Starting phenix.real_space_refine on Sat Sep 12 23:21:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pbe_20291/09_2026/6pbe_20291.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pbe_20291/09_2026/6pbe_20291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pbe_20291/09_2026/6pbe_20291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pbe_20291/09_2026/6pbe_20291.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pbe_20291/09_2026/6pbe_20291.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pbe_20291/09_2026/6pbe_20291.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pbe_20291/09_2026/6pbe_20291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pbe_20291/09_2026/6pbe_20291.map" } resolution = 3.78 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= 1.000 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: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 12608 2.51 5 N 3268 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19452 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4797 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'O6S': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.88, per 1000 atoms: 0.25 Number of scatterers: 19452 At special positions: 0 Unit cell: (135.128, 134.064, 125.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 3432 8.00 N 3268 7.00 C 12608 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: 1.65 Conformation dependent library (CDL) restraints added in 821.6 milliseconds 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 8 sheets defined 64.6% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.832A pdb=" N ASP A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 58 through 67 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.672A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.585A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.871A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.757A pdb=" N SER A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 310 through 325 removed outlier: 4.663A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 349 removed outlier: 4.447A pdb=" N VAL A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 379 through 408 Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 411 through 418 removed outlier: 4.168A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 removed outlier: 4.589A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 4.476A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 475 through 495 removed outlier: 3.926A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 512 removed outlier: 4.269A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 567 removed outlier: 4.179A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 4.185A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 4.852A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.832A pdb=" N ASP B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 58 through 67 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.672A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.586A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.872A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.757A pdb=" N SER B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 310 through 325 removed outlier: 4.663A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 349 removed outlier: 4.448A pdb=" N VAL B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 379 through 408 Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 411 through 418 removed outlier: 4.169A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 removed outlier: 4.589A pdb=" N ILE B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 4.476A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 475 through 495 removed outlier: 3.927A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 512 removed outlier: 4.269A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 567 removed outlier: 4.180A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 removed outlier: 4.185A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 4.852A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.832A pdb=" N ASP C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.672A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 119 through 128 Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.585A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 178 through 184 Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.872A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 261 through 263 No H-bonds generated for 'chain 'C' and resid 261 through 263' Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.757A pdb=" N SER C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 310 through 325 removed outlier: 4.663A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 349 removed outlier: 4.447A pdb=" N VAL C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 379 through 408 Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 411 through 418 removed outlier: 4.169A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 removed outlier: 4.588A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 4.476A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 475 through 495 removed outlier: 3.927A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 512 removed outlier: 4.269A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 507 " --> pdb=" O GLY C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 567 removed outlier: 4.180A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 585 removed outlier: 4.184A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 removed outlier: 4.853A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.831A pdb=" N ASP D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 39 " --> pdb=" O ARG D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 58 through 67 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.672A pdb=" N TYR D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.585A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 178 through 184 Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.873A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.757A pdb=" N SER D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 310 through 325 removed outlier: 4.663A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 349 removed outlier: 4.448A pdb=" N VAL D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 379 through 408 Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 411 through 418 removed outlier: 4.169A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 removed outlier: 4.589A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 4.475A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 475 through 495 removed outlier: 3.926A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 512 removed outlier: 4.269A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA D 507 " --> pdb=" O GLY D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 567 removed outlier: 4.179A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 585 removed outlier: 4.184A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 removed outlier: 4.852A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 5.528A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 276 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 5.527A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 276 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 5.527A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 removed outlier: 5.528A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR D 276 " --> pdb=" O VAL D 633 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1004 hydrogen bonds defined for protein. 2916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 2.19 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: 6165 1.34 - 1.46: 4021 1.46 - 1.58: 9498 1.58 - 1.69: 4 1.69 - 1.81: 240 Bond restraints: 19928 Sorted by residual: bond pdb=" C03 O6S D1002 " pdb=" C04 O6S D1002 " ideal model delta sigma weight residual 1.523 1.581 -0.058 2.00e-02 2.50e+03 8.38e+00 bond pdb=" C03 O6S B1002 " pdb=" C04 O6S B1002 " ideal model delta sigma weight residual 1.523 1.581 -0.058 2.00e-02 2.50e+03 8.30e+00 bond pdb=" C03 O6S A1002 " pdb=" C04 O6S A1002 " ideal model delta sigma weight residual 1.523 1.580 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" C03 O6S C1002 " pdb=" C04 O6S C1002 " ideal model delta sigma weight residual 1.523 1.580 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" C20 O6S A1001 " pdb=" N19 O6S A1001 " ideal model delta sigma weight residual 1.352 1.405 -0.053 2.00e-02 2.50e+03 7.01e+00 ... (remaining 19923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 25714 2.00 - 4.00: 1088 4.00 - 6.00: 187 6.00 - 8.00: 70 8.00 - 10.00: 25 Bond angle restraints: 27084 Sorted by residual: angle pdb=" C ASN C 208 " pdb=" N LYS C 209 " pdb=" CA LYS C 209 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C ASN A 208 " pdb=" N LYS A 209 " pdb=" CA LYS A 209 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASN B 208 " pdb=" N LYS B 209 " pdb=" CA LYS B 209 " ideal model delta sigma weight residual 121.54 130.02 -8.48 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASN D 208 " pdb=" N LYS D 209 " pdb=" CA LYS D 209 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C SER B 285 " pdb=" N TRP B 286 " pdb=" CA TRP B 286 " ideal model delta sigma weight residual 121.54 128.32 -6.78 1.91e+00 2.74e-01 1.26e+01 ... (remaining 27079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 10282 17.79 - 35.58: 1138 35.58 - 53.37: 216 53.37 - 71.15: 56 71.15 - 88.94: 32 Dihedral angle restraints: 11724 sinusoidal: 4668 harmonic: 7056 Sorted by residual: dihedral pdb=" CA CYS D 112 " pdb=" C CYS D 112 " pdb=" N GLU D 113 " pdb=" CA GLU D 113 " ideal model delta harmonic sigma weight residual -180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA CYS C 112 " pdb=" C CYS C 112 " pdb=" N GLU C 113 " pdb=" CA GLU C 113 " ideal model delta harmonic sigma weight residual 180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA CYS B 112 " pdb=" C CYS B 112 " pdb=" N GLU B 113 " pdb=" CA GLU B 113 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 11721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1769 0.040 - 0.080: 886 0.080 - 0.120: 295 0.120 - 0.161: 58 0.161 - 0.201: 40 Chirality restraints: 3048 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 3045 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 209 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C LYS C 209 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS C 209 " 0.017 2.00e-02 2.50e+03 pdb=" N THR C 210 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 209 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" C LYS D 209 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS D 209 " -0.017 2.00e-02 2.50e+03 pdb=" N THR D 210 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 209 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C LYS B 209 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS B 209 " -0.017 2.00e-02 2.50e+03 pdb=" N THR B 210 " -0.016 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4193 2.78 - 3.31: 17107 3.31 - 3.84: 30923 3.84 - 4.37: 33203 4.37 - 4.90: 58578 Nonbonded interactions: 144004 Sorted by model distance: nonbonded pdb=" O SER A 464 " pdb=" OG SER A 464 " model vdw 2.248 3.040 nonbonded pdb=" O SER C 464 " pdb=" OG SER C 464 " model vdw 2.249 3.040 nonbonded pdb=" O SER D 464 " pdb=" OG SER D 464 " model vdw 2.249 3.040 nonbonded pdb=" O SER B 464 " pdb=" OG SER B 464 " model vdw 2.249 3.040 nonbonded pdb=" OG SER A 506 " pdb=" OH TYR A 526 " model vdw 2.336 3.040 ... (remaining 143999 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.006 0.060 19928 Z= 0.288 Angle : 1.018 10.005 27084 Z= 0.513 Chirality : 0.054 0.201 3048 Planarity : 0.007 0.059 3416 Dihedral : 16.229 88.943 7164 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.18 % Allowed : 9.17 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.12), residues: 2400 helix: -2.71 (0.10), residues: 1452 sheet: -4.18 (0.58), residues: 40 loop : -4.21 (0.14), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.010 0.002 TYR C 222 PHE 0.012 0.002 PHE C 537 TRP 0.014 0.002 TRP D 613 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.29 (19928) covalent geometry : angle 1.01768 / 0.51 (27084) hydrogen bonds : bond 0.10999 / 7.66 ( 1004) hydrogen bonds : angle 5.86803 / 4.08 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 371 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7569 (mtp180) cc_final: 0.6980 (ttm170) REVERT: A 483 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8407 (tm-30) REVERT: A 628 ARG cc_start: 0.8030 (mtm180) cc_final: 0.7807 (mtp85) REVERT: B 113 GLU cc_start: 0.7301 (tp30) cc_final: 0.7089 (tp30) REVERT: B 483 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8371 (tm-30) REVERT: B 491 MET cc_start: 0.7342 (tpp) cc_final: 0.7095 (tpp) REVERT: B 495 TRP cc_start: 0.7649 (m100) cc_final: 0.7239 (m100) REVERT: C 483 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7686 (tt0) REVERT: C 495 TRP cc_start: 0.7772 (m100) cc_final: 0.7571 (m100) REVERT: C 515 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7431 (mm-30) REVERT: C 628 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7784 (mtp85) REVERT: D 483 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8346 (tm-30) REVERT: D 495 TRP cc_start: 0.7707 (m100) cc_final: 0.7328 (m100) REVERT: D 515 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7477 (mm-30) outliers start: 24 outliers final: 12 residues processed: 389 average time/residue: 0.1387 time to fit residues: 83.0355 Evaluate side-chains 293 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 281 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 394 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.0970 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN A 84 HIS A 509 HIS A 519 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 56 ASN B 84 HIS B 131 ASN B 369 GLN B 509 HIS B 519 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 84 HIS C 131 ASN C 509 HIS C 519 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 84 HIS D 131 ASN D 369 GLN D 509 HIS D 519 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.157389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132149 restraints weight = 23686.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.131624 restraints weight = 23738.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132644 restraints weight = 20676.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.132803 restraints weight = 17466.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132996 restraints weight = 16254.388| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19928 Z= 0.117 Angle : 0.584 7.629 27084 Z= 0.294 Chirality : 0.039 0.119 3048 Planarity : 0.005 0.040 3416 Dihedral : 8.585 79.716 2708 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.01 % Allowed : 17.45 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.16), residues: 2400 helix: -0.82 (0.13), residues: 1468 sheet: -4.50 (0.33), residues: 64 loop : -3.75 (0.16), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.019 0.001 TYR C 216 PHE 0.015 0.001 PHE A 574 TRP 0.006 0.001 TRP D 629 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (19928) covalent geometry : angle 0.58447 / 0.29 (27084) hydrogen bonds : bond 0.03976 / 2.71 ( 1004) hydrogen bonds : angle 4.45952 / 3.10 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 317 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7405 (mtp180) cc_final: 0.7126 (ttm170) REVERT: A 466 MET cc_start: 0.8573 (mmp) cc_final: 0.8157 (mmt) REVERT: A 483 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 601 THR cc_start: 0.7127 (m) cc_final: 0.5735 (p) REVERT: B 466 MET cc_start: 0.8523 (mmp) cc_final: 0.8112 (mmt) REVERT: B 483 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8449 (tm-30) REVERT: B 547 TYR cc_start: 0.6183 (m-80) cc_final: 0.5890 (m-80) REVERT: B 629 TRP cc_start: 0.9106 (m100) cc_final: 0.8529 (m100) REVERT: C 403 GLU cc_start: 0.7530 (tp30) cc_final: 0.7309 (tp30) REVERT: C 466 MET cc_start: 0.8547 (mmp) cc_final: 0.8158 (mmt) REVERT: C 483 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8310 (tm-30) REVERT: C 495 TRP cc_start: 0.7738 (m100) cc_final: 0.7508 (m100) REVERT: C 515 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7318 (mm-30) REVERT: C 601 THR cc_start: 0.7217 (m) cc_final: 0.5759 (p) REVERT: D 38 MET cc_start: 0.8083 (mmm) cc_final: 0.7751 (tpt) REVERT: D 466 MET cc_start: 0.8547 (mmp) cc_final: 0.8206 (mmt) REVERT: D 483 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8426 (tm-30) REVERT: D 495 TRP cc_start: 0.7765 (m100) cc_final: 0.7526 (m100) REVERT: D 515 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7471 (mm-30) REVERT: D 601 THR cc_start: 0.7176 (m) cc_final: 0.5665 (p) REVERT: D 629 TRP cc_start: 0.9113 (m100) cc_final: 0.8907 (m100) outliers start: 41 outliers final: 33 residues processed: 343 average time/residue: 0.1203 time to fit residues: 66.0930 Evaluate side-chains 319 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 201 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.156157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126760 restraints weight = 23754.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.129479 restraints weight = 14597.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130997 restraints weight = 10590.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132300 restraints weight = 8742.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132693 restraints weight = 7734.266| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19928 Z= 0.124 Angle : 0.560 8.363 27084 Z= 0.279 Chirality : 0.039 0.118 3048 Planarity : 0.004 0.038 3416 Dihedral : 8.435 74.585 2700 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.12 % Allowed : 17.70 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.17), residues: 2400 helix: -0.09 (0.14), residues: 1484 sheet: -4.53 (0.31), residues: 64 loop : -3.60 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 45 TYR 0.018 0.001 TYR D 216 PHE 0.016 0.001 PHE A 611 TRP 0.005 0.001 TRP A 583 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (19928) covalent geometry : angle 0.56014 / 0.28 (27084) hydrogen bonds : bond 0.03837 / 2.60 ( 1004) hydrogen bonds : angle 4.14621 / 2.88 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 307 time to evaluate : 0.716 Fit side-chains REVERT: A 146 ARG cc_start: 0.7622 (mtp180) cc_final: 0.7017 (ttm170) REVERT: A 403 GLU cc_start: 0.7412 (tp30) cc_final: 0.7160 (tp30) REVERT: A 483 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8461 (tm-30) REVERT: A 491 MET cc_start: 0.7891 (mmm) cc_final: 0.7239 (mmt) REVERT: A 547 TYR cc_start: 0.6110 (m-80) cc_final: 0.5845 (m-80) REVERT: A 601 THR cc_start: 0.6693 (m) cc_final: 0.5194 (p) REVERT: A 603 MET cc_start: 0.7360 (tmm) cc_final: 0.7044 (tmm) REVERT: B 353 LYS cc_start: 0.7147 (tttm) cc_final: 0.6853 (ptmt) REVERT: B 403 GLU cc_start: 0.7234 (tp30) cc_final: 0.7025 (tp30) REVERT: B 483 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8465 (tm-30) REVERT: B 491 MET cc_start: 0.7491 (tpp) cc_final: 0.7228 (mmt) REVERT: B 547 TYR cc_start: 0.6332 (m-80) cc_final: 0.6109 (m-80) REVERT: B 601 THR cc_start: 0.6554 (m) cc_final: 0.5119 (p) REVERT: B 629 TRP cc_start: 0.9154 (m100) cc_final: 0.8907 (m100) REVERT: C 353 LYS cc_start: 0.7017 (tttm) cc_final: 0.6660 (ptmt) REVERT: C 466 MET cc_start: 0.8280 (mmp) cc_final: 0.8031 (mmt) REVERT: C 483 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8362 (tm-30) REVERT: C 495 TRP cc_start: 0.7759 (m100) cc_final: 0.7544 (m100) REVERT: C 601 THR cc_start: 0.6802 (m) cc_final: 0.5257 (p) REVERT: D 38 MET cc_start: 0.8318 (mmm) cc_final: 0.7999 (tpt) REVERT: D 466 MET cc_start: 0.8389 (mmp) cc_final: 0.8097 (mmt) REVERT: D 483 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8452 (tm-30) REVERT: D 495 TRP cc_start: 0.7762 (m100) cc_final: 0.7544 (m100) REVERT: D 515 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7450 (mm-30) REVERT: D 601 THR cc_start: 0.6822 (m) cc_final: 0.5263 (p) REVERT: D 629 TRP cc_start: 0.9154 (m100) cc_final: 0.8877 (m100) outliers start: 84 outliers final: 61 residues processed: 362 average time/residue: 0.1120 time to fit residues: 66.9011 Evaluate side-chains 342 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 281 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 136 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 227 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 55 optimal weight: 0.0970 chunk 158 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 196 optimal weight: 0.2980 chunk 197 optimal weight: 5.9990 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131518 restraints weight = 23667.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130797 restraints weight = 22938.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131898 restraints weight = 23272.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132281 restraints weight = 18399.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132479 restraints weight = 16143.199| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19928 Z= 0.123 Angle : 0.560 9.986 27084 Z= 0.275 Chirality : 0.039 0.120 3048 Planarity : 0.004 0.040 3416 Dihedral : 8.108 66.507 2700 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.17 % Allowed : 19.61 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.17), residues: 2400 helix: 0.26 (0.14), residues: 1488 sheet: -4.01 (0.34), residues: 64 loop : -3.41 (0.17), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 628 TYR 0.010 0.001 TYR D 216 PHE 0.023 0.001 PHE A 611 TRP 0.007 0.001 TRP C 583 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (19928) covalent geometry : angle 0.56034 / 0.28 (27084) hydrogen bonds : bond 0.03692 / 2.50 ( 1004) hydrogen bonds : angle 4.06400 / 2.83 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 295 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7581 (mtp180) cc_final: 0.7191 (ttm170) REVERT: A 353 LYS cc_start: 0.7239 (tttm) cc_final: 0.6870 (ptmt) REVERT: A 403 GLU cc_start: 0.7522 (tp30) cc_final: 0.7271 (tp30) REVERT: A 483 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8526 (tm-30) REVERT: A 547 TYR cc_start: 0.6292 (m-80) cc_final: 0.6080 (m-80) REVERT: A 601 THR cc_start: 0.6943 (m) cc_final: 0.5448 (p) REVERT: B 403 GLU cc_start: 0.7380 (tp30) cc_final: 0.7139 (tp30) REVERT: B 483 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8513 (tm-30) REVERT: B 547 TYR cc_start: 0.6443 (m-80) cc_final: 0.6235 (m-80) REVERT: B 601 THR cc_start: 0.7086 (m) cc_final: 0.5615 (p) REVERT: C 483 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8393 (tm-30) REVERT: C 601 THR cc_start: 0.6927 (m) cc_final: 0.5370 (p) REVERT: D 38 MET cc_start: 0.8128 (mmm) cc_final: 0.7833 (tpt) REVERT: D 483 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8520 (tm-30) REVERT: D 515 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7421 (mm-30) REVERT: D 601 THR cc_start: 0.6949 (m) cc_final: 0.5362 (p) REVERT: D 629 TRP cc_start: 0.9137 (m100) cc_final: 0.8934 (m100) outliers start: 85 outliers final: 73 residues processed: 354 average time/residue: 0.1098 time to fit residues: 64.9045 Evaluate side-chains 351 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 278 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.149084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124635 restraints weight = 24178.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124340 restraints weight = 25469.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125051 restraints weight = 23438.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.125115 restraints weight = 21515.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125483 restraints weight = 19534.643| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19928 Z= 0.217 Angle : 0.688 9.792 27084 Z= 0.341 Chirality : 0.043 0.246 3048 Planarity : 0.005 0.044 3416 Dihedral : 7.711 64.677 2700 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.54 % Allowed : 20.15 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.17), residues: 2400 helix: 0.07 (0.14), residues: 1484 sheet: -3.99 (0.36), residues: 64 loop : -3.39 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 628 TYR 0.013 0.002 TYR B 222 PHE 0.021 0.002 PHE A 611 TRP 0.013 0.001 TRP C 583 HIS 0.005 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (19928) covalent geometry : angle 0.68782 / 0.34 (27084) hydrogen bonds : bond 0.05078 / 3.46 ( 1004) hydrogen bonds : angle 4.43064 / 3.08 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 266 time to evaluate : 0.754 Fit side-chains REVERT: A 146 ARG cc_start: 0.7802 (mtp180) cc_final: 0.7547 (ttm170) REVERT: A 353 LYS cc_start: 0.7349 (tttm) cc_final: 0.7048 (ptmt) REVERT: A 547 TYR cc_start: 0.6385 (m-80) cc_final: 0.6072 (m-80) REVERT: B 403 GLU cc_start: 0.7675 (tp30) cc_final: 0.7465 (tp30) REVERT: B 547 TYR cc_start: 0.6488 (m-80) cc_final: 0.6131 (m-80) REVERT: D 38 MET cc_start: 0.8148 (mmm) cc_final: 0.7897 (tpt) outliers start: 113 outliers final: 86 residues processed: 344 average time/residue: 0.1124 time to fit residues: 64.2878 Evaluate side-chains 338 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 252 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 45 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 596 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 HIS ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.155552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149732 restraints weight = 23518.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148666 restraints weight = 34881.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.147850 restraints weight = 37240.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146785 restraints weight = 40071.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.145983 restraints weight = 42886.501| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19928 Z= 0.103 Angle : 0.564 8.826 27084 Z= 0.273 Chirality : 0.039 0.265 3048 Planarity : 0.004 0.039 3416 Dihedral : 7.280 62.712 2700 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.53 % Allowed : 23.92 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.17), residues: 2400 helix: 0.63 (0.14), residues: 1460 sheet: -3.73 (0.39), residues: 64 loop : -3.13 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 45 TYR 0.014 0.001 TYR D 216 PHE 0.021 0.001 PHE A 611 TRP 0.019 0.001 TRP B 629 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (19928) covalent geometry : angle 0.56364 / 0.27 (27084) hydrogen bonds : bond 0.03392 / 2.29 ( 1004) hydrogen bonds : angle 4.06703 / 2.83 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 302 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 MET cc_start: 0.8528 (mmp) cc_final: 0.8295 (mmt) REVERT: A 483 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8694 (tm-30) REVERT: A 515 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: B 466 MET cc_start: 0.8427 (mmp) cc_final: 0.8217 (mmt) REVERT: B 483 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8556 (tm-30) REVERT: C 466 MET cc_start: 0.8476 (mmp) cc_final: 0.8242 (mmt) REVERT: C 483 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 515 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7133 (mm-30) REVERT: D 466 MET cc_start: 0.8547 (mmp) cc_final: 0.8285 (mmt) REVERT: D 483 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8611 (tm-30) REVERT: D 515 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7152 (mm-30) outliers start: 72 outliers final: 63 residues processed: 359 average time/residue: 0.1082 time to fit residues: 63.7902 Evaluate side-chains 342 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 278 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 369 GLN Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 462 TRP Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 72 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 178 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 235 optimal weight: 0.0050 chunk 129 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 overall best weight: 2.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.153510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3451 r_free = 0.3451 target = 0.128250 restraints weight = 23984.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129317 restraints weight = 17838.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129511 restraints weight = 14619.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129646 restraints weight = 13819.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129669 restraints weight = 13734.555| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19928 Z= 0.147 Angle : 0.608 8.838 27084 Z= 0.296 Chirality : 0.041 0.306 3048 Planarity : 0.004 0.039 3416 Dihedral : 7.158 63.154 2700 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.90 % Allowed : 23.09 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.17), residues: 2400 helix: 0.61 (0.14), residues: 1464 sheet: -3.65 (0.42), residues: 64 loop : -3.11 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.014 0.001 TYR C 216 PHE 0.018 0.001 PHE A 611 TRP 0.031 0.001 TRP B 629 HIS 0.003 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (19928) covalent geometry : angle 0.60777 / 0.30 (27084) hydrogen bonds : bond 0.04069 / 2.76 ( 1004) hydrogen bonds : angle 4.16094 / 2.90 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 273 time to evaluate : 0.656 Fit side-chains REVERT: A 341 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7970 (tp) REVERT: A 483 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8681 (tm-30) REVERT: A 554 MET cc_start: 0.7208 (tpp) cc_final: 0.7001 (tpp) REVERT: A 601 THR cc_start: 0.7200 (m) cc_final: 0.5645 (p) REVERT: B 483 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8626 (tm-30) REVERT: B 554 MET cc_start: 0.7237 (tpp) cc_final: 0.7023 (tpp) REVERT: B 601 THR cc_start: 0.7242 (m) cc_final: 0.5741 (p) REVERT: B 629 TRP cc_start: 0.8992 (m100) cc_final: 0.8758 (m100) REVERT: C 483 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8469 (tm-30) REVERT: C 491 MET cc_start: 0.7253 (tpp) cc_final: 0.7047 (tpp) REVERT: C 601 THR cc_start: 0.7251 (m) cc_final: 0.5767 (p) REVERT: D 483 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8607 (tm-30) REVERT: D 570 MET cc_start: 0.6657 (tpp) cc_final: 0.6432 (tpp) REVERT: D 601 THR cc_start: 0.7250 (m) cc_final: 0.5698 (p) outliers start: 100 outliers final: 87 residues processed: 346 average time/residue: 0.1087 time to fit residues: 63.2398 Evaluate side-chains 355 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 267 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 462 TRP Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 172 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.149080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124933 restraints weight = 24256.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125588 restraints weight = 17160.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125530 restraints weight = 14205.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125537 restraints weight = 13837.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125564 restraints weight = 13832.353| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 19928 Z= 0.227 Angle : 0.710 8.935 27084 Z= 0.349 Chirality : 0.044 0.250 3048 Planarity : 0.004 0.041 3416 Dihedral : 7.005 60.974 2700 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 5.49 % Allowed : 22.89 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.17), residues: 2400 helix: 0.32 (0.14), residues: 1460 sheet: -3.60 (0.43), residues: 64 loop : -3.13 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.012 0.002 TYR C 216 PHE 0.017 0.002 PHE A 611 TRP 0.033 0.001 TRP B 629 HIS 0.005 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (19928) covalent geometry : angle 0.71049 / 0.35 (27084) hydrogen bonds : bond 0.05189 / 3.53 ( 1004) hydrogen bonds : angle 4.51211 / 3.14 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 259 time to evaluate : 0.650 Fit side-chains REVERT: A 341 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7951 (tp) REVERT: A 466 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8258 (mmt) REVERT: A 554 MET cc_start: 0.7193 (tpp) cc_final: 0.6932 (tpp) REVERT: B 341 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7850 (tp) REVERT: B 466 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8251 (mmt) REVERT: B 483 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8628 (tm-30) REVERT: B 554 MET cc_start: 0.7291 (tpp) cc_final: 0.7027 (tpp) REVERT: C 466 MET cc_start: 0.8444 (mmp) cc_final: 0.8164 (mmt) REVERT: C 491 MET cc_start: 0.7398 (tpp) cc_final: 0.7154 (tpp) REVERT: D 341 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7909 (tp) REVERT: D 466 MET cc_start: 0.8536 (mmp) cc_final: 0.8273 (mmt) REVERT: D 570 MET cc_start: 0.6914 (tpp) cc_final: 0.6651 (tpp) outliers start: 112 outliers final: 90 residues processed: 347 average time/residue: 0.1087 time to fit residues: 63.0815 Evaluate side-chains 345 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 250 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 219 optimal weight: 0.9980 chunk 232 optimal weight: 0.4980 chunk 201 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 509 HIS ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 596 GLN ** 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 = 0.3711 r_free = 0.3711 target = 0.155812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150038 restraints weight = 23383.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.148699 restraints weight = 33619.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.147826 restraints weight = 35961.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.147287 restraints weight = 37182.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.146869 restraints weight = 38622.002| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19928 Z= 0.103 Angle : 0.583 12.677 27084 Z= 0.279 Chirality : 0.039 0.199 3048 Planarity : 0.004 0.038 3416 Dihedral : 6.599 62.680 2700 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.63 % Allowed : 25.39 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2400 helix: 0.77 (0.14), residues: 1464 sheet: -3.49 (0.45), residues: 64 loop : -3.00 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.012 0.001 TYR D 216 PHE 0.012 0.001 PHE A 611 TRP 0.021 0.001 TRP B 629 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (19928) covalent geometry : angle 0.58280 / 0.28 (27084) hydrogen bonds : bond 0.03295 / 2.23 ( 1004) hydrogen bonds : angle 4.07154 / 2.84 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 299 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8261 (tp) REVERT: A 466 MET cc_start: 0.8575 (mmp) cc_final: 0.8287 (mmt) REVERT: A 483 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8654 (tm-30) REVERT: B 341 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8162 (tp) REVERT: B 466 MET cc_start: 0.8546 (mmp) cc_final: 0.8294 (mmt) REVERT: B 483 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8568 (tm-30) REVERT: C 483 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8423 (tm-30) REVERT: D 483 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8658 (tm-30) REVERT: D 515 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7178 (mm-30) outliers start: 74 outliers final: 65 residues processed: 354 average time/residue: 0.1131 time to fit residues: 65.7857 Evaluate side-chains 352 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 285 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 462 TRP Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 597 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 201 optimal weight: 0.4980 chunk 185 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 234 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.156067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.150274 restraints weight = 23508.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.148539 restraints weight = 35233.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.147622 restraints weight = 39248.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.147004 restraints weight = 41322.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146134 restraints weight = 41009.797| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19928 Z= 0.104 Angle : 0.587 12.451 27084 Z= 0.277 Chirality : 0.039 0.167 3048 Planarity : 0.004 0.037 3416 Dihedral : 6.339 63.908 2700 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.09 % Allowed : 25.78 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.18), residues: 2400 helix: 0.93 (0.14), residues: 1472 sheet: -3.28 (0.46), residues: 64 loop : -2.94 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.011 0.001 TYR A 547 PHE 0.015 0.001 PHE A 611 TRP 0.022 0.001 TRP B 629 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (19928) covalent geometry : angle 0.58650 / 0.28 (27084) hydrogen bonds : bond 0.03306 / 2.23 ( 1004) hydrogen bonds : angle 3.98137 / 2.77 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 304 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 341 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8282 (tp) REVERT: A 466 MET cc_start: 0.8622 (mmp) cc_final: 0.8366 (mmt) REVERT: A 483 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8605 (tm-30) REVERT: B 466 MET cc_start: 0.8548 (mmp) cc_final: 0.8312 (mmt) REVERT: B 483 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8521 (tm-30) REVERT: C 466 MET cc_start: 0.8534 (mmp) cc_final: 0.8268 (mmt) REVERT: C 483 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8423 (tm-30) REVERT: D 466 MET cc_start: 0.8604 (mmp) cc_final: 0.8273 (mmt) REVERT: D 483 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8619 (tm-30) REVERT: D 515 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7178 (mm-30) outliers start: 63 outliers final: 60 residues processed: 354 average time/residue: 0.1130 time to fit residues: 66.3953 Evaluate side-chains 360 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 299 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 597 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 218 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 chunk 222 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.154847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149257 restraints weight = 23618.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148149 restraints weight = 33141.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.147029 restraints weight = 39626.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.145618 restraints weight = 41255.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138200 restraints weight = 49045.434| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19928 Z= 0.116 Angle : 0.604 12.597 27084 Z= 0.285 Chirality : 0.040 0.246 3048 Planarity : 0.004 0.038 3416 Dihedral : 6.239 63.748 2700 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.43 % Allowed : 25.98 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 2400 helix: 0.93 (0.14), residues: 1460 sheet: -3.12 (0.48), residues: 64 loop : -2.84 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.010 0.001 TYR D 216 PHE 0.015 0.001 PHE A 611 TRP 0.034 0.001 TRP B 629 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (19928) covalent geometry : angle 0.60403 / 0.28 (27084) hydrogen bonds : bond 0.03514 / 2.38 ( 1004) hydrogen bonds : angle 4.00031 / 2.79 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.08 seconds wall clock time: 48 minutes 8.35 seconds (2888.35 seconds total)