Starting phenix.real_space_refine on Mon May 4 22:40:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ubm_64011/05_2026/9ubm_64011_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ubm_64011/05_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_64011/05_2026/9ubm_64011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ubm_64011/05_2026/9ubm_64011.map" model { file = "/net/cci-nas-00/data/ceres_data/9ubm_64011/05_2026/9ubm_64011_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ubm_64011/05_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 5.78, per 1000 atoms: 0.24 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: 1.99 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: 0.84 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: 4.43 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8137 1.34 - 1.46: 4956 1.46 - 1.58: 11223 1.58 - 1.70: 45 1.70 - 1.82: 138 Bond restraints: 24499 Sorted by residual: bond pdb=" C ALA C 175 " pdb=" N PRO C 176 " ideal model delta sigma weight residual 1.335 1.356 -0.020 1.36e-02 5.41e+03 2.24e+00 bond pdb=" CB GLU E 308 " pdb=" CG GLU E 308 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" N ASP B 66 " pdb=" CA ASP B 66 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.11e+00 bond pdb=" CB GLU D 308 " pdb=" CG GLU D 308 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.83e+00 bond pdb=" C1' ATP B 701 " pdb=" O4' ATP B 701 " ideal model delta sigma weight residual 1.416 1.399 0.017 1.30e-02 5.92e+03 1.70e+00 ... (remaining 24494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 32839 2.01 - 4.02: 515 4.02 - 6.02: 80 6.02 - 8.03: 17 8.03 - 10.04: 7 Bond angle restraints: 33458 Sorted by residual: angle pdb=" CA MET A 19 " pdb=" CB MET A 19 " pdb=" CG MET A 19 " ideal model delta sigma weight residual 114.10 122.72 -8.62 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CA GLU B 435 " pdb=" CB GLU B 435 " pdb=" CG GLU B 435 " ideal model delta sigma weight residual 114.10 122.46 -8.36 2.00e+00 2.50e-01 1.75e+01 angle pdb=" C GLU D 52 " pdb=" N MET D 53 " pdb=" CA MET D 53 " ideal model delta sigma weight residual 121.94 113.83 8.11 2.00e+00 2.50e-01 1.64e+01 angle pdb=" N ALA C 320 " pdb=" CA ALA C 320 " pdb=" C ALA C 320 " ideal model delta sigma weight residual 113.18 108.40 4.78 1.33e+00 5.65e-01 1.29e+01 angle pdb=" N MET A 19 " pdb=" CA MET A 19 " pdb=" CB MET A 19 " ideal model delta sigma weight residual 110.16 115.41 -5.25 1.48e+00 4.57e-01 1.26e+01 ... (remaining 33453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 14192 34.83 - 69.67: 571 69.67 - 104.50: 43 104.50 - 139.34: 0 139.34 - 174.17: 1 Dihedral angle restraints: 14807 sinusoidal: 6113 harmonic: 8694 Sorted by residual: dihedral pdb=" CA GLU B 17 " pdb=" C GLU B 17 " pdb=" N ALA B 18 " pdb=" CA ALA B 18 " ideal model delta harmonic sigma weight residual -180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" C4' A Y 1 " pdb=" C3' A Y 1 " pdb=" O3' A Y 1 " pdb=" P A Y 2 " ideal model delta sinusoidal sigma weight residual -110.00 64.17 -174.17 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA MET B 53 " pdb=" C MET B 53 " pdb=" N HIS B 54 " pdb=" CA HIS B 54 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 14804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3233 0.058 - 0.116: 465 0.116 - 0.173: 33 0.173 - 0.231: 3 0.231 - 0.289: 16 Chirality restraints: 3750 Sorted by residual: chirality pdb=" C2' ATP E 701 " pdb=" C1' ATP E 701 " pdb=" C3' ATP E 701 " pdb=" O2' ATP E 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C3' ATP A 701 " pdb=" C2' ATP A 701 " pdb=" C4' ATP A 701 " pdb=" O3' ATP A 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' ATP C 701 " pdb=" C1' ATP C 701 " pdb=" C3' ATP C 701 " pdb=" O2' ATP C 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3747 not shown) Planarity restraints: 4311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 385 " -0.208 9.50e-02 1.11e+02 9.37e-02 6.45e+00 pdb=" NE ARG E 385 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG E 385 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG E 385 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 385 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 175 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO C 176 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 176 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 176 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 56 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 57 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.027 5.00e-02 4.00e+02 ... (remaining 4308 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 221 2.54 - 3.13: 18577 3.13 - 3.72: 38992 3.72 - 4.31: 53326 4.31 - 4.90: 90158 Nonbonded interactions: 201274 Sorted by model distance: nonbonded pdb=" O3G ATP B 701 " pdb="MG MG B 703 " model vdw 1.948 2.170 nonbonded pdb=" O3B ATP B 701 " pdb="MG MG B 703 " model vdw 1.968 2.170 nonbonded pdb=" O2B ATP A 701 " pdb="MG MG A 703 " model vdw 1.981 2.170 nonbonded pdb=" OD1 ASP B 548 " pdb="ZN ZN B 702 " model vdw 1.994 2.230 nonbonded pdb=" O2G ATP A 701 " pdb="MG MG A 703 " model vdw 2.053 2.170 ... (remaining 201269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 7 or resid 16 or (resid 17 through 18 and (name \ N or name CA or name C or name O or name CB )) or resid 19 through 38 or (resid \ 39 and (name N or name CA or name C or name O or name CB )) or resid 40 through \ 152 or resid 159 through 173 or resid 197 through 198 or (resid 199 and (name N \ or name CA or name C or name O or name CB )) or resid 200 through 327 or resid 3 \ 29 through 396 or (resid 397 through 398 and (name N or name CA or name C or nam \ e O or name CB )) or resid 399 through 433 or resid 446 through 608 or resid 701 \ through 703)) selection = (chain 'B' and (resid 1 through 16 or (resid 17 through 18 and (name N or name C \ A or name C or name O or name CB )) or resid 19 through 20 or (resid 21 and (nam \ e N or name CA or name C or name O or name CB )) or resid 22 through 26 or (resi \ d 27 and (name N or name CA or name C or name O or name CB )) or resid 28 throug \ h 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or re \ sid 52 through 66 or resid 68 through 69 or resid 72 through 91 or resid 94 thro \ ugh 102 or resid 107 through 159 or (resid 160 and (name N or name CA or name C \ or name O or name CB )) or resid 161 through 198 or (resid 199 and (name N or na \ me CA or name C or name O or name CB )) or resid 200 through 433 or resid 446 th \ rough 608 or resid 701 through 703)) selection = (chain 'C' and (resid 1 through 7 or resid 16 through 20 or (resid 21 and (name \ N or name CA or name C or name O or name CB )) or resid 22 through 26 or (resid \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 38 or (resid 39 and (name N or name CA or name C or name O or name CB )) or resi \ d 40 through 50 or (resid 51 and (name N or name CA or name C or name O or name \ CB )) or resid 52 through 66 or resid 68 through 69 or resid 72 through 91 or re \ sid 94 through 102 or resid 107 through 159 or (resid 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 through 173 or (resid 197 and (n \ ame N or name CA or name C or name O or name CB )) or resid 198 or (resid 199 an \ d (name N or name CA or name C or name O or name CB )) or resid 200 through 327 \ or resid 329 through 397 or (resid 398 and (name N or name CA or name C or name \ O or name CB )) or resid 399 through 703)) selection = (chain 'D' and (resid 1 through 7 or resid 16 or (resid 17 through 18 and (name \ N or name CA or name C or name O or name CB )) or resid 19 through 38 or (resid \ 39 and (name N or name CA or name C or name O or name CB )) or resid 40 through \ 102 or resid 107 through 152 or resid 159 through 173 or (resid 197 and (name N \ or name CA or name C or name O or name CB )) or resid 198 through 327 or resid 3 \ 29 through 396 or (resid 397 through 398 and (name N or name CA or name C or nam \ e O or name CB )) or resid 399 through 433 or resid 446 through 608 or resid 701 \ through 703)) } ncs_group { reference = (chain 'E' and (resid 220 through 396 or (resid 397 through 398 and (name N or n \ ame CA or name C or name O or name CB )) or resid 399 through 703)) selection = (chain 'F' and (resid 220 through 607 or resid 701 through 703)) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.610 Find NCS groups from input model: 0.680 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:8.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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= 0.179 Angle : 0.616 10.040 33458 Z= 0.322 Chirality : 0.044 0.289 3750 Planarity : 0.005 0.094 4311 Dihedral : 17.499 174.175 9147 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 2.26 % Allowed : 24.23 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 2951 helix: 1.80 (0.14), residues: 1404 sheet: 0.03 (0.30), residues: 346 loop : -0.15 (0.19), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 385 TYR 0.031 0.002 TYR D 356 PHE 0.019 0.001 PHE D 266 TRP 0.022 0.002 TRP A 237 HIS 0.013 0.001 HIS E 409 Details of bonding type rmsd covalent geometry : bond 0.00393 (24499) covalent geometry : angle 0.61574 (33458) hydrogen bonds : bond 0.16657 ( 1126) hydrogen bonds : angle 6.04685 ( 3174) metal coordination : bond 0.03318 ( 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 : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7443 (tpp) cc_final: 0.6336 (pp-130) REVERT: A 108 ILE cc_start: 0.3729 (OUTLIER) cc_final: 0.3519 (pp) REVERT: A 203 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8570 (tp30) REVERT: B 33 LEU cc_start: 0.9147 (tp) cc_final: 0.8946 (tp) REVERT: D 198 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6692 (tm) REVERT: D 203 GLU cc_start: 0.8186 (tp30) cc_final: 0.7935 (tp30) outliers start: 55 outliers final: 19 residues processed: 325 average time/residue: 0.8162 time to fit residues: 295.7407 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 : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 544 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 372 ASN E 376 GLN E 390 ASN E 473 GLN B 485 HIS 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.107715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.067337 restraints weight = 45712.442| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.07 r_work: 0.2739 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24517 Z= 0.191 Angle : 0.618 9.352 33458 Z= 0.308 Chirality : 0.042 0.215 3750 Planarity : 0.005 0.058 4311 Dihedral : 9.567 169.347 3641 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 4.39 % Allowed : 21.81 % Favored : 73.80 % 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: 1.33 (0.16), residues: 2951 helix: 1.95 (0.14), residues: 1441 sheet: -0.10 (0.29), residues: 355 loop : -0.09 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 49 TYR 0.011 0.001 TYR C 50 PHE 0.023 0.002 PHE A 79 TRP 0.026 0.001 TRP F 237 HIS 0.005 0.001 HIS E 409 Details of bonding type rmsd covalent geometry : bond 0.00445 (24499) covalent geometry : angle 0.61779 (33458) hydrogen bonds : bond 0.04264 ( 1126) hydrogen bonds : angle 4.93104 ( 3174) metal coordination : bond 0.00385 ( 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 303 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 196 time to evaluate : 0.852 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: 0.8491 (OUTLIER) cc_final: 0.8272 (ttt90) REVERT: F 237 TRP cc_start: 0.8804 (t-100) cc_final: 0.8418 (t-100) REVERT: F 258 GLU cc_start: 0.8722 (tp30) cc_final: 0.8365 (tp30) REVERT: F 421 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9079 (mtpp) REVERT: A 1 MET cc_start: 0.7203 (tpp) cc_final: 0.6512 (pp-130) REVERT: A 74 GLN cc_start: 0.8473 (mp10) cc_final: 0.7967 (tp40) REVERT: A 98 TYR cc_start: 0.8106 (m-80) cc_final: 0.7673 (m-80) REVERT: A 108 ILE cc_start: 0.3276 (OUTLIER) cc_final: 0.3073 (pp) REVERT: A 164 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8112 (tp30) REVERT: A 203 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8839 (tp30) REVERT: A 315 ASP cc_start: 0.9214 (OUTLIER) cc_final: 0.8871 (m-30) REVERT: A 434 PHE cc_start: 0.8726 (t80) cc_final: 0.8427 (t80) REVERT: A 443 MET cc_start: 0.9096 (mmp) cc_final: 0.8508 (mpt) REVERT: A 449 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7759 (tm-30) REVERT: B 2 ARG cc_start: 0.7770 (ptp90) cc_final: 0.7505 (ptp-110) REVERT: B 19 MET cc_start: 0.5793 (mpt) cc_final: 0.5272 (mpt) REVERT: B 33 LEU cc_start: 0.9260 (tp) cc_final: 0.9059 (tp) REVERT: B 50 TYR cc_start: 0.7014 (t80) cc_final: 0.6745 (t80) REVERT: B 308 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: B 466 ASP cc_start: 0.8667 (p0) cc_final: 0.8269 (t0) REVERT: B 544 THR cc_start: 0.9240 (m) cc_final: 0.8835 (p) REVERT: B 575 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: B 593 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: C 53 MET cc_start: 0.8570 (pmm) cc_final: 0.8365 (pp-130) REVERT: C 63 ARG cc_start: 0.7219 (mtp85) cc_final: 0.6850 (mtp180) REVERT: C 169 GLN cc_start: 0.9002 (mp10) cc_final: 0.8663 (mp10) REVERT: C 171 ARG cc_start: 0.8663 (mtp85) cc_final: 0.8427 (mtm110) REVERT: C 196 MET cc_start: 0.6893 (ttm) cc_final: 0.6627 (tpp) REVERT: C 248 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8660 (mtpp) REVERT: C 258 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8290 (mm-30) REVERT: C 568 CYS cc_start: 0.8823 (m) cc_final: 0.8608 (m) REVERT: D 198 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5784 (tm) outliers start: 107 outliers final: 28 residues processed: 291 average time/residue: 0.7312 time to fit residues: 239.8653 Evaluate side-chains 208 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 572 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 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 108 ILE 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 459 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 593 GLU 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 114 ARG 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: 0.9980 chunk 71 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 296 optimal weight: 0.4980 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN C 269 HIS C 390 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.068429 restraints weight = 45644.765| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.03 r_work: 0.2771 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1853 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= 0.157 Angle : 0.576 9.988 33458 Z= 0.283 Chirality : 0.041 0.222 3750 Planarity : 0.004 0.060 4311 Dihedral : 9.386 171.588 3623 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 3.28 % Allowed : 22.10 % Favored : 74.62 % 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: 1.40 (0.16), residues: 2951 helix: 2.03 (0.14), residues: 1445 sheet: -0.08 (0.29), residues: 350 loop : -0.08 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 405 TYR 0.011 0.001 TYR D 50 PHE 0.025 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 covalent geometry : bond 0.00362 (24499) covalent geometry : angle 0.57602 (33458) hydrogen bonds : bond 0.03801 ( 1126) hydrogen bonds : angle 4.67379 ( 3174) metal coordination : bond 0.00256 ( 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 267 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 187 time to evaluate : 0.895 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: E 575 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: F 237 TRP cc_start: 0.8830 (t-100) cc_final: 0.8415 (t-100) REVERT: F 258 GLU cc_start: 0.8684 (tp30) cc_final: 0.8397 (tp30) REVERT: F 421 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9069 (mtpp) REVERT: F 529 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: A 1 MET cc_start: 0.7220 (tpp) cc_final: 0.6478 (pp-130) REVERT: A 19 MET cc_start: 0.7257 (mpp) cc_final: 0.7044 (mpp) REVERT: A 75 ASP cc_start: 0.8601 (m-30) cc_final: 0.8337 (t0) REVERT: A 98 TYR cc_start: 0.8303 (m-80) cc_final: 0.7866 (m-80) REVERT: A 108 ILE cc_start: 0.3409 (OUTLIER) cc_final: 0.3111 (pp) REVERT: A 285 SER cc_start: 0.9527 (OUTLIER) cc_final: 0.9169 (m) REVERT: A 315 ASP cc_start: 0.9228 (OUTLIER) cc_final: 0.8891 (m-30) REVERT: A 425 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8647 (ptm-80) REVERT: A 434 PHE cc_start: 0.8824 (t80) cc_final: 0.8532 (t80) REVERT: A 437 ARG cc_start: 0.8897 (mtp-110) cc_final: 0.8501 (tpm170) REVERT: B 2 ARG cc_start: 0.7904 (ptp90) cc_final: 0.7678 (ptp-110) REVERT: B 50 TYR cc_start: 0.6821 (t80) cc_final: 0.6607 (t80) REVERT: B 59 PHE cc_start: 0.5463 (t80) cc_final: 0.4725 (t80) REVERT: B 308 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: B 459 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8840 (t) REVERT: B 466 ASP cc_start: 0.8686 (p0) cc_final: 0.8318 (t0) REVERT: B 544 THR cc_start: 0.9346 (m) cc_final: 0.9009 (p) REVERT: B 575 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: C 63 ARG cc_start: 0.7303 (mtp85) cc_final: 0.7046 (mtp180) REVERT: C 169 GLN cc_start: 0.9081 (mp10) cc_final: 0.8635 (mp10) REVERT: C 190 TRP cc_start: 0.7098 (m100) cc_final: 0.6808 (m100) REVERT: C 196 MET cc_start: 0.7114 (ttm) cc_final: 0.6668 (tpp) REVERT: C 248 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8702 (mtpp) REVERT: C 258 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8291 (mm-30) REVERT: C 469 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: D 198 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5842 (tm) outliers start: 80 outliers final: 32 residues processed: 259 average time/residue: 0.7387 time to fit residues: 215.5688 Evaluate side-chains 221 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 575 GLU 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 571 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 34 THR 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: 7.9990 chunk 137 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 287 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 219 optimal weight: 0.8980 chunk 255 optimal weight: 0.0970 chunk 264 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 269 HIS 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.072063 restraints weight = 46271.297| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.00 r_work: 0.2796 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24517 Z= 0.120 Angle : 0.553 10.287 33458 Z= 0.273 Chirality : 0.040 0.223 3750 Planarity : 0.004 0.056 4311 Dihedral : 9.233 172.386 3621 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 3.03 % Allowed : 22.18 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.16), residues: 2951 helix: 2.13 (0.14), residues: 1451 sheet: -0.02 (0.29), residues: 350 loop : 0.02 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 97 TYR 0.011 0.001 TYR D 50 PHE 0.028 0.001 PHE B 67 TRP 0.011 0.001 TRP C 364 HIS 0.008 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00273 (24499) covalent geometry : angle 0.55319 (33458) hydrogen bonds : bond 0.03310 ( 1126) hydrogen bonds : angle 4.44356 ( 3174) metal coordination : bond 0.00137 ( 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: 74 poor density : 191 time to evaluate : 0.788 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 461 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.7623 (m90) REVERT: E 477 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8643 (mppt) REVERT: E 575 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: F 237 TRP cc_start: 0.8847 (t-100) cc_final: 0.8425 (t-100) REVERT: F 258 GLU cc_start: 0.8567 (tp30) cc_final: 0.8323 (tp30) REVERT: F 421 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9054 (mtpp) REVERT: F 529 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8418 (pm20) REVERT: A 1 MET cc_start: 0.7293 (tpp) cc_final: 0.6472 (pp-130) REVERT: A 19 MET cc_start: 0.7330 (mpp) cc_final: 0.7078 (mpp) REVERT: A 74 GLN cc_start: 0.8436 (mp10) cc_final: 0.7844 (tp40) REVERT: A 75 ASP cc_start: 0.8661 (m-30) cc_final: 0.8348 (t0) REVERT: A 98 TYR cc_start: 0.8396 (m-80) cc_final: 0.7956 (m-80) REVERT: A 315 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8844 (m-30) REVERT: A 425 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8620 (ptm-80) REVERT: A 434 PHE cc_start: 0.8818 (t80) cc_final: 0.8521 (t80) REVERT: A 437 ARG cc_start: 0.8833 (mtp-110) cc_final: 0.8468 (tpm170) REVERT: B 2 ARG cc_start: 0.7864 (ptp90) cc_final: 0.7633 (ptp-110) REVERT: B 50 TYR cc_start: 0.6758 (t80) cc_final: 0.6540 (t80) REVERT: B 308 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: B 466 ASP cc_start: 0.8622 (p0) cc_final: 0.8233 (t0) REVERT: B 544 THR cc_start: 0.9343 (m) cc_final: 0.9013 (p) REVERT: B 575 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: B 578 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8462 (mtmm) REVERT: B 593 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: C 63 ARG cc_start: 0.7384 (mtp85) cc_final: 0.7038 (mtp180) REVERT: C 112 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8091 (ttp) REVERT: C 169 GLN cc_start: 0.9133 (mp10) cc_final: 0.8711 (mp10) REVERT: C 190 TRP cc_start: 0.7064 (m100) cc_final: 0.6742 (m100) REVERT: C 196 MET cc_start: 0.7238 (ttm) cc_final: 0.6766 (tpp) REVERT: C 203 GLU cc_start: 0.8970 (tp30) cc_final: 0.8703 (mm-30) REVERT: C 248 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8677 (mtpp) REVERT: C 258 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8297 (mm-30) REVERT: C 469 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: C 491 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8096 (mtt90) REVERT: C 523 GLU cc_start: 0.8665 (tt0) cc_final: 0.7934 (tm-30) REVERT: D 198 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5895 (tm) outliers start: 74 outliers final: 29 residues processed: 252 average time/residue: 0.6829 time to fit residues: 195.7718 Evaluate side-chains 219 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 575 GLU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 329 ARG Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 446 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 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 67 PHE 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 B residue 578 LYS Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 112 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 247 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 376 GLN A 76 HIS ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN C 269 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.108072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.067534 restraints weight = 45669.869| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.04 r_work: 0.2760 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24517 Z= 0.183 Angle : 0.574 11.337 33458 Z= 0.279 Chirality : 0.041 0.222 3750 Planarity : 0.004 0.055 4311 Dihedral : 9.150 172.996 3618 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.49 % Rotamer: Outliers : 3.40 % Allowed : 22.14 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.16), residues: 2951 helix: 2.13 (0.14), residues: 1449 sheet: 0.01 (0.29), residues: 352 loop : 0.03 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 440 TYR 0.012 0.001 TYR C 356 PHE 0.025 0.002 PHE B 59 TRP 0.012 0.001 TRP C 364 HIS 0.005 0.001 HIS E 409 Details of bonding type rmsd covalent geometry : bond 0.00429 (24499) covalent geometry : angle 0.57366 (33458) hydrogen bonds : bond 0.03584 ( 1126) hydrogen bonds : angle 4.42853 ( 3174) metal coordination : bond 0.00329 ( 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 266 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 183 time to evaluate : 0.880 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: 0.8367 (OUTLIER) cc_final: 0.8021 (tp30) REVERT: E 578 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: F 237 TRP cc_start: 0.8867 (t-100) cc_final: 0.8417 (t-100) REVERT: F 258 GLU cc_start: 0.8612 (tp30) cc_final: 0.8321 (tp30) REVERT: F 421 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9084 (mtpp) REVERT: F 529 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: F 575 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7868 (mt-10) REVERT: A 1 MET cc_start: 0.7305 (tpp) cc_final: 0.6458 (pp-130) REVERT: A 19 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7135 (mpp) REVERT: A 74 GLN cc_start: 0.8473 (mp10) cc_final: 0.8242 (tp40) REVERT: A 75 ASP cc_start: 0.8652 (m-30) cc_final: 0.8335 (t0) REVERT: A 98 TYR cc_start: 0.8444 (m-80) cc_final: 0.7981 (m-80) REVERT: A 112 MET cc_start: 0.9074 (mpm) cc_final: 0.8824 (mpp) REVERT: A 248 LYS cc_start: 0.8395 (ttpp) cc_final: 0.8168 (tttm) REVERT: A 315 ASP cc_start: 0.9212 (OUTLIER) cc_final: 0.8795 (m-30) REVERT: A 434 PHE cc_start: 0.8802 (t80) cc_final: 0.8526 (t80) REVERT: A 449 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 2 ARG cc_start: 0.7923 (ptp90) cc_final: 0.7705 (ptp-110) REVERT: B 86 TRP cc_start: 0.8944 (t60) cc_final: 0.8493 (t-100) REVERT: B 308 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: B 544 THR cc_start: 0.9343 (m) cc_final: 0.9032 (p) REVERT: B 575 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8413 (mt-10) REVERT: B 593 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: C 63 ARG cc_start: 0.7399 (mtp85) cc_final: 0.7012 (mtp180) REVERT: C 112 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8051 (ttp) REVERT: C 169 GLN cc_start: 0.9156 (mp10) cc_final: 0.8727 (mp10) REVERT: C 190 TRP cc_start: 0.7061 (m100) cc_final: 0.6792 (m100) REVERT: C 196 MET cc_start: 0.7226 (ttm) cc_final: 0.6842 (tpp) REVERT: C 248 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8725 (mtpp) REVERT: C 258 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8366 (mm-30) REVERT: C 491 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8041 (mtt90) REVERT: C 523 GLU cc_start: 0.8690 (tt0) cc_final: 0.8043 (tm-30) REVERT: C 525 GLN cc_start: 0.8284 (mp10) cc_final: 0.7591 (mp10) REVERT: D 53 MET cc_start: 0.8459 (ppp) cc_final: 0.8257 (ppp) REVERT: D 198 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5838 (tm) REVERT: D 324 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8380 (t70) outliers start: 83 outliers final: 35 residues processed: 253 average time/residue: 0.6930 time to fit residues: 199.4741 Evaluate side-chains 222 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 578 LYS Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 329 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 521 LEU 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 19 MET 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 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 6 CYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 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 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: 9.9990 chunk 221 optimal weight: 0.7980 chunk 289 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 chunk 284 optimal weight: 0.5980 chunk 190 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 217 optimal weight: 0.9980 chunk 233 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 376 GLN F 554 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.110376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.070878 restraints weight = 46486.594| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.03 r_work: 0.2793 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24517 Z= 0.118 Angle : 0.551 12.270 33458 Z= 0.266 Chirality : 0.040 0.247 3750 Planarity : 0.004 0.055 4311 Dihedral : 8.997 173.166 3612 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 2.75 % Allowed : 22.71 % 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: 1.64 (0.16), residues: 2951 helix: 2.21 (0.14), residues: 1444 sheet: 0.00 (0.29), residues: 348 loop : 0.07 (0.20), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 440 TYR 0.008 0.001 TYR D 50 PHE 0.026 0.001 PHE C 79 TRP 0.011 0.001 TRP C 364 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00271 (24499) covalent geometry : angle 0.55065 (33458) hydrogen bonds : bond 0.03157 ( 1126) hydrogen bonds : angle 4.28709 ( 3174) metal coordination : bond 0.00157 ( 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: 67 poor density : 184 time to evaluate : 0.917 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: 0.8373 (OUTLIER) cc_final: 0.8028 (tp30) REVERT: E 461 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.7623 (m90) REVERT: E 477 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8628 (mppt) REVERT: F 237 TRP cc_start: 0.8872 (t-100) cc_final: 0.8443 (t-100) REVERT: F 421 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9065 (mtpp) REVERT: F 529 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8450 (pm20) REVERT: A 1 MET cc_start: 0.7353 (tpp) cc_final: 0.6390 (pp-130) REVERT: A 19 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7193 (mpp) REVERT: A 74 GLN cc_start: 0.8512 (mp10) cc_final: 0.8201 (tm-30) REVERT: A 75 ASP cc_start: 0.8610 (m-30) cc_final: 0.8207 (t0) REVERT: A 98 TYR cc_start: 0.8409 (m-80) cc_final: 0.7885 (m-80) REVERT: A 112 MET cc_start: 0.9054 (mpm) cc_final: 0.8784 (mpp) REVERT: A 315 ASP cc_start: 0.9203 (OUTLIER) cc_final: 0.8838 (m-30) REVERT: A 434 PHE cc_start: 0.8817 (t80) cc_final: 0.8512 (t80) REVERT: A 443 MET cc_start: 0.9266 (mmm) cc_final: 0.8622 (mpt) REVERT: A 449 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 2 ARG cc_start: 0.7932 (ptp90) cc_final: 0.7714 (ptp-110) REVERT: B 40 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6491 (mm) REVERT: B 86 TRP cc_start: 0.8963 (t60) cc_final: 0.8500 (t-100) REVERT: B 308 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8090 (tp30) REVERT: B 544 THR cc_start: 0.9332 (m) cc_final: 0.9023 (p) REVERT: B 575 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: B 578 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8434 (mtmm) REVERT: B 593 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: C 63 ARG cc_start: 0.7385 (mtp85) cc_final: 0.7031 (mtp180) REVERT: C 112 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8047 (ttp) REVERT: C 169 GLN cc_start: 0.9158 (mp10) cc_final: 0.8732 (mp10) REVERT: C 190 TRP cc_start: 0.7074 (m100) cc_final: 0.6740 (m100) REVERT: C 196 MET cc_start: 0.7121 (ttm) cc_final: 0.6445 (tpp) REVERT: C 200 GLN cc_start: 0.9026 (mp10) cc_final: 0.8766 (mp10) REVERT: C 248 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8783 (mtpp) REVERT: C 258 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8378 (mm-30) REVERT: C 469 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: C 491 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8051 (mtt90) REVERT: C 523 GLU cc_start: 0.8669 (tt0) cc_final: 0.8131 (tm-30) REVERT: C 601 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8962 (mp) REVERT: D 53 MET cc_start: 0.8379 (ppp) cc_final: 0.8168 (ppp) REVERT: D 198 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5802 (tm) REVERT: D 203 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8083 (tp30) REVERT: D 324 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8329 (t70) outliers start: 67 outliers final: 23 residues processed: 240 average time/residue: 0.6921 time to fit residues: 189.7137 Evaluate side-chains 211 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain F residue 329 ARG Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 446 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 19 MET 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 40 ILE 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 578 LYS 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 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 459 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 131 optimal weight: 3.9990 chunk 288 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 41 optimal weight: 0.0000 chunk 19 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3635 r_free = 0.3635 target = 0.108566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.068983 restraints weight = 46874.984| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.00 r_work: 0.2759 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24517 Z= 0.186 Angle : 0.587 12.984 33458 Z= 0.284 Chirality : 0.041 0.215 3750 Planarity : 0.004 0.055 4311 Dihedral : 8.981 174.201 3612 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 2.99 % Allowed : 22.84 % Favored : 74.17 % 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: 1446 sheet: -0.02 (0.29), residues: 352 loop : 0.07 (0.20), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 440 TYR 0.014 0.001 TYR C 356 PHE 0.027 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 covalent geometry : bond 0.00437 (24499) covalent geometry : angle 0.58677 (33458) hydrogen bonds : bond 0.03602 ( 1126) hydrogen bonds : angle 4.35144 ( 3174) metal coordination : bond 0.00356 ( 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 251 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 178 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 461 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.7534 (m90) REVERT: E 578 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8418 (mtmm) REVERT: F 237 TRP cc_start: 0.8902 (t-100) cc_final: 0.8440 (t-100) REVERT: F 258 GLU cc_start: 0.8727 (tp30) cc_final: 0.8496 (tp30) REVERT: F 421 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9100 (mtpp) REVERT: F 461 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7951 (m90) REVERT: F 529 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8459 (pm20) REVERT: F 575 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7878 (mt-10) REVERT: A 1 MET cc_start: 0.7374 (tpp) cc_final: 0.6465 (pp-130) REVERT: A 19 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7200 (mpp) REVERT: A 74 GLN cc_start: 0.8493 (mp10) cc_final: 0.8167 (tp40) REVERT: A 75 ASP cc_start: 0.8596 (m-30) cc_final: 0.8310 (t0) REVERT: A 98 TYR cc_start: 0.8432 (m-80) cc_final: 0.8006 (m-80) REVERT: A 315 ASP cc_start: 0.9239 (OUTLIER) cc_final: 0.8812 (m-30) REVERT: A 434 PHE cc_start: 0.8803 (t80) cc_final: 0.8562 (t80) REVERT: A 443 MET cc_start: 0.9258 (mmm) cc_final: 0.8583 (mpt) REVERT: A 449 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7930 (tm-30) REVERT: B 2 ARG cc_start: 0.7930 (ptp90) cc_final: 0.7721 (ptp-110) REVERT: B 40 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6363 (pp) REVERT: B 86 TRP cc_start: 0.9011 (t60) cc_final: 0.8527 (t-100) REVERT: B 308 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: B 544 THR cc_start: 0.9325 (m) cc_final: 0.9016 (p) REVERT: B 575 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: B 593 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: C 63 ARG cc_start: 0.7415 (mtp85) cc_final: 0.7077 (mtp180) REVERT: C 112 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7957 (ttp) REVERT: C 169 GLN cc_start: 0.9200 (mp10) cc_final: 0.8763 (mp10) REVERT: C 190 TRP cc_start: 0.7090 (m100) cc_final: 0.6786 (m100) REVERT: C 196 MET cc_start: 0.7139 (ttm) cc_final: 0.6484 (tpp) REVERT: C 200 GLN cc_start: 0.9032 (mp10) cc_final: 0.8761 (mp10) REVERT: C 248 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8834 (mtpp) REVERT: C 258 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8390 (mm-30) REVERT: C 469 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: C 491 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8019 (mtt90) REVERT: C 523 GLU cc_start: 0.8686 (tt0) cc_final: 0.8233 (tm-30) REVERT: C 601 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9005 (mp) REVERT: D 53 MET cc_start: 0.8376 (ppp) cc_final: 0.8133 (ppp) REVERT: D 113 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8660 (tm-30) REVERT: D 203 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8152 (tp30) REVERT: D 324 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8415 (t70) outliers start: 73 outliers final: 29 residues processed: 240 average time/residue: 0.7410 time to fit residues: 201.7246 Evaluate side-chains 213 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 329 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 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 19 MET 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 40 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 ILE 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 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 113 GLN 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 466 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 138 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 282 optimal weight: 0.6980 chunk 241 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 376 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 269 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.107986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.067497 restraints weight = 45616.857| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.04 r_work: 0.2761 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2559 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= 0.166 Angle : 0.589 15.439 33458 Z= 0.283 Chirality : 0.041 0.210 3750 Planarity : 0.004 0.062 4311 Dihedral : 8.958 174.286 3610 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.13 % Favored : 95.80 % Rotamer: Outliers : 2.46 % Allowed : 23.74 % Favored : 73.80 % 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: 1.62 (0.16), residues: 2951 helix: 2.16 (0.14), residues: 1446 sheet: 0.01 (0.29), residues: 351 loop : 0.09 (0.20), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 440 TYR 0.012 0.001 TYR C 356 PHE 0.031 0.001 PHE B 79 TRP 0.012 0.001 TRP C 364 HIS 0.004 0.001 HIS E 409 Details of bonding type rmsd covalent geometry : bond 0.00389 (24499) covalent geometry : angle 0.58858 (33458) hydrogen bonds : bond 0.03415 ( 1126) hydrogen bonds : angle 4.32934 ( 3174) metal coordination : bond 0.00304 ( 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 232 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 240 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8482 (tp30) REVERT: E 461 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.7523 (m90) REVERT: F 237 TRP cc_start: 0.8901 (t-100) cc_final: 0.8421 (t-100) REVERT: F 258 GLU cc_start: 0.8708 (tp30) cc_final: 0.8455 (tp30) REVERT: F 421 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9093 (mtpp) REVERT: F 461 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.7846 (m90) REVERT: F 529 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8460 (pm20) REVERT: F 575 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7877 (mt-10) REVERT: A 1 MET cc_start: 0.7393 (tpp) cc_final: 0.6445 (pp-130) REVERT: A 19 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7254 (mpp) REVERT: A 74 GLN cc_start: 0.8544 (mp10) cc_final: 0.8203 (tp40) REVERT: A 75 ASP cc_start: 0.8592 (m-30) cc_final: 0.8287 (t0) REVERT: A 98 TYR cc_start: 0.8489 (m-80) cc_final: 0.7958 (m-80) REVERT: A 108 ILE cc_start: 0.3970 (OUTLIER) cc_final: 0.3414 (pp) REVERT: A 112 MET cc_start: 0.8995 (mpp) cc_final: 0.8787 (mpp) REVERT: A 315 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8809 (m-30) REVERT: A 434 PHE cc_start: 0.8790 (t80) cc_final: 0.8515 (t80) REVERT: A 443 MET cc_start: 0.9260 (mmm) cc_final: 0.8583 (mpt) REVERT: A 449 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 2 ARG cc_start: 0.7916 (ptp90) cc_final: 0.7706 (ptp-110) REVERT: B 40 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6311 (OUTLIER) REVERT: B 86 TRP cc_start: 0.8986 (t60) cc_final: 0.8504 (t-100) REVERT: B 308 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: B 544 THR cc_start: 0.9328 (m) cc_final: 0.9005 (p) REVERT: B 575 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8401 (mt-10) REVERT: B 593 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: C 63 ARG cc_start: 0.7427 (mtp85) cc_final: 0.7223 (mtp180) REVERT: C 80 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7550 (tp30) REVERT: C 112 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7992 (ttp) REVERT: C 169 GLN cc_start: 0.9206 (mp10) cc_final: 0.8776 (mp10) REVERT: C 190 TRP cc_start: 0.7098 (m100) cc_final: 0.6820 (m100) REVERT: C 196 MET cc_start: 0.7145 (ttm) cc_final: 0.6561 (tpp) REVERT: C 200 GLN cc_start: 0.9040 (mp10) cc_final: 0.8775 (mp10) REVERT: C 248 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8756 (mtpp) REVERT: C 258 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8388 (mm-30) REVERT: C 469 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: C 491 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8040 (mtt90) REVERT: C 523 GLU cc_start: 0.8637 (tt0) cc_final: 0.7900 (tm-30) REVERT: C 601 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8988 (mp) REVERT: D 198 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5807 (tm) REVERT: D 203 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8144 (tp30) REVERT: D 324 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8405 (t70) outliers start: 60 outliers final: 31 residues processed: 223 average time/residue: 0.7419 time to fit residues: 186.6256 Evaluate side-chains 215 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 329 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 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 19 MET Chi-restraints excluded: chain A residue 108 ILE 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 342 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 ILE 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 80 GLU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 459 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 149 optimal weight: 0.0050 chunk 250 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 288 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3632 r_free = 0.3632 target = 0.107649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.066922 restraints weight = 45381.681| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.04 r_work: 0.2744 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2605 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= 0.148 Angle : 0.597 15.684 33458 Z= 0.286 Chirality : 0.041 0.222 3750 Planarity : 0.004 0.055 4311 Dihedral : 8.939 173.956 3610 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 2.46 % Allowed : 23.86 % Favored : 73.68 % 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: 2.19 (0.14), residues: 1445 sheet: 0.01 (0.29), residues: 351 loop : 0.10 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 440 TYR 0.011 0.001 TYR C 356 PHE 0.035 0.001 PHE B 79 TRP 0.018 0.001 TRP D 86 HIS 0.004 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00347 (24499) covalent geometry : angle 0.59713 (33458) hydrogen bonds : bond 0.03342 ( 1126) hydrogen bonds : angle 4.30798 ( 3174) metal coordination : bond 0.00260 ( 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 229 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 240 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8371 (tp30) REVERT: E 461 HIS cc_start: 0.8682 (OUTLIER) cc_final: 0.7485 (m90) REVERT: E 477 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8400 (mttp) REVERT: F 237 TRP cc_start: 0.8892 (t-100) cc_final: 0.8414 (t-100) REVERT: F 258 GLU cc_start: 0.8684 (tp30) cc_final: 0.8397 (tp30) REVERT: F 421 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9106 (mtpp) REVERT: F 461 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.7754 (m90) REVERT: F 529 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8451 (pm20) REVERT: A 1 MET cc_start: 0.7406 (tpp) cc_final: 0.6600 (pp-130) REVERT: A 19 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7242 (mpp) REVERT: A 74 GLN cc_start: 0.8551 (mp10) cc_final: 0.8187 (tp40) REVERT: A 75 ASP cc_start: 0.8572 (m-30) cc_final: 0.8268 (t0) REVERT: A 98 TYR cc_start: 0.8378 (m-80) cc_final: 0.7970 (m-80) REVERT: A 108 ILE cc_start: 0.3782 (OUTLIER) cc_final: 0.3237 (pp) REVERT: A 315 ASP cc_start: 0.9216 (OUTLIER) cc_final: 0.8788 (m-30) REVERT: A 434 PHE cc_start: 0.8713 (t80) cc_final: 0.8432 (t80) REVERT: A 443 MET cc_start: 0.9263 (mmm) cc_final: 0.8589 (mpt) REVERT: A 449 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 2 ARG cc_start: 0.7893 (ptp90) cc_final: 0.7681 (ptp-110) REVERT: B 86 TRP cc_start: 0.8991 (t60) cc_final: 0.8497 (t-100) REVERT: B 308 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: B 544 THR cc_start: 0.9287 (m) cc_final: 0.8950 (p) REVERT: B 575 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: B 593 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: C 112 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8087 (ttp) REVERT: C 169 GLN cc_start: 0.9199 (mp10) cc_final: 0.8758 (mp10) REVERT: C 190 TRP cc_start: 0.7101 (m100) cc_final: 0.6821 (m100) REVERT: C 196 MET cc_start: 0.7114 (ttm) cc_final: 0.6640 (tpp) REVERT: C 200 GLN cc_start: 0.9040 (mp10) cc_final: 0.8792 (mp10) REVERT: C 248 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8790 (mtpp) REVERT: C 258 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8358 (mm-30) REVERT: C 469 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: C 491 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8007 (mtt90) REVERT: C 523 GLU cc_start: 0.8621 (tt0) cc_final: 0.7984 (tm-30) REVERT: C 601 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8947 (mp) REVERT: D 198 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5785 (tm) REVERT: D 203 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8165 (tp30) REVERT: D 324 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8349 (t70) outliers start: 60 outliers final: 33 residues processed: 223 average time/residue: 0.6876 time to fit residues: 175.0035 Evaluate side-chains 213 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 329 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 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 19 MET Chi-restraints excluded: chain A residue 108 ILE 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 342 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 ILE 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 105 TYR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 85 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 190 optimal weight: 20.0000 chunk 175 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 188 optimal weight: 0.0010 chunk 151 optimal weight: 0.9990 chunk 126 optimal weight: 0.0040 chunk 280 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3657 r_free = 0.3657 target = 0.109190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068605 restraints weight = 45286.930| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.07 r_work: 0.2778 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24517 Z= 0.105 Angle : 0.590 16.112 33458 Z= 0.281 Chirality : 0.040 0.199 3750 Planarity : 0.004 0.057 4311 Dihedral : 8.791 169.509 3610 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.34 % Favored : 95.59 % Rotamer: Outliers : 2.05 % Allowed : 24.31 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.17), residues: 2951 helix: 2.26 (0.14), residues: 1443 sheet: 0.13 (0.30), residues: 334 loop : 0.14 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 440 TYR 0.007 0.001 TYR A 531 PHE 0.034 0.001 PHE B 79 TRP 0.019 0.001 TRP D 86 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00240 (24499) covalent geometry : angle 0.59048 (33458) hydrogen bonds : bond 0.02934 ( 1126) hydrogen bonds : angle 4.19407 ( 3174) metal coordination : bond 0.00110 ( 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 223 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 240 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8375 (tp30) REVERT: E 430 ASP cc_start: 0.8999 (t0) cc_final: 0.8228 (t0) REVERT: E 461 HIS cc_start: 0.8656 (OUTLIER) cc_final: 0.7423 (m90) REVERT: E 477 LYS cc_start: 0.8996 (mtpt) cc_final: 0.8443 (mttp) REVERT: F 237 TRP cc_start: 0.8892 (t-100) cc_final: 0.8448 (t-100) REVERT: F 258 GLU cc_start: 0.8622 (tp30) cc_final: 0.8315 (tp30) REVERT: F 421 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9080 (mtpp) REVERT: F 461 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.7745 (m90) REVERT: F 529 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: A 1 MET cc_start: 0.7377 (tpp) cc_final: 0.6543 (pp-130) REVERT: A 19 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7218 (mpp) REVERT: A 74 GLN cc_start: 0.8533 (mp10) cc_final: 0.8197 (tp40) REVERT: A 75 ASP cc_start: 0.8549 (m-30) cc_final: 0.8247 (t0) REVERT: A 98 TYR cc_start: 0.8576 (m-80) cc_final: 0.8119 (m-80) REVERT: A 108 ILE cc_start: 0.4001 (OUTLIER) cc_final: 0.3568 (pp) REVERT: A 285 SER cc_start: 0.9488 (OUTLIER) cc_final: 0.9247 (m) REVERT: A 315 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8752 (m-30) REVERT: A 342 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8721 (t0) REVERT: A 434 PHE cc_start: 0.8747 (t80) cc_final: 0.8491 (t80) REVERT: A 443 MET cc_start: 0.9257 (mmm) cc_final: 0.8596 (mpt) REVERT: A 449 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 2 ARG cc_start: 0.7910 (ptp90) cc_final: 0.7666 (ptp-110) REVERT: B 53 MET cc_start: 0.6666 (ppp) cc_final: 0.6003 (pmt) REVERT: B 86 TRP cc_start: 0.8986 (t60) cc_final: 0.8506 (t-100) REVERT: B 308 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8028 (tp30) REVERT: B 544 THR cc_start: 0.9296 (m) cc_final: 0.8991 (p) REVERT: B 593 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: C 53 MET cc_start: 0.8327 (pp-130) cc_final: 0.8126 (ppp) REVERT: C 112 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8092 (ttp) REVERT: C 169 GLN cc_start: 0.9183 (mp10) cc_final: 0.8751 (mp10) REVERT: C 196 MET cc_start: 0.7146 (ttm) cc_final: 0.6673 (tpp) REVERT: C 200 GLN cc_start: 0.9035 (mp10) cc_final: 0.8811 (mp10) REVERT: C 248 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8784 (mtpp) REVERT: C 258 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8237 (mm-30) REVERT: C 469 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8065 (tm-30) REVERT: C 491 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8037 (mtt90) REVERT: C 523 GLU cc_start: 0.8651 (tt0) cc_final: 0.8023 (tm-30) REVERT: C 575 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7788 (mp0) REVERT: C 601 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8850 (mp) REVERT: D 198 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5671 (tm) REVERT: D 203 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8154 (tp30) REVERT: D 324 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8288 (t70) REVERT: D 440 ARG cc_start: 0.6314 (ptm160) cc_final: 0.5957 (ptm160) outliers start: 50 outliers final: 22 residues processed: 215 average time/residue: 0.6764 time to fit residues: 166.1159 Evaluate side-chains 204 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain F residue 329 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 461 HIS Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain A residue 19 MET 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 352 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 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 593 GLU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 109 SER 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: 0.6980 chunk 176 optimal weight: 1.9990 chunk 180 optimal weight: 0.4980 chunk 209 optimal weight: 0.8980 chunk 101 optimal weight: 0.0980 chunk 265 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 376 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.108954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.068636 restraints weight = 45247.426| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.05 r_work: 0.2778 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24517 Z= 0.109 Angle : 0.593 16.032 33458 Z= 0.282 Chirality : 0.040 0.197 3750 Planarity : 0.004 0.055 4311 Dihedral : 8.710 165.550 3610 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 1.72 % Allowed : 24.76 % 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: 1.75 (0.16), residues: 2951 helix: 2.27 (0.14), residues: 1443 sheet: 0.14 (0.30), residues: 339 loop : 0.13 (0.19), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 440 TYR 0.014 0.001 TYR E 356 PHE 0.035 0.001 PHE B 79 TRP 0.016 0.001 TRP D 86 HIS 0.003 0.000 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00251 (24499) covalent geometry : angle 0.59303 (33458) hydrogen bonds : bond 0.02935 ( 1126) hydrogen bonds : angle 4.16826 ( 3174) metal coordination : bond 0.00139 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6913.66 seconds wall clock time: 118 minutes 45.45 seconds (7125.45 seconds total)