Starting phenix.real_space_refine on Sun Sep 13 17:06:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ubm_64011/09_2026/9ubm_64011_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ubm_64011/09_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_64011/09_2026/9ubm_64011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ubm_64011/09_2026/9ubm_64011.map" model { file = "/net/cci-nas-00/data/ceres_data/9ubm_64011/09_2026/9ubm_64011_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ubm_64011/09_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-2.2.1-6174/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: 5.60, 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 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: 0.75 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: 4.62 Time building geometry restraints manager: 2.75 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=" C2' A Y 1 " pdb=" C1' A Y 1 " ideal model delta sigma weight residual 1.526 1.539 -0.013 8.00e-03 1.56e+04 2.63e+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 ... (remaining 24494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 32818 2.01 - 4.02: 536 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=" O4' A Y 1 " pdb=" C1' A Y 1 " pdb=" N9 A Y 1 " ideal model delta sigma weight residual 108.20 104.93 3.27 8.00e-01 1.56e+00 1.67e+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 ... (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: 3219 0.058 - 0.116: 471 0.116 - 0.173: 41 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.820 Find NCS groups from input model: 0.800 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- 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= 0.181 Angle : 0.619 10.040 33458 Z= 0.332 Chirality : 0.045 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 0.61937 / 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 : 0.922 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: 0.3520 (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: 0.8239 time to fit residues: 300.4509 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 : 0.947 ------------------------------------------------------------------------------- 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: 2.9990 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 = 0.109044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.068773 restraints weight = 45949.315| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.08 r_work: 0.2745 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24517 Z= 0.197 Angle : 0.626 10.245 33458 Z= 0.315 Chirality : 0.043 0.393 3750 Planarity : 0.005 0.060 4311 Dihedral : 9.596 171.636 3641 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 4.10 % Allowed : 22.30 % Favored : 73.60 % 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: 1.28 (0.16), residues: 2951 helix: 1.88 (0.14), residues: 1453 sheet: -0.04 (0.29), residues: 347 loop : -0.14 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 573 TYR 0.010 0.001 TYR C 50 PHE 0.020 0.002 PHE A 79 TRP 0.032 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 0.62579 / 0.32 (33458) hydrogen bonds : bond 0.04706 / 3.16 ( 1126) hydrogen bonds : angle 5.07971 / 3.73 ( 3174) metal coordination : bond 0.00340 / 0.19 ( 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 292 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 192 time to evaluate : 0.872 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: 0.8515 (OUTLIER) cc_final: 0.8307 (ttt90) REVERT: F 237 TRP cc_start: 0.8791 (t-100) cc_final: 0.8395 (t-100) REVERT: F 258 GLU cc_start: 0.8739 (tp30) cc_final: 0.8385 (tp30) REVERT: F 421 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9087 (mtpp) REVERT: A 1 MET cc_start: 0.7140 (tpp) cc_final: 0.6515 (pp-130) REVERT: A 74 GLN cc_start: 0.8459 (mp10) cc_final: 0.7952 (tp40) REVERT: A 98 TYR cc_start: 0.8081 (m-80) cc_final: 0.7608 (m-80) REVERT: A 203 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8847 (tp30) REVERT: A 285 SER cc_start: 0.9520 (OUTLIER) cc_final: 0.9184 (m) REVERT: A 315 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8868 (m-30) REVERT: A 443 MET cc_start: 0.9140 (mmp) cc_final: 0.8700 (mpt) REVERT: A 449 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 2 ARG cc_start: 0.7743 (ptp90) cc_final: 0.7513 (ptp-110) REVERT: B 19 MET cc_start: 0.5696 (mpt) cc_final: 0.5131 (mpt) REVERT: B 50 TYR cc_start: 0.6900 (t80) cc_final: 0.6673 (t80) REVERT: B 308 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8078 (tp30) REVERT: B 358 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8384 (p) REVERT: B 434 PHE cc_start: 0.8376 (p90) cc_final: 0.8172 (p90) REVERT: B 466 ASP cc_start: 0.8630 (p0) cc_final: 0.8332 (t0) REVERT: B 544 THR cc_start: 0.9196 (m) cc_final: 0.8768 (p) REVERT: B 575 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: C 169 GLN cc_start: 0.8986 (mp10) cc_final: 0.8516 (mp10) REVERT: C 171 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8420 (mtm110) REVERT: C 196 MET cc_start: 0.6830 (ttm) cc_final: 0.6486 (tpp) REVERT: C 248 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8598 (mtpp) REVERT: C 258 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8136 (mm-30) REVERT: D 198 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5800 (tm) REVERT: D 203 GLU cc_start: 0.8722 (tp30) cc_final: 0.8189 (tp30) outliers start: 100 outliers final: 25 residues processed: 279 average time/residue: 0.7246 time to fit residues: 229.9109 Evaluate side-chains 208 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 459 THR 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 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: 0.2980 chunk 71 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 296 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN B 580 GLN C 269 HIS ** 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 = 0.3657 r_free = 0.3657 target = 0.109361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.069070 restraints weight = 45402.543| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.06 r_work: 0.2772 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24517 Z= 0.142 Angle : 0.578 10.843 33458 Z= 0.286 Chirality : 0.041 0.405 3750 Planarity : 0.004 0.055 4311 Dihedral : 9.501 173.725 3620 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 3.20 % Allowed : 22.30 % 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: 1.38 (0.16), residues: 2951 helix: 2.02 (0.14), residues: 1441 sheet: -0.11 (0.29), residues: 359 loop : -0.10 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 491 TYR 0.010 0.001 TYR D 50 PHE 0.036 0.002 PHE B 59 TRP 0.012 0.001 TRP C 364 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24499) covalent geometry : angle 0.57838 / 0.29 (33458) hydrogen bonds : bond 0.03901 / 2.63 ( 1126) hydrogen bonds : angle 4.76133 / 3.47 ( 3174) metal coordination : bond 0.00215 / 0.11 ( 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 274 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 196 time to evaluate : 0.995 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: F 237 TRP cc_start: 0.8863 (t-100) cc_final: 0.8431 (t-100) REVERT: F 258 GLU cc_start: 0.8697 (tp30) cc_final: 0.8379 (tp30) REVERT: F 421 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9062 (mtpp) REVERT: A 1 MET cc_start: 0.7219 (tpp) cc_final: 0.6507 (pp-130) REVERT: A 19 MET cc_start: 0.7198 (mpp) cc_final: 0.6985 (mpp) REVERT: A 74 GLN cc_start: 0.8486 (mp10) cc_final: 0.7930 (tp40) REVERT: A 75 ASP cc_start: 0.8623 (m-30) cc_final: 0.8332 (t0) REVERT: A 98 TYR cc_start: 0.8221 (m-80) cc_final: 0.7752 (m-80) REVERT: A 108 ILE cc_start: 0.3295 (OUTLIER) cc_final: 0.3007 (pp) REVERT: A 315 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8869 (m-30) REVERT: A 434 PHE cc_start: 0.8822 (t80) cc_final: 0.8531 (t80) REVERT: A 437 ARG cc_start: 0.8901 (mtp-110) cc_final: 0.8567 (tpm170) REVERT: A 449 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7876 (tm-30) REVERT: B 2 ARG cc_start: 0.7829 (ptp90) cc_final: 0.7628 (ptp-110) REVERT: B 50 TYR cc_start: 0.6749 (t80) cc_final: 0.6497 (t80) REVERT: B 59 PHE cc_start: 0.5355 (t80) cc_final: 0.4588 (t80) REVERT: B 308 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: B 434 PHE cc_start: 0.8435 (p90) cc_final: 0.8081 (p90) REVERT: B 459 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8859 (t) REVERT: B 466 ASP cc_start: 0.8629 (p0) cc_final: 0.8268 (t0) REVERT: B 544 THR cc_start: 0.9313 (m) cc_final: 0.8955 (p) REVERT: B 575 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: B 593 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: C 53 MET cc_start: 0.8541 (pmm) cc_final: 0.8314 (pp-130) REVERT: C 80 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: C 169 GLN cc_start: 0.9055 (mp10) cc_final: 0.8691 (mp10) REVERT: C 190 TRP cc_start: 0.7086 (m100) cc_final: 0.6863 (m100) REVERT: C 196 MET cc_start: 0.6953 (ttm) cc_final: 0.6639 (tpp) REVERT: C 248 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8647 (mtpp) REVERT: C 258 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8294 (mm-30) REVERT: C 469 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: C 568 CYS cc_start: 0.8830 (m) cc_final: 0.8590 (m) REVERT: D 198 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5836 (tm) outliers start: 78 outliers final: 28 residues processed: 263 average time/residue: 0.7535 time to fit residues: 225.1968 Evaluate side-chains 216 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 108 ILE 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 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 B residue 593 GLU 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 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: 10.0000 chunk 137 optimal weight: 30.0000 chunk 163 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 255 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 269 HIS E 376 GLN B 485 HIS 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.070885 restraints weight = 46436.538| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.00 r_work: 0.2771 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24517 Z= 0.173 Angle : 0.575 11.367 33458 Z= 0.282 Chirality : 0.041 0.410 3750 Planarity : 0.004 0.056 4311 Dihedral : 9.359 175.409 3620 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 3.16 % Allowed : 22.26 % Favored : 74.58 % 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: 2.05 (0.14), residues: 1446 sheet: -0.02 (0.29), residues: 353 loop : -0.05 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 97 TYR 0.013 0.001 TYR D 50 PHE 0.024 0.001 PHE A 79 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 0.00402 / 0.17 (24499) covalent geometry : angle 0.57504 / 0.28 (33458) hydrogen bonds : bond 0.03741 / 2.54 ( 1126) hydrogen bonds : angle 4.60244 / 3.35 ( 3174) metal coordination : bond 0.00297 / 0.16 ( 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 265 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 188 time to evaluate : 0.968 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: F 237 TRP cc_start: 0.8865 (t-100) cc_final: 0.8410 (t-100) REVERT: F 258 GLU cc_start: 0.8636 (tp30) cc_final: 0.8393 (tp30) REVERT: F 421 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9060 (mtpp) REVERT: F 529 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: F 575 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7824 (mt-10) REVERT: A 1 MET cc_start: 0.7263 (tpp) cc_final: 0.6499 (pp-130) REVERT: A 19 MET cc_start: 0.7339 (mpp) cc_final: 0.7101 (mpp) REVERT: A 75 ASP cc_start: 0.8651 (m-30) cc_final: 0.8294 (t0) REVERT: A 98 TYR cc_start: 0.8259 (m-80) cc_final: 0.7749 (m-80) REVERT: A 248 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8157 (tttm) REVERT: A 285 SER cc_start: 0.9535 (OUTLIER) cc_final: 0.9213 (m) REVERT: A 315 ASP cc_start: 0.9216 (OUTLIER) cc_final: 0.8867 (m-30) REVERT: A 425 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8532 (ptm-80) REVERT: A 434 PHE cc_start: 0.8821 (t80) cc_final: 0.8553 (t80) REVERT: A 437 ARG cc_start: 0.8860 (mtp-110) cc_final: 0.8534 (tpm170) REVERT: A 449 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 2 ARG cc_start: 0.7922 (ptp90) cc_final: 0.7712 (ptp-110) REVERT: B 50 TYR cc_start: 0.6757 (t80) cc_final: 0.6535 (t80) REVERT: B 308 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: B 434 PHE cc_start: 0.8471 (p90) cc_final: 0.8132 (p90) REVERT: B 466 ASP cc_start: 0.8696 (p0) cc_final: 0.8326 (t0) REVERT: B 544 THR cc_start: 0.9335 (m) cc_final: 0.9007 (p) REVERT: B 575 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: C 169 GLN cc_start: 0.9123 (mp10) cc_final: 0.8703 (mp10) REVERT: C 190 TRP cc_start: 0.6933 (m100) cc_final: 0.6708 (m100) REVERT: C 196 MET cc_start: 0.7166 (ttm) cc_final: 0.6796 (tpp) REVERT: C 248 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8697 (mtpp) REVERT: C 258 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8313 (mm-30) REVERT: C 469 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: C 491 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8076 (mtt90) REVERT: C 568 CYS cc_start: 0.8813 (m) cc_final: 0.8579 (m) REVERT: D 2 ARG cc_start: 0.7922 (mpt-90) cc_final: 0.7673 (mmm160) REVERT: D 198 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5819 (tm) outliers start: 77 outliers final: 33 residues processed: 252 average time/residue: 0.7238 time to fit residues: 208.3931 Evaluate side-chains 217 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 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 315 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 393 LEU 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 396 THR Chi-restraints excluded: chain B residue 439 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 198 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 571 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 247 optimal weight: 0.5980 chunk 191 optimal weight: 0.0040 chunk 204 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 277 optimal weight: 8.9990 chunk 239 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN F 554 GLN ** 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** ** 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 = 0.3651 r_free = 0.3651 target = 0.109935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.070421 restraints weight = 46278.299| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.98 r_work: 0.2784 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2123 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= 0.139 Angle : 0.563 12.116 33458 Z= 0.275 Chirality : 0.041 0.412 3750 Planarity : 0.004 0.055 4311 Dihedral : 9.277 176.232 3618 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.51 % Favored : 95.43 % Rotamer: Outliers : 3.08 % Allowed : 22.39 % 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: 1.52 (0.16), residues: 2951 helix: 2.12 (0.14), residues: 1439 sheet: 0.00 (0.29), residues: 353 loop : -0.01 (0.20), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 290 TYR 0.016 0.001 TYR D 50 PHE 0.028 0.001 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 0.00320 / 0.14 (24499) covalent geometry : angle 0.56300 / 0.27 (33458) hydrogen bonds : bond 0.03505 / 2.40 ( 1126) hydrogen bonds : angle 4.49745 / 3.27 ( 3174) metal coordination : bond 0.00217 / 0.11 ( 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 250 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 175 time to evaluate : 0.996 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 240 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: F 237 TRP cc_start: 0.8852 (t-100) cc_final: 0.8377 (t-100) REVERT: F 258 GLU cc_start: 0.8581 (tp30) cc_final: 0.8276 (tp30) REVERT: F 421 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9062 (mtpp) REVERT: F 529 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: A 1 MET cc_start: 0.7281 (tpp) cc_final: 0.6455 (pp-130) REVERT: A 75 ASP cc_start: 0.8518 (m-30) cc_final: 0.8309 (t0) REVERT: A 98 TYR cc_start: 0.8380 (m-80) cc_final: 0.7894 (m-80) REVERT: A 315 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8823 (m-30) REVERT: A 425 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8625 (ptm-80) REVERT: A 434 PHE cc_start: 0.8794 (t80) cc_final: 0.8527 (t80) REVERT: A 437 ARG cc_start: 0.8908 (mtp-110) cc_final: 0.8567 (tpm170) REVERT: A 449 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 2 ARG cc_start: 0.7923 (ptp90) cc_final: 0.7705 (ptp-110) REVERT: B 33 LEU cc_start: 0.9203 (tp) cc_final: 0.8809 (mt) REVERT: B 53 MET cc_start: 0.6675 (ppp) cc_final: 0.6452 (ppp) REVERT: B 308 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8072 (tp30) REVERT: B 434 PHE cc_start: 0.8452 (p90) cc_final: 0.8113 (p90) REVERT: B 544 THR cc_start: 0.9322 (m) cc_final: 0.8983 (p) REVERT: B 575 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: B 593 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: C 169 GLN cc_start: 0.9136 (mp10) cc_final: 0.8697 (mp10) REVERT: C 196 MET cc_start: 0.7203 (ttm) cc_final: 0.6831 (tpp) REVERT: C 248 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8678 (mtpp) REVERT: C 258 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8335 (mm-30) REVERT: C 469 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: C 568 CYS cc_start: 0.8791 (m) cc_final: 0.8561 (m) REVERT: D 2 ARG cc_start: 0.7939 (mpt-90) cc_final: 0.7646 (mmm160) REVERT: D 19 MET cc_start: 0.7367 (pmm) cc_final: 0.7071 (pmm) REVERT: D 198 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5858 (tm) REVERT: D 324 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8339 (t70) outliers start: 75 outliers final: 36 residues processed: 239 average time/residue: 0.6954 time to fit residues: 190.9793 Evaluate side-chains 216 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 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 393 LEU 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 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 B residue 593 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 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 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 Chi-restraints excluded: chain D residue 571 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 189 optimal weight: 5.9990 chunk 221 optimal weight: 0.6980 chunk 289 optimal weight: 3.9990 chunk 249 optimal weight: 20.0000 chunk 284 optimal weight: 0.8980 chunk 190 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 217 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 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 = 0.3632 r_free = 0.3632 target = 0.107985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.067632 restraints weight = 45693.385| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.02 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: 0.8293 moved from start: 0.2238 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= 0.177 Angle : 0.575 13.220 33458 Z= 0.281 Chirality : 0.041 0.410 3750 Planarity : 0.004 0.053 4311 Dihedral : 9.194 175.879 3618 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 3.12 % Allowed : 22.59 % Favored : 74.29 % 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: 1.52 (0.16), residues: 2951 helix: 2.10 (0.14), residues: 1439 sheet: 0.00 (0.29), residues: 355 loop : 0.00 (0.20), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 290 TYR 0.015 0.001 TYR D 50 PHE 0.029 0.002 PHE C 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 0.00414 / 0.18 (24499) covalent geometry : angle 0.57454 / 0.28 (33458) hydrogen bonds : bond 0.03615 / 2.48 ( 1126) hydrogen bonds : angle 4.46406 / 3.24 ( 3174) metal coordination : bond 0.00314 / 0.17 ( 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 251 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 175 time to evaluate : 1.052 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 578 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8397 (mtmm) REVERT: F 237 TRP cc_start: 0.8896 (t-100) cc_final: 0.8427 (t-100) REVERT: F 258 GLU cc_start: 0.8608 (tp30) cc_final: 0.8323 (tp30) REVERT: F 421 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9077 (mtpp) REVERT: F 529 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: F 575 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 1 MET cc_start: 0.7324 (tpp) cc_final: 0.6408 (pp-130) REVERT: A 19 MET cc_start: 0.7200 (mtm) cc_final: 0.6837 (mpp) REVERT: A 75 ASP cc_start: 0.8513 (m-30) cc_final: 0.8245 (t0) REVERT: A 98 TYR cc_start: 0.8366 (m-80) cc_final: 0.7880 (m-80) REVERT: A 248 LYS cc_start: 0.8398 (ttpp) cc_final: 0.8168 (tttm) REVERT: A 285 SER cc_start: 0.9531 (OUTLIER) cc_final: 0.9244 (m) REVERT: A 315 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8789 (m-30) REVERT: A 434 PHE cc_start: 0.8805 (t80) cc_final: 0.8527 (t80) REVERT: A 449 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 2 ARG cc_start: 0.7908 (ptp90) cc_final: 0.7697 (ptp-110) REVERT: B 86 TRP cc_start: 0.8978 (t60) cc_final: 0.8461 (t-100) REVERT: B 308 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: B 434 PHE cc_start: 0.8491 (p90) cc_final: 0.8182 (p90) REVERT: B 544 THR cc_start: 0.9326 (m) cc_final: 0.9016 (p) REVERT: B 575 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: B 593 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8405 (mt-10) REVERT: C 169 GLN cc_start: 0.9168 (mp10) cc_final: 0.8716 (mp10) REVERT: C 196 MET cc_start: 0.7340 (ttm) cc_final: 0.7006 (tpp) REVERT: C 248 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8705 (mtpp) REVERT: C 258 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8362 (mm-30) REVERT: C 469 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: C 491 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8016 (mtt90) REVERT: C 601 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9020 (mp) REVERT: D 19 MET cc_start: 0.7362 (pmm) cc_final: 0.7115 (pmm) REVERT: D 198 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5830 (tm) REVERT: D 324 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8389 (t70) outliers start: 76 outliers final: 32 residues processed: 243 average time/residue: 0.6894 time to fit residues: 192.1356 Evaluate side-chains 214 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 E residue 578 LYS 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 342 ASP Chi-restraints excluded: chain A residue 352 SER 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 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 B residue 593 GLU 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 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 324 ASP Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 571 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 131 optimal weight: 0.9980 chunk 288 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 213 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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 = 0.3667 r_free = 0.3667 target = 0.110472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.070751 restraints weight = 45895.248| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.02 r_work: 0.2790 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24517 Z= 0.120 Angle : 0.567 15.477 33458 Z= 0.275 Chirality : 0.040 0.414 3750 Planarity : 0.004 0.063 4311 Dihedral : 9.109 177.065 3614 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 2.67 % Allowed : 23.08 % Favored : 74.25 % 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: 2.16 (0.14), residues: 1443 sheet: -0.07 (0.29), residues: 359 loop : 0.05 (0.20), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 58 TYR 0.011 0.001 TYR D 50 PHE 0.028 0.001 PHE A 79 TRP 0.015 0.001 TRP C 190 HIS 0.003 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (24499) covalent geometry : angle 0.56703 / 0.27 (33458) hydrogen bonds : bond 0.03263 / 2.23 ( 1126) hydrogen bonds : angle 4.34357 / 3.14 ( 3174) metal coordination : bond 0.00175 / 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 249 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 0.708 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: 0.8684 (mm-30) cc_final: 0.8388 (tp30) REVERT: E 461 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.7541 (m90) REVERT: E 477 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8676 (mppt) REVERT: E 578 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: F 237 TRP cc_start: 0.8896 (t-100) cc_final: 0.8437 (t-100) REVERT: F 421 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9073 (mtpp) REVERT: F 529 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: A 1 MET cc_start: 0.7349 (tpp) cc_final: 0.6408 (pp-130) REVERT: A 19 MET cc_start: 0.7227 (mtt) cc_final: 0.6905 (mpp) REVERT: A 75 ASP cc_start: 0.8496 (m-30) cc_final: 0.8224 (t0) REVERT: A 98 TYR cc_start: 0.8424 (m-80) cc_final: 0.7931 (m-80) REVERT: A 285 SER cc_start: 0.9528 (OUTLIER) cc_final: 0.9266 (m) REVERT: A 315 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8839 (m-30) REVERT: A 434 PHE cc_start: 0.8799 (t80) cc_final: 0.8529 (t80) REVERT: A 443 MET cc_start: 0.9244 (mmm) cc_final: 0.8579 (mpt) REVERT: A 449 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7904 (tm-30) REVERT: B 2 ARG cc_start: 0.7968 (ptp90) cc_final: 0.7749 (ptp-110) REVERT: B 86 TRP cc_start: 0.8965 (t60) cc_final: 0.8444 (t-100) REVERT: B 308 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: B 434 PHE cc_start: 0.8433 (p90) cc_final: 0.8016 (p90) REVERT: B 544 THR cc_start: 0.9334 (m) cc_final: 0.9032 (p) REVERT: B 575 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: B 593 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8408 (mt-10) REVERT: C 112 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8047 (ttp) REVERT: C 169 GLN cc_start: 0.9159 (mp10) cc_final: 0.8697 (mp10) REVERT: C 196 MET cc_start: 0.7278 (ttm) cc_final: 0.6584 (tpp) REVERT: C 200 GLN cc_start: 0.9027 (mp10) cc_final: 0.8760 (mp10) REVERT: C 248 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8706 (mtpp) REVERT: C 258 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8345 (mm-30) REVERT: C 403 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6408 (mtt180) REVERT: C 469 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: C 491 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8050 (mtt90) REVERT: C 523 GLU cc_start: 0.8640 (tt0) cc_final: 0.8045 (tm-30) REVERT: C 568 CYS cc_start: 0.8791 (m) cc_final: 0.8571 (m) REVERT: C 601 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8993 (mp) REVERT: D 203 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8079 (tp30) REVERT: D 324 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8351 (t70) outliers start: 65 outliers final: 26 residues processed: 240 average time/residue: 0.7249 time to fit residues: 198.4700 Evaluate side-chains 210 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 572 THR Chi-restraints excluded: chain E residue 578 LYS 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 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 B residue 593 GLU Chi-restraints excluded: chain C residue 6 CYS 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 403 ARG 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 459 THR Chi-restraints excluded: chain D residue 571 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 138 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 282 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.107436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.066819 restraints weight = 45646.254| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.04 r_work: 0.2747 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24517 Z= 0.206 Angle : 0.603 14.771 33458 Z= 0.293 Chirality : 0.042 0.398 3750 Planarity : 0.004 0.056 4311 Dihedral : 9.041 178.036 3610 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 2.38 % Allowed : 23.53 % Favored : 74.09 % 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: 1.53 (0.16), residues: 2951 helix: 2.13 (0.14), residues: 1438 sheet: -0.08 (0.29), residues: 351 loop : 0.04 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 440 TYR 0.016 0.001 TYR C 356 PHE 0.029 0.002 PHE A 79 TRP 0.019 0.001 TRP C 190 HIS 0.005 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (24499) covalent geometry : angle 0.60300 / 0.29 (33458) hydrogen bonds : bond 0.03702 / 2.53 ( 1126) hydrogen bonds : angle 4.43258 / 3.21 ( 3174) metal coordination : bond 0.00366 / 0.20 ( 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 233 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 175 time to evaluate : 0.970 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: 0.8656 (mm-30) cc_final: 0.8260 (tp30) REVERT: E 578 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: F 237 TRP cc_start: 0.8899 (t-100) cc_final: 0.8401 (t-100) REVERT: F 258 GLU cc_start: 0.8769 (tp30) cc_final: 0.8525 (tp30) REVERT: F 421 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9104 (mtpp) REVERT: F 461 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.7934 (m90) REVERT: F 529 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8462 (pm20) REVERT: F 575 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7875 (mt-10) REVERT: A 1 MET cc_start: 0.7359 (tpp) cc_final: 0.6435 (pp-130) REVERT: A 19 MET cc_start: 0.7203 (mtt) cc_final: 0.6873 (mpp) REVERT: A 75 ASP cc_start: 0.8492 (m-30) cc_final: 0.8265 (t0) REVERT: A 98 TYR cc_start: 0.8423 (m-80) cc_final: 0.7966 (m-80) REVERT: A 285 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.9274 (m) REVERT: A 315 ASP cc_start: 0.9236 (OUTLIER) cc_final: 0.8771 (m-30) REVERT: A 434 PHE cc_start: 0.8760 (t80) cc_final: 0.8514 (t80) REVERT: A 443 MET cc_start: 0.9247 (mmm) cc_final: 0.8587 (mpt) REVERT: A 449 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7921 (tm-30) REVERT: B 2 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7725 (ptp-110) REVERT: B 86 TRP cc_start: 0.8973 (t60) cc_final: 0.8434 (t-100) REVERT: B 308 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8069 (tp30) REVERT: B 434 PHE cc_start: 0.8511 (p90) cc_final: 0.8103 (p90) REVERT: B 544 THR cc_start: 0.9318 (m) cc_final: 0.9008 (p) REVERT: B 575 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: B 593 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8426 (mt-10) REVERT: C 169 GLN cc_start: 0.9197 (mp10) cc_final: 0.8756 (mp10) REVERT: C 196 MET cc_start: 0.7207 (ttm) cc_final: 0.6537 (tpp) REVERT: C 200 GLN cc_start: 0.9035 (mp10) cc_final: 0.8760 (mp10) REVERT: C 248 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8749 (mtpp) REVERT: C 258 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8431 (mm-30) REVERT: C 491 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8033 (mtt90) REVERT: C 523 GLU cc_start: 0.8662 (tt0) cc_final: 0.8027 (tm-30) REVERT: C 601 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9019 (mp) REVERT: D 198 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5751 (tm) REVERT: D 203 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8147 (tp30) REVERT: D 324 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8422 (t70) outliers start: 58 outliers final: 29 residues processed: 224 average time/residue: 0.7175 time to fit residues: 183.5855 Evaluate side-chains 212 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 E residue 578 LYS 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 B residue 593 GLU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 248 LYS 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 Chi-restraints excluded: chain D residue 571 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 149 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 288 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 197 optimal weight: 0.4980 chunk 192 optimal weight: 10.0000 chunk 28 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.108863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.068568 restraints weight = 45677.597| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.04 r_work: 0.2778 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24517 Z= 0.127 Angle : 0.582 16.057 33458 Z= 0.281 Chirality : 0.040 0.395 3750 Planarity : 0.004 0.056 4311 Dihedral : 8.985 177.273 3610 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 2.17 % Allowed : 23.78 % Favored : 74.05 % 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: 1.61 (0.16), residues: 2951 helix: 2.17 (0.14), residues: 1442 sheet: -0.08 (0.29), residues: 346 loop : 0.10 (0.20), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 440 TYR 0.010 0.001 TYR B 50 PHE 0.031 0.001 PHE B 79 TRP 0.024 0.001 TRP C 190 HIS 0.003 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (24499) covalent geometry : angle 0.58154 / 0.28 (33458) hydrogen bonds : bond 0.03254 / 2.23 ( 1126) hydrogen bonds : angle 4.32744 / 3.13 ( 3174) metal coordination : bond 0.00214 / 0.11 ( 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 225 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 0.941 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: 0.8653 (mm-30) cc_final: 0.8284 (tp30) REVERT: E 461 HIS cc_start: 0.8691 (OUTLIER) cc_final: 0.7399 (m90) REVERT: E 578 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8353 (mtmm) REVERT: F 237 TRP cc_start: 0.8890 (t-100) cc_final: 0.8416 (t-100) REVERT: F 258 GLU cc_start: 0.8707 (tp30) cc_final: 0.8437 (tp30) REVERT: F 421 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9077 (mtpp) REVERT: F 461 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.7917 (m90) REVERT: F 529 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: A 1 MET cc_start: 0.7344 (tpp) cc_final: 0.6378 (pp-130) REVERT: A 19 MET cc_start: 0.7267 (mtt) cc_final: 0.6952 (mpp) REVERT: A 75 ASP cc_start: 0.8497 (m-30) cc_final: 0.8226 (t0) REVERT: A 98 TYR cc_start: 0.8466 (m-80) cc_final: 0.7868 (m-80) REVERT: A 108 ILE cc_start: 0.4010 (OUTLIER) cc_final: 0.3764 (pp) REVERT: A 285 SER cc_start: 0.9520 (OUTLIER) cc_final: 0.9271 (m) REVERT: A 315 ASP cc_start: 0.9212 (OUTLIER) cc_final: 0.8777 (m-30) REVERT: A 434 PHE cc_start: 0.8787 (t80) cc_final: 0.8518 (t80) REVERT: A 443 MET cc_start: 0.9256 (mmm) cc_final: 0.8616 (mpt) REVERT: A 449 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 2 ARG cc_start: 0.7969 (ptp90) cc_final: 0.7747 (ptp-110) REVERT: B 86 TRP cc_start: 0.8970 (t60) cc_final: 0.8411 (t-100) REVERT: B 308 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: B 434 PHE cc_start: 0.8388 (p90) cc_final: 0.8113 (p90) REVERT: B 544 THR cc_start: 0.9338 (m) cc_final: 0.9034 (p) REVERT: B 575 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: B 593 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8409 (mt-10) REVERT: C 53 MET cc_start: 0.8334 (pp-130) cc_final: 0.8101 (ppp) REVERT: C 169 GLN cc_start: 0.9181 (mp10) cc_final: 0.8750 (mp10) REVERT: C 196 MET cc_start: 0.7112 (ttm) cc_final: 0.6530 (tpp) REVERT: C 200 GLN cc_start: 0.9037 (mp10) cc_final: 0.8775 (mp10) REVERT: C 248 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8745 (mtpp) REVERT: C 258 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8401 (mm-30) REVERT: C 469 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: C 491 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8058 (mtt90) REVERT: C 523 GLU cc_start: 0.8653 (tt0) cc_final: 0.7971 (tm-30) REVERT: C 601 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8984 (mp) REVERT: D 198 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5743 (tm) REVERT: D 203 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8132 (tp30) REVERT: D 324 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8385 (t70) outliers start: 53 outliers final: 26 residues processed: 218 average time/residue: 0.6846 time to fit residues: 171.2066 Evaluate side-chains 207 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 E residue 578 LYS 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 285 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 342 ASP 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 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain C residue 6 CYS 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 313 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 571 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 85 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 285 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.108439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.067801 restraints weight = 45324.477| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.05 r_work: 0.2758 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24517 Z= 0.125 Angle : 0.585 15.865 33458 Z= 0.282 Chirality : 0.040 0.382 3750 Planarity : 0.004 0.056 4311 Dihedral : 8.896 175.253 3610 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 1.93 % Allowed : 24.23 % Favored : 73.84 % 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: 1.64 (0.16), residues: 2951 helix: 2.20 (0.14), residues: 1442 sheet: -0.11 (0.29), residues: 344 loop : 0.12 (0.20), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 440 TYR 0.016 0.001 TYR B 50 PHE 0.030 0.001 PHE A 79 TRP 0.012 0.001 TRP C 364 HIS 0.003 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (24499) covalent geometry : angle 0.58475 / 0.28 (33458) hydrogen bonds : bond 0.03198 / 2.19 ( 1126) hydrogen bonds : angle 4.30566 / 3.12 ( 3174) metal coordination : bond 0.00191 / 0.10 ( 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 212 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 240 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8225 (tp30) REVERT: E 461 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.7356 (m90) REVERT: E 477 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8640 (mppt) REVERT: E 578 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8305 (mtmm) REVERT: F 237 TRP cc_start: 0.8881 (t-100) cc_final: 0.8407 (t-100) REVERT: F 258 GLU cc_start: 0.8671 (tp30) cc_final: 0.8383 (tp30) REVERT: F 421 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9091 (mtpp) REVERT: F 461 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.7833 (m90) REVERT: F 529 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8427 (pm20) REVERT: A 1 MET cc_start: 0.7406 (tpp) cc_final: 0.6581 (pp-130) REVERT: A 75 ASP cc_start: 0.8475 (m-30) cc_final: 0.8215 (t0) REVERT: A 98 TYR cc_start: 0.8426 (m-80) cc_final: 0.7988 (m-80) REVERT: A 108 ILE cc_start: 0.3931 (OUTLIER) cc_final: 0.3665 (pp) REVERT: A 285 SER cc_start: 0.9510 (OUTLIER) cc_final: 0.9266 (m) REVERT: A 315 ASP cc_start: 0.9208 (OUTLIER) cc_final: 0.8746 (m-30) REVERT: A 434 PHE cc_start: 0.8728 (t80) cc_final: 0.8462 (t80) REVERT: A 443 MET cc_start: 0.9258 (mmm) cc_final: 0.8613 (mpt) REVERT: A 449 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 2 ARG cc_start: 0.7996 (ptp90) cc_final: 0.7773 (ptp-110) REVERT: B 86 TRP cc_start: 0.8992 (t60) cc_final: 0.8426 (t-100) REVERT: B 308 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: B 434 PHE cc_start: 0.8434 (p90) cc_final: 0.8182 (p90) REVERT: B 544 THR cc_start: 0.9297 (m) cc_final: 0.8980 (p) REVERT: B 575 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: B 593 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: C 53 MET cc_start: 0.8373 (pp-130) cc_final: 0.8151 (ppp) REVERT: C 112 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8010 (ttp) REVERT: C 169 GLN cc_start: 0.9178 (mp10) cc_final: 0.8736 (mp10) REVERT: C 196 MET cc_start: 0.7074 (ttm) cc_final: 0.6512 (tpp) REVERT: C 200 GLN cc_start: 0.9036 (mp10) cc_final: 0.8770 (mp10) REVERT: C 248 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8721 (mtpp) REVERT: C 258 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8285 (mm-30) REVERT: C 491 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8020 (mtt90) REVERT: C 523 GLU cc_start: 0.8674 (tt0) cc_final: 0.8038 (tm-30) REVERT: C 525 GLN cc_start: 0.8289 (mp10) cc_final: 0.7673 (mp10) REVERT: C 601 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8927 (mp) REVERT: D 198 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5689 (tm) REVERT: D 203 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8142 (tp30) REVERT: D 324 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8288 (t70) outliers start: 47 outliers final: 22 residues processed: 207 average time/residue: 0.6994 time to fit residues: 165.8365 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 : 0.826 ------------------------------------------------------------------------------- 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 572 THR Chi-restraints excluded: chain E residue 578 LYS 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 285 SER Chi-restraints excluded: chain A residue 315 ASP 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 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 593 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 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 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: 0.2980 chunk 176 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 101 optimal weight: 0.0670 chunk 265 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 232 optimal weight: 0.0470 chunk 104 optimal weight: 0.6980 chunk 258 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 376 GLN A 452 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.109537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.068970 restraints weight = 45113.576| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.06 r_work: 0.2777 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24517 Z= 0.102 Angle : 0.582 16.232 33458 Z= 0.279 Chirality : 0.040 0.366 3750 Planarity : 0.004 0.057 4311 Dihedral : 8.781 169.280 3610 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 1.72 % Allowed : 24.68 % Favored : 73.60 % 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: 1.70 (0.17), residues: 2951 helix: 2.24 (0.14), residues: 1442 sheet: 0.06 (0.30), residues: 330 loop : 0.12 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 440 TYR 0.047 0.001 TYR B 50 PHE 0.031 0.001 PHE A 79 TRP 0.013 0.001 TRP C 190 HIS 0.003 0.000 HIS E 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (24499) covalent geometry : angle 0.58238 / 0.28 (33458) hydrogen bonds : bond 0.02970 / 2.05 ( 1126) hydrogen bonds : angle 4.21946 / 3.05 ( 3174) metal coordination : bond 0.00113 / 0.05 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6818.13 seconds wall clock time: 117 minutes 29.91 seconds (7049.91 seconds total)