487 Evaluate side-chains 140 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 86 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN D 84 ASN D 95 ASN D 351 ASN E 435 GLN E 717 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.185750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142484 restraints weight = 15580.176| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.04 r_work: 0.3135 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13462 Z= 0.168 Angle : 0.536 7.918 18198 Z= 0.278 Chirality : 0.040 0.141 2005 Planarity : 0.005 0.055 2299 Dihedral : 6.244 80.302 1805 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.11 % Allowed : 6.87 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.36 (0.22), residues: 1570 helix: 2.73 (0.16), residues: 937 sheet: 1.25 (0.39), residues: 176 loop : -0.90 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 296 TYR 0.020 0.001 TYR D 169 PHE 0.023 0.002 PHE B 27 TRP 0.013 0.001 TRP E 267 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (13462) covalent geometry : angle 0.53615 / 0.28 (18198) hydrogen bonds : bond 0.05346 / 3.51 ( 832) hydrogen bonds : angle 3.70355 / 2.74 ( 2604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: D 54 GLU cc_start: 0.8104 (tt0) cc_final: 0.7829 (tt0) REVERT: D 86 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.7036 (pttt) REVERT: D 90 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7146 (mtmm) REVERT: D 141 VAL cc_start: 0.8972 (m) cc_final: 0.8606 (p) REVERT: D 173 PHE cc_start: 0.7711 (t80) cc_final: 0.7288 (t80) REVERT: D 343 PHE cc_start: 0.7663 (m-80) cc_final: 0.7264 (m-80) REVERT: E 323 LYS cc_start: 0.7849 (ttmm) cc_final: 0.7411 (ptmt) REVERT: E 717 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6595 (t0) outliers start: 16 outliers final: 10 residues processed: 156 average time/residue: 0.1203 time to fit residues: 27.4304 Evaluate side-chains 147 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 666 THR Chi-restraints excluded: chain E residue 717 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 70 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 717 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.187199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144800 restraints weight = 15771.788| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.01 r_work: 0.3161 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13462 Z= 0.115 Angle : 0.468 6.479 18198 Z= 0.243 Chirality : 0.038 0.147 2005 Planarity : 0.004 0.051 2299 Dihedral : 5.774 73.615 1804 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.25 % Allowed : 8.74 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.63 (0.22), residues: 1570 helix: 2.93 (0.17), residues: 943 sheet: 1.31 (0.40), residues: 176 loop : -0.79 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 689 TYR 0.019 0.001 TYR D 169 PHE 0.016 0.001 PHE B 53 TRP 0.015 0.001 TRP E 267 HIS 0.002 0.001 HIS D 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (13462) covalent geometry : angle 0.46804 / 0.24 (18198) hydrogen bonds : bond 0.04670 / 3.07 ( 832) hydrogen bonds : angle 3.47652 / 2.57 ( 2604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.514 Fit side-chains REVERT: A 70 MET cc_start: 0.6182 (tpp) cc_final: 0.5906 (tpp) REVERT: D 54 GLU cc_start: 0.8110 (tt0) cc_final: 0.7841 (tt0) REVERT: D 86 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7101 (pttt) REVERT: D 141 VAL cc_start: 0.8941 (m) cc_final: 0.8579 (p) REVERT: D 173 PHE cc_start: 0.7716 (t80) cc_final: 0.7354 (t80) REVERT: D 343 PHE cc_start: 0.7661 (m-80) cc_final: 0.7258 (m-80) REVERT: E 149 ARG cc_start: 0.7791 (mmm160) cc_final: 0.7580 (mmm160) REVERT: E 323 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7419 (ptmt) outliers start: 18 outliers final: 13 residues processed: 157 average time/residue: 0.1194 time to fit residues: 27.5126 Evaluate side-chains 151 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 647 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 114 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 0.0870 chunk 69 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 111 GLN E 717 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.188163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144180 restraints weight = 15770.780| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.07 r_work: 0.3175 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13462 Z= 0.104 Angle : 0.453 7.484 18198 Z= 0.233 Chirality : 0.037 0.146 2005 Planarity : 0.004 0.052 2299 Dihedral : 5.409 68.241 1802 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.32 % Allowed : 9.72 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.81 (0.22), residues: 1570 helix: 3.06 (0.17), residues: 943 sheet: 1.41 (0.40), residues: 176 loop : -0.71 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 196 TYR 0.018 0.001 TYR D 169 PHE 0.015 0.001 PHE B 53 TRP 0.015 0.001 TRP E 267 HIS 0.002 0.000 HIS E 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (13462) covalent geometry : angle 0.45258 / 0.23 (18198) hydrogen bonds : bond 0.04236 / 2.79 ( 832) hydrogen bonds : angle 3.33006 / 2.47 ( 2604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.531 Fit side-chains REVERT: A 70 MET cc_start: 0.6468 (tpp) cc_final: 0.6236 (tpp) REVERT: D 54 GLU cc_start: 0.8008 (tt0) cc_final: 0.7762 (tt0) REVERT: D 141 VAL cc_start: 0.8909 (m) cc_final: 0.8555 (p) REVERT: D 173 PHE cc_start: 0.7756 (t80) cc_final: 0.7429 (t80) REVERT: D 343 PHE cc_start: 0.7704 (m-80) cc_final: 0.7305 (m-80) REVERT: E 323 LYS cc_start: 0.7851 (ttmm) cc_final: 0.7457 (ptmt) outliers start: 19 outliers final: 15 residues processed: 147 average time/residue: 0.1139 time to fit residues: 24.7096 Evaluate side-chains 145 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 717 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 152 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.186947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145189 restraints weight = 15814.299| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.04 r_work: 0.3151 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13462 Z= 0.127 Angle : 0.473 8.525 18198 Z= 0.244 Chirality : 0.038 0.140 2005 Planarity : 0.004 0.051 2299 Dihedral : 5.382 64.885 1798 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.25 % Allowed : 11.03 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.75 (0.22), residues: 1570 helix: 3.03 (0.16), residues: 943 sheet: 1.33 (0.40), residues: 176 loop : -0.73 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 196 TYR 0.019 0.001 TYR D 169 PHE 0.020 0.001 PHE D 205 TRP 0.012 0.001 TRP E 267 HIS 0.002 0.001 HIS D 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (13462) covalent geometry : angle 0.47308 / 0.24 (18198) hydrogen bonds : bond 0.04508 / 2.98 ( 832) hydrogen bonds : angle 3.36867 / 2.49 ( 2604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.529 Fit side-chains REVERT: A 70 MET cc_start: 0.6639 (tpp) cc_final: 0.6418 (mmt) REVERT: D 141 VAL cc_start: 0.8910 (m) cc_final: 0.8552 (p) REVERT: D 173 PHE cc_start: 0.7763 (t80) cc_final: 0.7433 (t80) REVERT: D 343 PHE cc_start: 0.7723 (m-80) cc_final: 0.7341 (m-80) REVERT: E 323 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7482 (ptmt) outliers start: 18 outliers final: 16 residues processed: 144 average time/residue: 0.1109 time to fit residues: 23.6794 Evaluate side-chains 151 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 123 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 80 optimal weight: 0.0060 chunk 110 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 826 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.186895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146426 restraints weight = 15682.549| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.91 r_work: 0.3168 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13462 Z= 0.119 Angle : 0.466 9.949 18198 Z= 0.241 Chirality : 0.038 0.141 2005 Planarity : 0.004 0.050 2299 Dihedral : 5.285 60.547 1798 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.60 % Allowed : 11.52 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.80 (0.22), residues: 1570 helix: 3.05 (0.16), residues: 947 sheet: 1.33 (0.40), residues: 176 loop : -0.70 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 196 TYR 0.017 0.001 TYR D 169 PHE 0.016 0.001 PHE B 53 TRP 0.013 0.001 TRP E 267 HIS 0.002 0.001 HIS D 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13462) covalent geometry : angle 0.46591 / 0.24 (18198) hydrogen bonds : bond 0.04404 / 2.91 ( 832) hydrogen bonds : angle 3.32425 / 2.46 ( 2604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.543 Fit side-chains REVERT: A 70 MET cc_start: 0.6669 (tpp) cc_final: 0.6460 (mmt) REVERT: D 141 VAL cc_start: 0.8922 (m) cc_final: 0.8548 (p) REVERT: D 173 PHE cc_start: 0.7766 (t80) cc_final: 0.7441 (t80) REVERT: D 343 PHE cc_start: 0.7732 (m-80) cc_final: 0.7335 (m-80) REVERT: D 527 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8914 (mp) REVERT: E 323 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7497 (ptmt) outliers start: 23 outliers final: 17 residues processed: 154 average time/residue: 0.1073 time to fit residues: 24.5557 Evaluate side-chains 154 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 96 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.184965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142316 restraints weight = 15680.003| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.99 r_work: 0.3096 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13462 Z= 0.167 Angle : 0.528 10.500 18198 Z= 0.273 Chirality : 0.040 0.139 2005 Planarity : 0.005 0.051 2299 Dihedral : 5.521 61.021 1798 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.39 % Allowed : 12.14 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.55 (0.22), residues: 1570 helix: 2.87 (0.16), residues: 943 sheet: 1.13 (0.40), residues: 178 loop : -0.76 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 196 TYR 0.020 0.001 TYR D 169 PHE 0.017 0.002 PHE B 53 TRP 0.011 0.001 TRP E 440 HIS 0.003 0.001 HIS D 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (13462) covalent geometry : angle 0.52805 / 0.27 (18198) hydrogen bonds : bond 0.05221 / 3.46 ( 832) hydrogen bonds : angle 3.51181 / 2.59 ( 2604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.514 Fit side-chains REVERT: A 70 MET cc_start: 0.6720 (tpp) cc_final: 0.6508 (mmt) REVERT: D 141 VAL cc_start: 0.8929 (m) cc_final: 0.8587 (p) REVERT: D 173 PHE cc_start: 0.7837 (t80) cc_final: 0.7529 (t80) REVERT: D 343 PHE cc_start: 0.7665 (m-80) cc_final: 0.7305 (m-80) REVERT: D 527 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8959 (mp) REVERT: E 323 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7498 (ptmt) outliers start: 20 outliers final: 19 residues processed: 151 average time/residue: 0.1090 time to fit residues: 24.5287 Evaluate side-chains 152 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 666 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 64 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 66 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.187763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147657 restraints weight = 15655.578| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.90 r_work: 0.3177 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13462 Z= 0.103 Angle : 0.459 9.082 18198 Z= 0.237 Chirality : 0.037 0.145 2005 Planarity : 0.004 0.051 2299 Dihedral : 5.258 59.644 1798 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.39 % Allowed : 12.91 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.83 (0.22), residues: 1570 helix: 3.09 (0.16), residues: 943 sheet: 1.39 (0.40), residues: 174 loop : -0.70 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 689 TYR 0.017 0.001 TYR D 169 PHE 0.016 0.001 PHE B 53 TRP 0.018 0.001 TRP E 267 HIS 0.002 0.000 HIS D 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (13462) covalent geometry : angle 0.45918 / 0.24 (18198) hydrogen bonds : bond 0.04190 / 2.77 ( 832) hydrogen bonds : angle 3.30500 / 2.44 ( 2604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.528 Fit side-chains REVERT: C 70 MET cc_start: 0.4969 (ttt) cc_final: 0.4668 (ptp) REVERT: D 141 VAL cc_start: 0.8909 (m) cc_final: 0.8536 (p) REVERT: D 173 PHE cc_start: 0.7779 (t80) cc_final: 0.7508 (t80) REVERT: D 343 PHE cc_start: 0.7762 (m-80) cc_final: 0.7330 (m-80) REVERT: D 527 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8882 (mp) REVERT: D 585 MET cc_start: 0.6678 (ptm) cc_final: 0.6350 (ppp) REVERT: E 323 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7497 (ptmt) outliers start: 20 outliers final: 17 residues processed: 150 average time/residue: 0.1089 time to fit residues: 24.1523 Evaluate side-chains 153 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 137 optimal weight: 0.0770 chunk 15 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.187040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133187 restraints weight = 15393.963| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.14 r_work: 0.3110 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13462 Z= 0.102 Angle : 0.470 11.956 18198 Z= 0.239 Chirality : 0.037 0.147 2005 Planarity : 0.004 0.050 2299 Dihedral : 5.093 59.189 1798 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.18 % Allowed : 13.39 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 3.01 (0.22), residues: 1570 helix: 3.19 (0.16), residues: 941 sheet: 1.40 (0.40), residues: 176 loop : -0.47 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 196 TYR 0.016 0.001 TYR D 169 PHE 0.023 0.001 PHE D 205 TRP 0.016 0.001 TRP E 267 HIS 0.002 0.000 HIS E 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (13462) covalent geometry : angle 0.46969 / 0.24 (18198) hydrogen bonds : bond 0.04018 / 2.66 ( 832) hydrogen bonds : angle 3.24564 / 2.40 ( 2604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.497 Fit side-chains REVERT: B 53 PHE cc_start: 0.6968 (m-80) cc_final: 0.6406 (m-80) REVERT: B 81 HIS cc_start: 0.6065 (m-70) cc_final: 0.5840 (m-70) REVERT: C 70 MET cc_start: 0.4970 (ttt) cc_final: 0.4730 (ptp) REVERT: D 141 VAL cc_start: 0.8871 (m) cc_final: 0.8509 (p) REVERT: D 173 PHE cc_start: 0.7786 (t80) cc_final: 0.7542 (t80) REVERT: D 343 PHE cc_start: 0.7711 (m-80) cc_final: 0.7311 (m-80) REVERT: D 527 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8860 (mp) REVERT: D 585 MET cc_start: 0.6601 (ptm) cc_final: 0.6276 (ppp) REVERT: E 323 LYS cc_start: 0.7891 (ttmm) cc_final: 0.7488 (ptmt) outliers start: 17 outliers final: 15 residues processed: 148 average time/residue: 0.1099 time to fit residues: 23.9040 Evaluate side-chains 148 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.185500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.144004 restraints weight = 15700.954| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.00 r_work: 0.3110 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13462 Z= 0.164 Angle : 0.529 11.542 18198 Z= 0.271 Chirality : 0.040 0.160 2005 Planarity : 0.005 0.051 2299 Dihedral : 5.382 62.283 1798 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.32 % Allowed : 13.46 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.67 (0.22), residues: 1570 helix: 2.96 (0.16), residues: 947 sheet: 1.14 (0.40), residues: 178 loop : -0.72 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 302 TYR 0.020 0.001 TYR D 169 PHE 0.024 0.002 PHE D 205 TRP 0.009 0.001 TRP E 440 HIS 0.003 0.001 HIS D 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (13462) covalent geometry : angle 0.52920 / 0.27 (18198) hydrogen bonds : bond 0.04897 / 3.25 ( 832) hydrogen bonds : angle 3.44054 / 2.54 ( 2604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.549 Fit side-chains REVERT: D 141 VAL cc_start: 0.8896 (m) cc_final: 0.8560 (p) REVERT: D 173 PHE cc_start: 0.7846 (t80) cc_final: 0.7565 (t80) REVERT: D 343 PHE cc_start: 0.7711 (m-80) cc_final: 0.7319 (m-80) REVERT: D 527 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8932 (mp) REVERT: D 585 MET cc_start: 0.6539 (ptm) cc_final: 0.6272 (ppp) REVERT: E 323 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7520 (ptmt) outliers start: 19 outliers final: 17 residues processed: 145 average time/residue: 0.1002 time to fit residues: 21.7470 Evaluate side-chains 147 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 647 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 117 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 92 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.186991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134840 restraints weight = 15303.500| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.13 r_work: 0.3167 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13462 Z= 0.101 Angle : 0.471 11.020 18198 Z= 0.240 Chirality : 0.037 0.147 2005 Planarity : 0.004 0.051 2299 Dihedral : 5.111 60.023 1798 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.97 % Allowed : 13.60 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 3.00 (0.22), residues: 1570 helix: 3.19 (0.16), residues: 940 sheet: 1.42 (0.40), residues: 174 loop : -0.49 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 689 TYR 0.016 0.001 TYR D 169 PHE 0.023 0.001 PHE D 205 TRP 0.019 0.001 TRP E 267 HIS 0.002 0.000 HIS D 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (13462) covalent geometry : angle 0.47129 / 0.24 (18198) hydrogen bonds : bond 0.03998 / 2.63 ( 832) hydrogen bonds : angle 3.27668 / 2.42 ( 2604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3947.74 seconds wall clock time: 68 minutes 6.89 seconds (4086.89 seconds total)