Starting phenix.real_space_refine on Sun Jul 5 01:23:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ubm_64011/07_2026/9ubm_64011_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ubm_64011/07_2026/9ubm_64011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ubm_64011/07_2026/9ubm_64011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ubm_64011/07_2026/9ubm_64011.map" model { file = "/net/cci-nas-00/data/ceres_data/9ubm_64011/07_2026/9ubm_64011_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ubm_64011/07_2026/9ubm_64011_trim.cif" } resolution = 2.94 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= 0.020 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 30 5.49 5 Mg 6 5.21 5 S 99 5.16 5 C 15011 2.51 5 N 4367 2.21 5 O 4403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s 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: 23922 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3015 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 359} Chain: "F" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3048 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 365} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "Y" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 2} Link IDs: {'rna2p': 3, 'rna3p': 2} Chain: "A" Number of atoms: 4317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4317 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 519} Chain breaks: 8 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 4317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4317 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 516} Chain breaks: 6 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4436 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 529} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 4327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4327 Classifications: {'peptide': 556} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 520} Chain breaks: 8 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.59, per 1000 atoms: 0.23 Number of scatterers: 23922 At special positions: 0 Unit cell: (97.86, 147.256, 215.292, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 99 16.00 P 30 15.00 Mg 6 11.99 O 4403 8.00 N 4367 7.00 C 15011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 461 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 260 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 262 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 262 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 260 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 461 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 262 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 461 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 260 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 461 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 260 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 262 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 262 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 260 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 461 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 260 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 262 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 461 " 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5660 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 11 sheets defined 56.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 231 through 239 Processing helix chain 'E' and resid 247 through 254 Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.630A pdb=" N HIS E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 306 through 313 Processing helix chain 'E' and resid 320 through 323 removed outlier: 3.825A pdb=" N LYS E 323 " --> pdb=" O ALA E 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 320 through 323' Processing helix chain 'E' and resid 324 through 342 Processing helix chain 'E' and resid 352 through 357 Processing helix chain 'E' and resid 362 through 380 Processing helix chain 'E' and resid 381 through 386 removed outlier: 6.061A pdb=" N ASP E 384 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 420 Processing helix chain 'E' and resid 432 through 435 removed outlier: 3.855A pdb=" N GLU E 435 " --> pdb=" O ALA E 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 432 through 435' Processing helix chain 'E' and resid 436 through 446 removed outlier: 3.565A pdb=" N ALA E 442 " --> pdb=" O THR E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 455 Processing helix chain 'E' and resid 467 through 477 Processing helix chain 'E' and resid 488 through 491 removed outlier: 3.704A pdb=" N ARG E 491 " --> pdb=" O HIS E 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 488 through 491' Processing helix chain 'E' and resid 492 through 503 Processing helix chain 'E' and resid 509 through 517 Processing helix chain 'E' and resid 532 through 540 Processing helix chain 'E' and resid 549 through 554 Processing helix chain 'E' and resid 556 through 568 removed outlier: 4.303A pdb=" N ALA E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG E 566 " --> pdb=" O LEU E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 587 removed outlier: 3.520A pdb=" N VAL E 576 " --> pdb=" O THR E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 602 Processing helix chain 'F' and resid 224 through 230 removed outlier: 3.651A pdb=" N ALA F 228 " --> pdb=" O PRO F 225 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA F 229 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP F 230 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 247 through 254 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 269 through 279 removed outlier: 3.601A pdb=" N LEU F 273 " --> pdb=" O HIS F 269 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'F' and resid 305 through 313 removed outlier: 4.106A pdb=" N ARG F 309 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 323 removed outlier: 3.792A pdb=" N LYS F 323 " --> pdb=" O ALA F 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 320 through 323' Processing helix chain 'F' and resid 324 through 342 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 362 through 381 Processing helix chain 'F' and resid 382 through 386 Processing helix chain 'F' and resid 403 through 420 removed outlier: 3.597A pdb=" N ALA F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU F 418 " --> pdb=" O ILE F 414 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 435 No H-bonds generated for 'chain 'F' and resid 433 through 435' Processing helix chain 'F' and resid 436 through 446 Processing helix chain 'F' and resid 448 through 454 Processing helix chain 'F' and resid 467 through 477 Processing helix chain 'F' and resid 492 through 503 Processing helix chain 'F' and resid 509 through 517 Processing helix chain 'F' and resid 532 through 539 Processing helix chain 'F' and resid 549 through 554 Processing helix chain 'F' and resid 556 through 568 removed outlier: 4.829A pdb=" N ALA F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG F 566 " --> pdb=" O LEU F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 587 Processing helix chain 'F' and resid 590 through 602 Processing helix chain 'A' and resid 14 through 23 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 73 through 91 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 167 through 172 removed outlier: 4.173A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 215 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.735A pdb=" N GLU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 320 through 323 removed outlier: 3.837A pdb=" N LYS A 323 " --> pdb=" O ALA A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 324 through 342 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.581A pdb=" N ALA A 357 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.525A pdb=" N THR A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.362A pdb=" N GLU A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.813A pdb=" N PHE A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Proline residue: A 450 - end of helix removed outlier: 3.581A pdb=" N ARG A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.825A pdb=" N ILE A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.698A pdb=" N THR A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.565A pdb=" N LEU B 21 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B 22 " --> pdb=" O MET B 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 22' Processing helix chain 'B' and resid 39 through 53 removed outlier: 4.538A pdb=" N GLY B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 91 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.849A pdb=" N MET B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.914A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.578A pdb=" N ALA B 228 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 247 through 254 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 326 through 327 No H-bonds generated for 'chain 'B' and resid 326 through 327' Processing helix chain 'B' and resid 329 through 329 No H-bonds generated for 'chain 'B' and resid 329 through 329' Processing helix chain 'B' and resid 330 through 342 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 362 through 380 Processing helix chain 'B' and resid 404 through 420 removed outlier: 4.000A pdb=" N GLU B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 removed outlier: 5.035A pdb=" N PHE B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 492 through 503 Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.550A pdb=" N THR B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 587 Processing helix chain 'B' and resid 590 through 602 Processing helix chain 'C' and resid 14 through 20 Processing helix chain 'C' and resid 39 through 53 removed outlier: 4.399A pdb=" N GLY C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.821A pdb=" N LEU C 78 " --> pdb=" O GLN C 74 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE C 79 " --> pdb=" O ASP C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 105 through 120 Processing helix chain 'C' and resid 144 through 152 Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.999A pdb=" N LEU C 172 " --> pdb=" O PRO C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 215 removed outlier: 4.117A pdb=" N GLN C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 247 through 254 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 269 through 278 removed outlier: 4.027A pdb=" N LEU C 273 " --> pdb=" O HIS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 306 through 313 Processing helix chain 'C' and resid 324 through 342 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 362 through 381 Processing helix chain 'C' and resid 382 through 386 Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 467 through 477 removed outlier: 3.615A pdb=" N ILE C 471 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 492 through 503 Processing helix chain 'C' and resid 509 through 517 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 549 through 554 removed outlier: 3.531A pdb=" N GLN C 554 " --> pdb=" O LEU C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 568 removed outlier: 4.070A pdb=" N ALA C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 587 Processing helix chain 'C' and resid 590 through 602 Processing helix chain 'D' and resid 14 through 23 removed outlier: 3.853A pdb=" N LEU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 54 removed outlier: 3.549A pdb=" N HIS D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 167 through 173 removed outlier: 3.530A pdb=" N LEU D 172 " --> pdb=" O PRO D 168 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 173 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 216 Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 247 through 254 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 270 through 279 Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 306 through 313 Processing helix chain 'D' and resid 324 through 342 Processing helix chain 'D' and resid 352 through 357 Processing helix chain 'D' and resid 362 through 380 Processing helix chain 'D' and resid 403 through 420 Processing helix chain 'D' and resid 441 through 445 Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'D' and resid 467 through 477 removed outlier: 4.379A pdb=" N ILE D 471 " --> pdb=" O ASP D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 503 Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.612A pdb=" N THR D 564 " --> pdb=" O ASN D 560 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 587 Processing helix chain 'D' and resid 590 through 602 Processing sheet with id=AA1, first strand: chain 'E' and resid 256 through 257 removed outlier: 7.392A pdb=" N LYS E 256 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA E 347 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N CYS E 261 " --> pdb=" O ARG E 350 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 256 through 257 removed outlier: 7.392A pdb=" N LYS E 256 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA E 347 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA E 345 " --> pdb=" O HIS E 388 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASN E 390 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA E 347 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU E 392 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE E 349 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR E 394 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N CYS E 351 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 11.840A pdb=" N VAL E 389 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N GLY E 428 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU E 391 " --> pdb=" O GLY E 428 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP E 430 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU E 393 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL E 458 " --> pdb=" O ARG E 482 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLY E 484 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL E 460 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU E 483 " --> pdb=" O GLU E 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 256 through 262 removed outlier: 4.582A pdb=" N VAL F 257 " --> pdb=" O TYR F 346 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLU F 348 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU F 259 " --> pdb=" O GLU F 348 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG F 350 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS F 261 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA F 345 " --> pdb=" O HIS F 388 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN F 390 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA F 347 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU F 392 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE F 349 " --> pdb=" O LEU F 392 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR F 394 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS F 351 " --> pdb=" O THR F 394 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL F 426 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU F 391 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY F 428 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL F 458 " --> pdb=" O ARG F 482 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLY F 484 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL F 460 " --> pdb=" O GLY F 484 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 63 removed outlier: 3.594A pdb=" N SER A 62 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 3 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N CYS A 100 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU A 5 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG A 97 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE A 125 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE A 99 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU A 123 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY A 162 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE A 125 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG A 160 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 256 through 262 removed outlier: 6.059A pdb=" N LYS A 256 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 346 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N HIS A 260 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ARG A 350 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N HIS A 262 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A 426 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 391 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 428 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 458 " --> pdb=" O ARG A 482 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N GLY A 484 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 460 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 483 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.294A pdb=" N LEU B 4 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B 33 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS B 6 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 3 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N CYS B 100 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU B 5 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG B 97 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE B 125 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE B 99 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 256 through 262 removed outlier: 7.244A pdb=" N LYS B 256 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA B 347 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU B 258 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE B 349 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N HIS B 260 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N CYS B 351 " --> pdb=" O HIS B 260 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N HIS B 262 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B 388 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 426 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 391 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 428 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL B 458 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLY B 484 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 460 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.695A pdb=" N ARG C 97 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE C 125 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE C 99 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 30 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER C 62 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 32 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL C 64 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR C 34 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 256 through 262 removed outlier: 4.458A pdb=" N VAL C 257 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLU C 348 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU C 259 " --> pdb=" O GLU C 348 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG C 350 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS C 261 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 345 " --> pdb=" O HIS C 388 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASN C 390 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA C 347 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU C 392 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE C 349 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR C 394 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS C 351 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 426 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU C 391 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 428 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 457 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL C 458 " --> pdb=" O ARG C 482 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY C 484 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 460 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 483 " --> pdb=" O GLU C 507 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 63 removed outlier: 6.393A pdb=" N ILE D 3 " --> pdb=" O TYR D 98 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N CYS D 100 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU D 5 " --> pdb=" O CYS D 100 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG D 97 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE D 125 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE D 99 " --> pdb=" O PHE D 125 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N CYS D 122 " --> pdb=" O PRO D 163 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D 124 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 256 through 262 removed outlier: 5.996A pdb=" N LYS D 256 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR D 346 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS D 260 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG D 350 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N HIS D 262 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL D 426 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU D 391 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY D 428 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL D 427 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N THR D 459 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 429 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N HIS D 461 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU D 431 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL D 458 " --> pdb=" O ARG D 482 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLY D 484 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 460 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU D 483 " --> pdb=" O GLU D 507 " (cutoff:3.500A) 1126 hydrogen bonds defined for protein. 3174 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: 4.20 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8137 1.34 - 1.46: 4956 1.46 - 1.58: 11223 1.58 - 1.70: 45 1.70 - 1.82: 138 Bond restraints: 24499 Sorted by residual: bond pdb=" N9 A Y 4 " pdb=" C4 A Y 4 " ideal model delta sigma weight residual 1.374 1.386 -0.012 6.00e-03 2.78e+04 4.14e+00 bond pdb=" C ALA C 175 " pdb=" N PRO C 176 " ideal model delta sigma weight residual 1.335 1.356 -0.020 1.36e-02 5.41e+03 2.24e+00 bond pdb=" CB GLU E 308 " pdb=" CG GLU E 308 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" N ASP B 66 " pdb=" CA ASP B 66 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.11e+00 bond pdb=" CB GLU D 308 " pdb=" CG GLU D 308 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.83e+00 ... (remaining 24494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 32839 2.01 - 4.02: 515 4.02 - 6.02: 80 6.02 - 8.03: 17 8.03 - 10.04: 7 Bond angle restraints: 33458 Sorted by residual: angle pdb=" CA MET A 19 " pdb=" CB MET A 19 " pdb=" CG MET A 19 " ideal model delta sigma weight residual 114.10 122.72 -8.62 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CA GLU B 435 " pdb=" CB GLU B 435 " pdb=" CG GLU B 435 " ideal model delta sigma weight residual 114.10 122.46 -8.36 2.00e+00 2.50e-01 1.75e+01 angle pdb=" C GLU D 52 " pdb=" N MET D 53 " pdb=" CA MET D 53 " ideal model delta sigma weight residual 121.94 113.83 8.11 2.00e+00 2.50e-01 1.64e+01 angle pdb=" N ALA C 320 " pdb=" CA ALA C 320 " pdb=" C ALA C 320 " ideal model delta sigma weight residual 113.18 108.40 4.78 1.33e+00 5.65e-01 1.29e+01 angle pdb=" N MET A 19 " pdb=" CA MET A 19 " pdb=" CB MET A 19 " ideal model delta sigma weight residual 110.16 115.41 -5.25 1.48e+00 4.57e-01 1.26e+01 ... (remaining 33453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 14192 34.83 - 69.67: 571 69.67 - 104.50: 43 104.50 - 139.34: 0 139.34 - 174.17: 1 Dihedral angle restraints: 14807 sinusoidal: 6113 harmonic: 8694 Sorted by residual: dihedral pdb=" CA GLU B 17 " pdb=" C GLU B 17 " pdb=" N ALA B 18 " pdb=" CA ALA B 18 " ideal model delta harmonic sigma weight residual -180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" C4' A Y 1 " pdb=" C3' A Y 1 " pdb=" O3' A Y 1 " pdb=" P A Y 2 " ideal model delta sinusoidal sigma weight residual -110.00 64.17 -174.17 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA MET B 53 " pdb=" C MET B 53 " pdb=" N HIS B 54 " pdb=" CA HIS B 54 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 14804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3233 0.058 - 0.116: 465 0.116 - 0.173: 33 0.173 - 0.231: 3 0.231 - 0.289: 16 Chirality restraints: 3750 Sorted by residual: chirality pdb=" C2' ATP E 701 " pdb=" C1' ATP E 701 " pdb=" C3' ATP E 701 " pdb=" O2' ATP E 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C3' ATP A 701 " pdb=" C2' ATP A 701 " pdb=" C4' ATP A 701 " pdb=" O3' ATP A 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' ATP C 701 " pdb=" C1' ATP C 701 " pdb=" C3' ATP C 701 " pdb=" O2' ATP C 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3747 not shown) Planarity restraints: 4311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 385 " -0.208 9.50e-02 1.11e+02 9.37e-02 6.45e+00 pdb=" NE ARG E 385 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG E 385 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG E 385 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 385 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 175 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO C 176 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 176 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 176 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 56 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 57 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.027 5.00e-02 4.00e+02 ... (remaining 4308 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 221 2.54 - 3.13: 18577 3.13 - 3.72: 38992 3.72 - 4.31: 53326 4.31 - 4.90: 90158 Nonbonded interactions: 201274 Sorted by model distance: nonbonded pdb=" O3G ATP B 701 " pdb="MG MG B 703 " model vdw 1.948 2.170 nonbonded pdb=" O3B ATP B 701 " pdb="MG MG B 703 " model vdw 1.968 2.170 nonbonded pdb=" O2B ATP A 701 " pdb="MG MG A 703 " model vdw 1.981 2.170 nonbonded pdb=" OD1 ASP B 548 " pdb="ZN ZN B 702 " model vdw 1.994 2.230 nonbonded pdb=" O2G ATP A 701 " pdb="MG MG A 703 " model vdw 2.053 2.170 ... (remaining 201269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 7 or resid 16 or (resid 17 through 18 and (name \ N or name CA or name C or name O or name CB )) or resid 19 through 38 or (resid \ 39 and (name N or name CA or name C or name O or name CB )) or resid 40 through \ 152 or resid 159 through 173 or resid 197 through 198 or (resid 199 and (name N \ or name CA or name C or name O or name CB )) or resid 200 through 327 or resid 3 \ 29 through 396 or (resid 397 through 398 and (name N or name CA or name C or nam \ e O or name CB )) or resid 399 through 433 or resid 446 through 608 or resid 701 \ through 703)) selection = (chain 'B' and (resid 1 through 16 or (resid 17 through 18 and (name N or name C \ A or name C or name O or name CB )) or resid 19 through 20 or (resid 21 and (nam \ e N or name CA or name C or name O or name CB )) or resid 22 through 26 or (resi \ d 27 and (name N or name CA or name C or name O or name CB )) or resid 28 throug \ h 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or re \ sid 52 through 66 or resid 68 through 69 or resid 72 through 91 or resid 94 thro \ ugh 102 or resid 107 through 159 or (resid 160 and (name N or name CA or name C \ or name O or name CB )) or resid 161 through 198 or (resid 199 and (name N or na \ me CA or name C or name O or name CB )) or resid 200 through 433 or resid 446 th \ rough 608 or resid 701 through 703)) selection = (chain 'C' and (resid 1 through 7 or resid 16 through 20 or (resid 21 and (name \ N or name CA or name C or name O or name CB )) or resid 22 through 26 or (resid \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 38 or (resid 39 and (name N or name CA or name C or name O or name CB )) or resi \ d 40 through 50 or (resid 51 and (name N or name CA or name C or name O or name \ CB )) or resid 52 through 66 or resid 68 through 69 or resid 72 through 91 or re \ sid 94 through 102 or resid 107 through 159 or (resid 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 through 173 or (resid 197 and (n \ ame N or name CA or name C or name O or name CB )) or resid 198 or (resid 199 an \ d (name N or name CA or name C or name O or name CB )) or resid 200 through 327 \ or resid 329 through 397 or (resid 398 and (name N or name CA or name C or name \ O or name CB )) or resid 399 through 703)) selection = (chain 'D' and (resid 1 through 7 or resid 16 or (resid 17 through 18 and (name \ N or name CA or name C or name O or name CB )) or resid 19 through 38 or (resid \ 39 and (name N or name CA or name C or name O or name CB )) or resid 40 through \ 102 or resid 107 through 152 or resid 159 through 173 or (resid 197 and (name N \ or name CA or name C or name O or name CB )) or resid 198 through 327 or resid 3 \ 29 through 396 or (resid 397 through 398 and (name N or name CA or name C or nam \ e O or name CB )) or resid 399 through 433 or resid 446 through 608 or resid 701 \ through 703)) } ncs_group { reference = (chain 'E' and (resid 220 through 396 or (resid 397 through 398 and (name N or n \ ame CA or name C or name O or name CB )) or resid 399 through 703)) selection = (chain 'F' and (resid 220 through 607 or resid 701 through 703)) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 4.260 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.350 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 0.140 24517 Z= 0.180 Angle : 0.616 10.040 33458 Z= 0.326 Chirality : 0.044 0.289 3750 Planarity : 0.005 0.094 4311 Dihedral : 17.499 174.175 9147 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 2.26 % Allowed : 24.23 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 2951 helix: 1.80 (0.14), residues: 1404 sheet: 0.03 (0.30), residues: 346 loop : -0.15 (0.19), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 385 TYR 0.031 0.002 TYR D 356 PHE 0.019 0.001 PHE D 266 TRP 0.022 0.002 TRP A 237 HIS 0.013 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (24499) covalent geometry : angle 0.61574 / 0.33 (33458) hydrogen bonds : bond 0.16657 / 10.96 ( 1126) hydrogen bonds : angle 6.04685 / 4.48 ( 3174) metal coordination : bond 0.03318 / 2.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7443 (tpp) cc_final: 0.6336 (pp-130) REVERT: A 108 ILE cc_start: 0.3729 (OUTLIER) cc_final: 0.3519 (pp) REVERT: A 203 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8570 (tp30) REVERT: B 33 LEU cc_start: 0.9147 (tp) cc_final: 0.8946 (tp) REVERT: D 198 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6692 (tm) REVERT: D 203 GLU cc_start: 0.8186 (tp30) cc_final: 0.7935 (tp30) outliers start: 55 outliers final: 19 residues processed: 325 average time/residue: 0.8169 time to fit residues: 297.3575 Evaluate side-chains 202 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 544 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 372 ASN E 376 GLN E 390 ASN E 473 GLN B 580 GLN C 113 GLN C 269 HIS C 488 HIS ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.109051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.068774 restraints weight = 45967.221| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.08 r_work: 0.2745 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24517 Z= 0.195 Angle : 0.636 10.479 33458 Z= 0.319 Chirality : 0.043 0.205 3750 Planarity : 0.005 0.059 4311 Dihedral : 9.595 169.311 3641 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 4.14 % Allowed : 22.22 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.16), residues: 2951 helix: 1.87 (0.14), residues: 1453 sheet: -0.07 (0.29), residues: 349 loop : -0.18 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 49 TYR 0.010 0.001 TYR C 50 PHE 0.020 0.002 PHE A 79 TRP 0.034 0.001 TRP F 237 HIS 0.006 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (24499) covalent geometry : angle 0.63574 / 0.32 (33458) hydrogen bonds : bond 0.04508 / 3.03 ( 1126) hydrogen bonds : angle 5.08424 / 3.73 ( 3174) metal coordination : bond 0.00561 / 0.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 195 time to evaluate : 0.855 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: E 600 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8300 (ttt90) REVERT: F 237 TRP cc_start: 0.8781 (t-100) cc_final: 0.8383 (t-100) REVERT: F 258 GLU cc_start: 0.8735 (tp30) cc_final: 0.8376 (tp30) REVERT: F 421 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9087 (mtpp) REVERT: A 1 MET cc_start: 0.7146 (tpp) cc_final: 0.6513 (pp-130) REVERT: A 74 GLN cc_start: 0.8455 (mp10) cc_final: 0.7955 (tp40) REVERT: A 98 TYR cc_start: 0.8092 (m-80) cc_final: 0.7568 (m-80) REVERT: A 203 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8847 (tp30) REVERT: A 285 SER cc_start: 0.9518 (OUTLIER) cc_final: 0.9174 (m) REVERT: A 315 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8867 (m-30) REVERT: A 443 MET cc_start: 0.9098 (mmp) cc_final: 0.8585 (mpt) REVERT: A 449 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 2 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7516 (ptp-110) REVERT: B 19 MET cc_start: 0.5727 (mpt) cc_final: 0.5154 (mpt) REVERT: B 50 TYR cc_start: 0.6977 (t80) cc_final: 0.6713 (t80) REVERT: B 308 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: B 358 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8379 (p) REVERT: B 466 ASP cc_start: 0.8645 (p0) cc_final: 0.8348 (t0) REVERT: B 544 THR cc_start: 0.9191 (m) cc_final: 0.8762 (p) REVERT: B 575 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: C 63 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6726 (mtp180) REVERT: C 169 GLN cc_start: 0.8987 (mp10) cc_final: 0.8523 (mp10) REVERT: C 171 ARG cc_start: 0.8655 (mtp85) cc_final: 0.8433 (mtm110) REVERT: C 196 MET cc_start: 0.6804 (ttm) cc_final: 0.6465 (tpp) REVERT: C 248 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8595 (mtpp) REVERT: C 258 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8139 (mm-30) REVERT: D 90 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7712 (mmm160) REVERT: D 198 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5800 (tm) REVERT: D 203 GLU cc_start: 0.8724 (tp30) cc_final: 0.8192 (tp30) outliers start: 101 outliers final: 24 residues processed: 283 average time/residue: 0.7236 time to fit residues: 232.2650 Evaluate side-chains 212 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 459 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 161 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 296 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN B 580 GLN C 269 HIS C 390 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.068310 restraints weight = 45791.944| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.05 r_work: 0.2764 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24517 Z= 0.171 Angle : 0.590 11.656 33458 Z= 0.292 Chirality : 0.041 0.218 3750 Planarity : 0.005 0.057 4311 Dihedral : 9.491 171.041 3620 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Rotamer: Outliers : 3.65 % Allowed : 21.85 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.16), residues: 2951 helix: 1.99 (0.14), residues: 1440 sheet: -0.15 (0.29), residues: 359 loop : -0.12 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 405 TYR 0.012 0.001 TYR D 310 PHE 0.033 0.002 PHE B 59 TRP 0.012 0.001 TRP C 364 HIS 0.006 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (24499) covalent geometry : angle 0.58974 / 0.29 (33458) hydrogen bonds : bond 0.04021 / 2.72 ( 1126) hydrogen bonds : angle 4.77943 / 3.48 ( 3174) metal coordination : bond 0.00298 / 0.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 191 time to evaluate : 0.999 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: E 600 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8235 (ttt90) REVERT: F 237 TRP cc_start: 0.8849 (t-100) cc_final: 0.8405 (t-100) REVERT: F 258 GLU cc_start: 0.8702 (tp30) cc_final: 0.8412 (tp30) REVERT: F 421 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9065 (mtpp) REVERT: A 1 MET cc_start: 0.7211 (tpp) cc_final: 0.6506 (pp-130) REVERT: A 19 MET cc_start: 0.7191 (mpp) cc_final: 0.6969 (mpp) REVERT: A 74 GLN cc_start: 0.8465 (mp10) cc_final: 0.7924 (tp40) REVERT: A 75 ASP cc_start: 0.8633 (m-30) cc_final: 0.8328 (t0) REVERT: A 98 TYR cc_start: 0.8187 (m-80) cc_final: 0.7709 (m-80) REVERT: A 108 ILE cc_start: 0.3314 (OUTLIER) cc_final: 0.3016 (pp) REVERT: A 203 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8829 (tp30) REVERT: A 285 SER cc_start: 0.9530 (OUTLIER) cc_final: 0.9171 (m) REVERT: A 315 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8894 (m-30) REVERT: A 434 PHE cc_start: 0.8803 (t80) cc_final: 0.8545 (t80) REVERT: A 437 ARG cc_start: 0.8901 (mtp-110) cc_final: 0.8563 (tpm170) REVERT: A 449 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 2 ARG cc_start: 0.7828 (ptp90) cc_final: 0.7620 (ptp-110) REVERT: B 50 TYR cc_start: 0.6780 (t80) cc_final: 0.6542 (t80) REVERT: B 59 PHE cc_start: 0.5303 (t80) cc_final: 0.4564 (t80) REVERT: B 308 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8059 (tp30) REVERT: B 466 ASP cc_start: 0.8664 (p0) cc_final: 0.8266 (t0) REVERT: B 544 THR cc_start: 0.9314 (m) cc_final: 0.8971 (p) REVERT: B 575 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: C 27 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.5597 (m-10) REVERT: C 53 MET cc_start: 0.8558 (pmm) cc_final: 0.8331 (pp-130) REVERT: C 63 ARG cc_start: 0.7297 (mtp85) cc_final: 0.7000 (mtp180) REVERT: C 80 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: C 169 GLN cc_start: 0.9065 (mp10) cc_final: 0.8700 (mp10) REVERT: C 190 TRP cc_start: 0.7076 (m100) cc_final: 0.6857 (m100) REVERT: C 196 MET cc_start: 0.7018 (ttm) cc_final: 0.6566 (tpp) REVERT: C 248 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8715 (mtpp) REVERT: C 258 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8318 (mm-30) REVERT: C 469 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: C 568 CYS cc_start: 0.8823 (m) cc_final: 0.8585 (m) REVERT: D 90 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7720 (mmm160) REVERT: D 198 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5844 (tm) outliers start: 89 outliers final: 33 residues processed: 267 average time/residue: 0.7299 time to fit residues: 221.1647 Evaluate side-chains 219 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 466 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 111 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 255 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 269 HIS E 376 GLN B 580 GLN C 269 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.109171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.068785 restraints weight = 45612.917| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.04 r_work: 0.2782 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24517 Z= 0.132 Angle : 0.562 11.866 33458 Z= 0.276 Chirality : 0.040 0.222 3750 Planarity : 0.004 0.057 4311 Dihedral : 9.313 171.943 3620 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % Rotamer: Outliers : 3.20 % Allowed : 22.26 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.16), residues: 2951 helix: 2.07 (0.14), residues: 1446 sheet: -0.04 (0.29), residues: 353 loop : -0.05 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 97 TYR 0.014 0.001 TYR D 50 PHE 0.025 0.001 PHE A 79 TRP 0.012 0.001 TRP C 364 HIS 0.005 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (24499) covalent geometry : angle 0.56178 / 0.28 (33458) hydrogen bonds : bond 0.03528 / 2.40 ( 1126) hydrogen bonds : angle 4.55813 / 3.31 ( 3174) metal coordination : bond 0.00215 / 0.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 192 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 237 TRP cc_start: 0.8854 (t-100) cc_final: 0.8397 (t-100) REVERT: F 258 GLU cc_start: 0.8604 (tp30) cc_final: 0.8358 (tp30) REVERT: F 421 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9046 (mtpp) REVERT: F 529 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8419 (pm20) REVERT: A 1 MET cc_start: 0.7238 (tpp) cc_final: 0.6456 (pp-130) REVERT: A 19 MET cc_start: 0.7388 (mpp) cc_final: 0.7155 (mpp) REVERT: A 75 ASP cc_start: 0.8655 (m-30) cc_final: 0.8295 (t0) REVERT: A 98 TYR cc_start: 0.8290 (m-80) cc_final: 0.7788 (m-80) REVERT: A 315 ASP cc_start: 0.9215 (OUTLIER) cc_final: 0.8867 (m-30) REVERT: A 434 PHE cc_start: 0.8815 (t80) cc_final: 0.8509 (t80) REVERT: A 437 ARG cc_start: 0.8876 (mtp-110) cc_final: 0.8526 (tpm170) REVERT: A 449 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 50 TYR cc_start: 0.6762 (t80) cc_final: 0.6539 (t80) REVERT: B 308 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: B 466 ASP cc_start: 0.8679 (p0) cc_final: 0.8315 (t0) REVERT: B 544 THR cc_start: 0.9333 (m) cc_final: 0.9015 (p) REVERT: B 575 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: C 63 ARG cc_start: 0.7387 (mtp85) cc_final: 0.7025 (mtp180) REVERT: C 169 GLN cc_start: 0.9115 (mp10) cc_final: 0.8701 (mp10) REVERT: C 190 TRP cc_start: 0.7055 (m100) cc_final: 0.6755 (m100) REVERT: C 196 MET cc_start: 0.7178 (ttm) cc_final: 0.6718 (tpp) REVERT: C 248 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8696 (mtpp) REVERT: C 258 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8290 (mm-30) REVERT: C 469 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: C 491 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8077 (mtt90) REVERT: C 568 CYS cc_start: 0.8817 (m) cc_final: 0.8596 (m) REVERT: D 2 ARG cc_start: 0.7931 (mpt-90) cc_final: 0.7669 (mmm160) REVERT: D 198 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5795 (tm) outliers start: 78 outliers final: 32 residues processed: 257 average time/residue: 0.7175 time to fit residues: 210.4283 Evaluate side-chains 213 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 459 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 247 optimal weight: 0.1980 chunk 191 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 277 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN B 485 HIS B 580 GLN C 269 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.108165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.067522 restraints weight = 45594.295| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.04 r_work: 0.2759 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24517 Z= 0.190 Angle : 0.581 12.864 33458 Z= 0.284 Chirality : 0.041 0.222 3750 Planarity : 0.004 0.054 4311 Dihedral : 9.206 172.352 3614 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 3.24 % Allowed : 22.10 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.16), residues: 2951 helix: 2.08 (0.14), residues: 1439 sheet: -0.02 (0.29), residues: 353 loop : -0.03 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 2 TYR 0.017 0.001 TYR D 50 PHE 0.028 0.002 PHE B 59 TRP 0.012 0.001 TRP C 364 HIS 0.005 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (24499) covalent geometry : angle 0.58099 / 0.28 (33458) hydrogen bonds : bond 0.03686 / 2.51 ( 1126) hydrogen bonds : angle 4.54309 / 3.30 ( 3174) metal coordination : bond 0.00360 / 0.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 170 time to evaluate : 0.986 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: E 240 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: F 237 TRP cc_start: 0.8866 (t-100) cc_final: 0.8389 (t-100) REVERT: F 258 GLU cc_start: 0.8617 (tp30) cc_final: 0.8334 (tp30) REVERT: F 421 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9072 (mtpp) REVERT: F 529 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8437 (pm20) REVERT: F 575 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7871 (mt-10) REVERT: A 1 MET cc_start: 0.7249 (tpp) cc_final: 0.6486 (pp-130) REVERT: A 75 ASP cc_start: 0.8527 (m-30) cc_final: 0.8315 (t0) REVERT: A 98 TYR cc_start: 0.8393 (m-80) cc_final: 0.7917 (m-80) REVERT: A 248 LYS cc_start: 0.8395 (ttpp) cc_final: 0.8166 (tttm) REVERT: A 285 SER cc_start: 0.9535 (OUTLIER) cc_final: 0.9229 (m) REVERT: A 315 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8824 (m-30) REVERT: A 434 PHE cc_start: 0.8786 (t80) cc_final: 0.8510 (t80) REVERT: A 437 ARG cc_start: 0.8878 (mtp-110) cc_final: 0.8507 (tpm170) REVERT: A 449 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 33 LEU cc_start: 0.9207 (tp) cc_final: 0.8812 (mt) REVERT: B 53 MET cc_start: 0.6676 (ppp) cc_final: 0.6454 (ppp) REVERT: B 308 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8050 (tp30) REVERT: B 544 THR cc_start: 0.9335 (m) cc_final: 0.9021 (p) REVERT: B 575 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: C 22 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8257 (tm) REVERT: C 63 ARG cc_start: 0.7445 (mtp85) cc_final: 0.7083 (mtp180) REVERT: C 112 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8056 (ttp) REVERT: C 169 GLN cc_start: 0.9148 (mp10) cc_final: 0.8680 (mp10) REVERT: C 190 TRP cc_start: 0.7037 (m100) cc_final: 0.6804 (m100) REVERT: C 196 MET cc_start: 0.7259 (ttm) cc_final: 0.6887 (tpp) REVERT: C 248 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8699 (mtpp) REVERT: C 258 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8393 (mm-30) REVERT: C 469 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: C 491 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8082 (mtt90) REVERT: C 568 CYS cc_start: 0.8803 (m) cc_final: 0.8572 (m) REVERT: D 2 ARG cc_start: 0.7933 (mpt-90) cc_final: 0.7634 (mmm160) REVERT: D 198 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5840 (tm) REVERT: D 203 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8077 (tp30) REVERT: D 324 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8387 (t70) outliers start: 79 outliers final: 33 residues processed: 238 average time/residue: 0.6765 time to fit residues: 184.8108 Evaluate side-chains 212 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 459 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 189 optimal weight: 20.0000 chunk 221 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 284 optimal weight: 0.4980 chunk 190 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN F 554 GLN A 76 HIS ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN C 269 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.108753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.068332 restraints weight = 45572.380| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.04 r_work: 0.2774 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24517 Z= 0.137 Angle : 0.566 15.242 33458 Z= 0.275 Chirality : 0.040 0.227 3750 Planarity : 0.004 0.056 4311 Dihedral : 9.145 172.471 3614 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 3.16 % Allowed : 22.39 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.16), residues: 2951 helix: 2.12 (0.14), residues: 1439 sheet: -0.01 (0.29), residues: 355 loop : 0.02 (0.20), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 2 TYR 0.023 0.001 TYR B 50 PHE 0.029 0.001 PHE C 79 TRP 0.012 0.001 TRP C 364 HIS 0.004 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (24499) covalent geometry : angle 0.56605 / 0.28 (33458) hydrogen bonds : bond 0.03412 / 2.35 ( 1126) hydrogen bonds : angle 4.42851 / 3.21 ( 3174) metal coordination : bond 0.00240 / 0.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 178 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 237 TRP cc_start: 0.8893 (t-100) cc_final: 0.8429 (t-100) REVERT: F 421 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9069 (mtpp) REVERT: F 529 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: A 1 MET cc_start: 0.7327 (tpp) cc_final: 0.6408 (pp-130) REVERT: A 19 MET cc_start: 0.7087 (mtt) cc_final: 0.6728 (mpp) REVERT: A 75 ASP cc_start: 0.8492 (m-30) cc_final: 0.8261 (t0) REVERT: A 98 TYR cc_start: 0.8381 (m-80) cc_final: 0.7900 (m-80) REVERT: A 285 SER cc_start: 0.9532 (OUTLIER) cc_final: 0.9252 (m) REVERT: A 315 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8809 (m-30) REVERT: A 434 PHE cc_start: 0.8797 (t80) cc_final: 0.8529 (t80) REVERT: A 437 ARG cc_start: 0.8892 (mtp-110) cc_final: 0.8480 (tpm170) REVERT: A 449 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 86 TRP cc_start: 0.8981 (t60) cc_final: 0.8472 (t-100) REVERT: B 308 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: B 544 THR cc_start: 0.9338 (m) cc_final: 0.9019 (p) REVERT: B 575 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: C 63 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7163 (mtp180) REVERT: C 112 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8137 (ttp) REVERT: C 169 GLN cc_start: 0.9152 (mp10) cc_final: 0.8707 (mp10) REVERT: C 190 TRP cc_start: 0.7087 (m100) cc_final: 0.6759 (m100) REVERT: C 196 MET cc_start: 0.7220 (ttm) cc_final: 0.6486 (tpp) REVERT: C 200 GLN cc_start: 0.9028 (mp10) cc_final: 0.8778 (mp10) REVERT: C 248 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8704 (mtpp) REVERT: C 258 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8303 (mm-30) REVERT: C 469 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: C 491 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (mtt90) REVERT: C 568 CYS cc_start: 0.8799 (m) cc_final: 0.8580 (m) REVERT: C 601 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9006 (mp) REVERT: D 2 ARG cc_start: 0.7897 (mpt-90) cc_final: 0.7571 (mmm160) REVERT: D 198 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5811 (tm) REVERT: D 203 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8076 (tp30) REVERT: D 324 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8384 (t70) outliers start: 77 outliers final: 31 residues processed: 248 average time/residue: 0.6516 time to fit residues: 185.9843 Evaluate side-chains 212 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 459 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 131 optimal weight: 0.5980 chunk 288 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 175 optimal weight: 0.3980 chunk 154 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN A 76 HIS ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.110311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.070664 restraints weight = 45954.341| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.02 r_work: 0.2786 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24517 Z= 0.125 Angle : 0.575 15.053 33458 Z= 0.278 Chirality : 0.040 0.224 3750 Planarity : 0.004 0.062 4311 Dihedral : 9.035 172.186 3612 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 2.54 % Allowed : 23.25 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.16), residues: 2951 helix: 2.15 (0.14), residues: 1443 sheet: -0.11 (0.29), residues: 360 loop : 0.07 (0.20), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 58 TYR 0.036 0.001 TYR B 50 PHE 0.028 0.001 PHE A 79 TRP 0.013 0.001 TRP C 86 HIS 0.004 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (24499) covalent geometry : angle 0.57494 / 0.28 (33458) hydrogen bonds : bond 0.03284 / 2.25 ( 1126) hydrogen bonds : angle 4.35617 / 3.15 ( 3174) metal coordination : bond 0.00179 / 0.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 0.877 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: E 240 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8389 (tp30) REVERT: E 461 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.7514 (m90) REVERT: F 237 TRP cc_start: 0.8885 (t-100) cc_final: 0.8409 (t-100) REVERT: F 258 GLU cc_start: 0.8737 (tp30) cc_final: 0.8438 (tp30) REVERT: F 421 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9074 (mtpp) REVERT: F 529 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: A 1 MET cc_start: 0.7335 (tpp) cc_final: 0.6375 (pp-130) REVERT: A 19 MET cc_start: 0.7213 (mtt) cc_final: 0.6898 (mpp) REVERT: A 75 ASP cc_start: 0.8499 (m-30) cc_final: 0.8225 (t0) REVERT: A 98 TYR cc_start: 0.8434 (m-80) cc_final: 0.7833 (m-80) REVERT: A 285 SER cc_start: 0.9529 (OUTLIER) cc_final: 0.9264 (m) REVERT: A 315 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8818 (m-30) REVERT: A 434 PHE cc_start: 0.8798 (t80) cc_final: 0.8532 (t80) REVERT: A 443 MET cc_start: 0.9237 (mmm) cc_final: 0.8561 (mpt) REVERT: A 449 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7904 (tm-30) REVERT: B 86 TRP cc_start: 0.8965 (t60) cc_final: 0.8456 (t-100) REVERT: B 308 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8084 (tp30) REVERT: B 544 THR cc_start: 0.9331 (m) cc_final: 0.9028 (p) REVERT: B 575 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: C 63 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7386 (mtp180) REVERT: C 112 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8099 (ttp) REVERT: C 169 GLN cc_start: 0.9155 (mp10) cc_final: 0.8703 (mp10) REVERT: C 190 TRP cc_start: 0.7141 (m100) cc_final: 0.6702 (m100) REVERT: C 196 MET cc_start: 0.7200 (ttm) cc_final: 0.6480 (tpp) REVERT: C 200 GLN cc_start: 0.9022 (mp10) cc_final: 0.8758 (mp10) REVERT: C 248 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8704 (mtpp) REVERT: C 258 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8270 (mm-30) REVERT: C 469 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: C 491 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8085 (mtt90) REVERT: C 523 GLU cc_start: 0.8634 (tt0) cc_final: 0.8008 (tm-30) REVERT: C 568 CYS cc_start: 0.8777 (m) cc_final: 0.8562 (m) REVERT: C 601 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8991 (mp) REVERT: D 203 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8081 (tp30) REVERT: D 324 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8352 (t70) outliers start: 62 outliers final: 29 residues processed: 234 average time/residue: 0.7062 time to fit residues: 189.6203 Evaluate side-chains 207 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 446 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 138 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 193 optimal weight: 0.1980 chunk 77 optimal weight: 20.0000 chunk 256 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 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 = 0.3634 r_free = 0.3634 target = 0.107996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.067533 restraints weight = 45557.816| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.03 r_work: 0.2760 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24517 Z= 0.179 Angle : 0.598 15.093 33458 Z= 0.289 Chirality : 0.041 0.238 3750 Planarity : 0.004 0.056 4311 Dihedral : 9.009 173.760 3610 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 2.50 % Allowed : 23.62 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.16), residues: 2951 helix: 2.15 (0.14), residues: 1439 sheet: -0.13 (0.29), residues: 357 loop : 0.04 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 58 TYR 0.042 0.001 TYR B 50 PHE 0.030 0.002 PHE A 79 TRP 0.012 0.001 TRP C 364 HIS 0.004 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (24499) covalent geometry : angle 0.59808 / 0.29 (33458) hydrogen bonds : bond 0.03506 / 2.40 ( 1126) hydrogen bonds : angle 4.39472 / 3.19 ( 3174) metal coordination : bond 0.00316 / 0.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 240 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8294 (tp30) REVERT: E 461 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.7503 (m90) REVERT: F 237 TRP cc_start: 0.8890 (t-100) cc_final: 0.8387 (t-100) REVERT: F 258 GLU cc_start: 0.8756 (tp30) cc_final: 0.8478 (tp30) REVERT: F 421 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9085 (mtpp) REVERT: F 461 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.7928 (m90) REVERT: F 529 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8462 (pm20) REVERT: F 575 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7840 (mt-10) REVERT: A 1 MET cc_start: 0.7337 (tpp) cc_final: 0.6489 (pp-130) REVERT: A 19 MET cc_start: 0.7271 (mtt) cc_final: 0.6946 (mpp) REVERT: A 75 ASP cc_start: 0.8520 (m-30) cc_final: 0.8239 (t0) REVERT: A 98 TYR cc_start: 0.8367 (m-80) cc_final: 0.7927 (m-80) REVERT: A 285 SER cc_start: 0.9542 (OUTLIER) cc_final: 0.9281 (m) REVERT: A 315 ASP cc_start: 0.9228 (OUTLIER) cc_final: 0.8788 (m-30) REVERT: A 434 PHE cc_start: 0.8774 (t80) cc_final: 0.8503 (t80) REVERT: A 443 MET cc_start: 0.9246 (mmm) cc_final: 0.8578 (mpt) REVERT: A 449 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 86 TRP cc_start: 0.8974 (t60) cc_final: 0.8442 (t-100) REVERT: B 308 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: B 544 THR cc_start: 0.9321 (m) cc_final: 0.9002 (p) REVERT: B 575 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: C 112 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8072 (ttp) REVERT: C 169 GLN cc_start: 0.9175 (mp10) cc_final: 0.8742 (mp10) REVERT: C 190 TRP cc_start: 0.7169 (m100) cc_final: 0.6799 (m100) REVERT: C 196 MET cc_start: 0.7163 (ttm) cc_final: 0.6570 (tpp) REVERT: C 200 GLN cc_start: 0.9029 (mp10) cc_final: 0.8759 (mp10) REVERT: C 248 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8747 (mtpp) REVERT: C 258 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8391 (mm-30) REVERT: C 469 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: C 491 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8061 (mtt90) REVERT: C 523 GLU cc_start: 0.8666 (tt0) cc_final: 0.8011 (tm-30) REVERT: C 601 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8995 (mp) REVERT: D 198 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5789 (tm) REVERT: D 203 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8074 (tp30) REVERT: D 324 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8398 (t70) outliers start: 61 outliers final: 31 residues processed: 225 average time/residue: 0.6740 time to fit residues: 173.9010 Evaluate side-chains 210 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 311 MET Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 466 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 149 optimal weight: 0.0770 chunk 250 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 288 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 269 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.108692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.068304 restraints weight = 45731.551| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.06 r_work: 0.2778 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24517 Z= 0.129 Angle : 0.587 15.884 33458 Z= 0.283 Chirality : 0.040 0.219 3750 Planarity : 0.004 0.056 4311 Dihedral : 8.965 172.902 3610 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 2.17 % Allowed : 23.90 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.16), residues: 2951 helix: 2.18 (0.14), residues: 1443 sheet: -0.13 (0.29), residues: 353 loop : 0.09 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 58 TYR 0.049 0.001 TYR B 50 PHE 0.031 0.001 PHE B 79 TRP 0.020 0.001 TRP D 86 HIS 0.003 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (24499) covalent geometry : angle 0.58714 / 0.28 (33458) hydrogen bonds : bond 0.03253 / 2.23 ( 1126) hydrogen bonds : angle 4.32818 / 3.13 ( 3174) metal coordination : bond 0.00203 / 0.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 240 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8288 (tp30) REVERT: E 461 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.7388 (m90) REVERT: F 237 TRP cc_start: 0.8886 (t-100) cc_final: 0.8398 (t-100) REVERT: F 258 GLU cc_start: 0.8715 (tp30) cc_final: 0.8442 (tp30) REVERT: F 421 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9078 (mtpp) REVERT: F 461 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.7902 (m90) REVERT: F 529 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: A 1 MET cc_start: 0.7298 (tpp) cc_final: 0.6440 (pp-130) REVERT: A 19 MET cc_start: 0.7175 (mtt) cc_final: 0.6967 (mpp) REVERT: A 75 ASP cc_start: 0.8500 (m-30) cc_final: 0.8234 (t0) REVERT: A 98 TYR cc_start: 0.8442 (m-80) cc_final: 0.7955 (m-80) REVERT: A 108 ILE cc_start: 0.3933 (OUTLIER) cc_final: 0.3490 (pp) REVERT: A 285 SER cc_start: 0.9521 (OUTLIER) cc_final: 0.9269 (m) REVERT: A 315 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8776 (m-30) REVERT: A 434 PHE cc_start: 0.8773 (t80) cc_final: 0.8510 (t80) REVERT: A 443 MET cc_start: 0.9256 (mmm) cc_final: 0.8612 (mpt) REVERT: A 449 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 86 TRP cc_start: 0.8982 (t60) cc_final: 0.8445 (t-100) REVERT: B 308 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8085 (tp30) REVERT: B 544 THR cc_start: 0.9324 (m) cc_final: 0.9017 (p) REVERT: B 575 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8355 (mt-10) REVERT: C 53 MET cc_start: 0.8375 (pp-130) cc_final: 0.8137 (ppp) REVERT: C 112 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8079 (ttp) REVERT: C 169 GLN cc_start: 0.9174 (mp10) cc_final: 0.8743 (mp10) REVERT: C 190 TRP cc_start: 0.7042 (m100) cc_final: 0.6790 (m100) REVERT: C 196 MET cc_start: 0.7169 (ttm) cc_final: 0.6590 (tpp) REVERT: C 200 GLN cc_start: 0.9038 (mp10) cc_final: 0.8778 (mp10) REVERT: C 248 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8744 (mtpp) REVERT: C 258 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8396 (mm-30) REVERT: C 469 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: C 491 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8086 (mtt90) REVERT: C 523 GLU cc_start: 0.8660 (tt0) cc_final: 0.7978 (tm-30) REVERT: C 568 CYS cc_start: 0.8781 (m) cc_final: 0.8556 (m) REVERT: C 601 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8982 (mp) REVERT: D 198 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5770 (tm) REVERT: D 203 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8073 (tp30) REVERT: D 324 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8375 (t70) outliers start: 53 outliers final: 25 residues processed: 215 average time/residue: 0.7153 time to fit residues: 176.6285 Evaluate side-chains 202 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 85 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 285 optimal weight: 0.6980 chunk 190 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 151 optimal weight: 0.2980 chunk 126 optimal weight: 4.9990 chunk 280 optimal weight: 0.9990 chunk 149 optimal weight: 0.0020 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.068967 restraints weight = 45608.322| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.06 r_work: 0.2789 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24517 Z= 0.113 Angle : 0.603 16.056 33458 Z= 0.289 Chirality : 0.040 0.219 3750 Planarity : 0.004 0.057 4311 Dihedral : 8.941 173.442 3610 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 1.80 % Allowed : 24.48 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.16), residues: 2951 helix: 2.19 (0.14), residues: 1443 sheet: 0.05 (0.30), residues: 324 loop : 0.11 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 440 TYR 0.056 0.001 TYR B 50 PHE 0.031 0.001 PHE B 79 TRP 0.020 0.001 TRP D 86 HIS 0.003 0.001 HIS E 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (24499) covalent geometry : angle 0.60291 / 0.29 (33458) hydrogen bonds : bond 0.03137 / 2.15 ( 1126) hydrogen bonds : angle 4.29925 / 3.11 ( 3174) metal coordination : bond 0.00141 / 0.07 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 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: E 240 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8281 (tp30) REVERT: E 461 HIS cc_start: 0.8653 (OUTLIER) cc_final: 0.7422 (m90) REVERT: F 237 TRP cc_start: 0.8885 (t-100) cc_final: 0.8393 (t-100) REVERT: F 258 GLU cc_start: 0.8674 (tp30) cc_final: 0.8405 (tp30) REVERT: F 421 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9063 (mtpp) REVERT: F 461 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.7820 (m90) REVERT: F 529 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8464 (pm20) REVERT: A 1 MET cc_start: 0.7306 (tpp) cc_final: 0.6431 (pp-130) REVERT: A 19 MET cc_start: 0.7171 (mtt) cc_final: 0.6872 (mpp) REVERT: A 75 ASP cc_start: 0.8494 (m-30) cc_final: 0.8226 (t0) REVERT: A 98 TYR cc_start: 0.8453 (m-80) cc_final: 0.7962 (m-80) REVERT: A 108 ILE cc_start: 0.4007 (OUTLIER) cc_final: 0.3578 (pp) REVERT: A 315 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8802 (m-30) REVERT: A 434 PHE cc_start: 0.8776 (t80) cc_final: 0.8515 (t80) REVERT: A 443 MET cc_start: 0.9256 (mmm) cc_final: 0.8619 (mpt) REVERT: A 449 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 53 MET cc_start: 0.6409 (ppp) cc_final: 0.5731 (pmt) REVERT: B 86 TRP cc_start: 0.8985 (t60) cc_final: 0.8437 (t-100) REVERT: B 308 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8093 (tp30) REVERT: B 544 THR cc_start: 0.9342 (m) cc_final: 0.9052 (p) REVERT: B 575 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: C 53 MET cc_start: 0.8388 (pp-130) cc_final: 0.8174 (ppp) REVERT: C 112 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8094 (ttp) REVERT: C 169 GLN cc_start: 0.9170 (mp10) cc_final: 0.8737 (mp10) REVERT: C 190 TRP cc_start: 0.7055 (m100) cc_final: 0.6820 (m100) REVERT: C 196 MET cc_start: 0.7132 (ttm) cc_final: 0.6554 (tpp) REVERT: C 200 GLN cc_start: 0.9035 (mp10) cc_final: 0.8771 (mp10) REVERT: C 248 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8740 (mtpp) REVERT: C 258 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8396 (mm-30) REVERT: C 469 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: C 491 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8067 (mtt90) REVERT: C 523 GLU cc_start: 0.8675 (tt0) cc_final: 0.7929 (tm-30) REVERT: C 568 CYS cc_start: 0.8772 (m) cc_final: 0.8544 (m) REVERT: C 601 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8943 (mp) REVERT: D 198 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5771 (tm) REVERT: D 203 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8070 (tp30) REVERT: D 324 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8328 (t70) outliers start: 44 outliers final: 24 residues processed: 206 average time/residue: 0.6604 time to fit residues: 156.3116 Evaluate side-chains 201 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 459 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 218 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 101 optimal weight: 0.0050 chunk 265 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 50 optimal weight: 0.0970 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 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 = 0.3647 r_free = 0.3647 target = 0.108500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.067882 restraints weight = 45133.180| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.06 r_work: 0.2752 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24517 Z= 0.130 Angle : 0.599 15.715 33458 Z= 0.287 Chirality : 0.040 0.212 3750 Planarity : 0.004 0.056 4311 Dihedral : 8.896 172.994 3610 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 1.85 % Allowed : 24.60 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.16), residues: 2951 helix: 2.22 (0.14), residues: 1442 sheet: 0.05 (0.30), residues: 330 loop : 0.12 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 440 TYR 0.052 0.001 TYR B 50 PHE 0.032 0.001 PHE B 79 TRP 0.018 0.001 TRP D 86 HIS 0.004 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (24499) covalent geometry : angle 0.59925 / 0.29 (33458) hydrogen bonds : bond 0.03205 / 2.21 ( 1126) hydrogen bonds : angle 4.28195 / 3.10 ( 3174) metal coordination : bond 0.00199 / 0.11 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7268.83 seconds wall clock time: 124 minutes 52.19 seconds (7492.19 seconds total)