Starting phenix.real_space_refine on Thu Mar 5 04:25:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pbe_20291/03_2026/6pbe_20291.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pbe_20291/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pbe_20291/03_2026/6pbe_20291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pbe_20291/03_2026/6pbe_20291.map" model { file = "/net/cci-nas-00/data/ceres_data/6pbe_20291/03_2026/6pbe_20291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pbe_20291/03_2026/6pbe_20291.cif" } 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-dev-5986/lib/python3.9/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: 4.10, per 1000 atoms: 0.21 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: 1.60 Conformation dependent library (CDL) restraints added in 914.6 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: 0.58 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: 3.00 Time building geometry restraints manager: 2.10 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 - 31.71: 11260 31.71 - 63.43: 456 63.43 - 95.14: 52 95.14 - 126.85: 0 126.85 - 158.57: 4 Dihedral angle restraints: 11772 sinusoidal: 4716 harmonic: 7056 Sorted by residual: dihedral pdb=" C03 O6S A1001 " pdb=" C02 O6S A1001 " pdb=" O16 O6S A1001 " pdb=" C17 O6S A1001 " ideal model delta sinusoidal sigma weight residual 178.86 -22.57 -158.57 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C03 O6S B1001 " pdb=" C02 O6S B1001 " pdb=" O16 O6S B1001 " pdb=" C17 O6S B1001 " ideal model delta sinusoidal sigma weight residual 178.86 -22.57 -158.57 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C03 O6S C1001 " pdb=" C02 O6S C1001 " pdb=" O16 O6S C1001 " pdb=" C17 O6S C1001 " ideal model delta sinusoidal sigma weight residual 178.86 -22.58 -158.56 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 11769 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: 0.460 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.170 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 16.964 158.568 7212 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 covalent geometry : bond 0.00644 (19928) covalent geometry : angle 1.01768 (27084) hydrogen bonds : bond 0.10999 ( 1004) hydrogen bonds : angle 5.86803 ( 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 : 0.658 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: 0.1390 time to fit residues: 82.9422 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 : 0.791 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 56 ASN 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134108 restraints weight = 23712.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.133435 restraints weight = 24480.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134228 restraints weight = 23720.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134558 restraints weight = 19686.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134754 restraints weight = 17814.311| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19928 Z= 0.120 Angle : 0.589 7.491 27084 Z= 0.296 Chirality : 0.039 0.119 3048 Planarity : 0.005 0.041 3416 Dihedral : 11.929 170.770 2756 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.06 % Allowed : 17.40 % 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: -2.98 (0.16), residues: 2400 helix: -0.85 (0.13), residues: 1468 sheet: -4.51 (0.33), residues: 64 loop : -3.76 (0.16), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.016 0.001 TYR C 216 PHE 0.016 0.001 PHE A 574 TRP 0.006 0.001 TRP C 286 HIS 0.002 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00266 (19928) covalent geometry : angle 0.58872 (27084) hydrogen bonds : bond 0.04020 ( 1004) hydrogen bonds : angle 4.48526 ( 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 356 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 314 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7389 (mtp180) cc_final: 0.7129 (ttm170) REVERT: A 466 MET cc_start: 0.8586 (mmp) cc_final: 0.8137 (mmt) REVERT: A 483 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 491 MET cc_start: 0.7281 (tpp) cc_final: 0.7047 (mmt) REVERT: A 601 THR cc_start: 0.7126 (m) cc_final: 0.5742 (p) REVERT: B 466 MET cc_start: 0.8534 (mmp) cc_final: 0.8107 (mmt) REVERT: B 483 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 547 TYR cc_start: 0.6184 (m-80) cc_final: 0.5881 (m-80) REVERT: B 629 TRP cc_start: 0.9106 (m100) cc_final: 0.8532 (m100) REVERT: C 403 GLU cc_start: 0.7532 (tp30) cc_final: 0.7296 (tp30) REVERT: C 466 MET cc_start: 0.8548 (mmp) cc_final: 0.8152 (mmt) REVERT: C 483 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8313 (tm-30) REVERT: C 495 TRP cc_start: 0.7742 (m100) cc_final: 0.7512 (m100) REVERT: C 515 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7301 (mm-30) REVERT: C 601 THR cc_start: 0.7206 (m) cc_final: 0.5748 (p) REVERT: D 38 MET cc_start: 0.8023 (mmm) cc_final: 0.7682 (tpt) REVERT: D 466 MET cc_start: 0.8544 (mmp) cc_final: 0.8196 (mmt) REVERT: D 483 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8421 (tm-30) REVERT: D 495 TRP cc_start: 0.7776 (m100) cc_final: 0.7377 (m100) REVERT: D 515 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7473 (mm-30) REVERT: D 601 THR cc_start: 0.7017 (m) cc_final: 0.5509 (p) REVERT: D 629 TRP cc_start: 0.9110 (m100) cc_final: 0.8901 (m100) outliers start: 42 outliers final: 32 residues processed: 342 average time/residue: 0.1212 time to fit residues: 66.2248 Evaluate side-chains 318 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 57 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 11 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** 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 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 = 0.3740 r_free = 0.3740 target = 0.156315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131890 restraints weight = 23735.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131422 restraints weight = 26718.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132107 restraints weight = 26259.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132416 restraints weight = 21649.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132817 restraints weight = 19529.064| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19928 Z= 0.130 Angle : 0.566 7.965 27084 Z= 0.283 Chirality : 0.039 0.119 3048 Planarity : 0.004 0.039 3416 Dihedral : 11.590 179.761 2748 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.92 % Allowed : 17.84 % Favored : 78.24 % 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: -2.19 (0.17), residues: 2400 helix: -0.15 (0.14), residues: 1484 sheet: -4.52 (0.31), residues: 64 loop : -3.61 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 45 TYR 0.015 0.001 TYR D 216 PHE 0.016 0.001 PHE A 611 TRP 0.006 0.001 TRP A 583 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00303 (19928) covalent geometry : angle 0.56575 (27084) hydrogen bonds : bond 0.03935 ( 1004) hydrogen bonds : angle 4.18716 ( 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 376 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 296 time to evaluate : 0.459 Fit side-chains REVERT: A 146 ARG cc_start: 0.7507 (mtp180) cc_final: 0.7191 (ttm170) REVERT: A 403 GLU cc_start: 0.7575 (tp30) cc_final: 0.7325 (tp30) REVERT: A 483 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 547 TYR cc_start: 0.6068 (m-80) cc_final: 0.5800 (m-80) REVERT: A 601 THR cc_start: 0.6970 (m) cc_final: 0.5475 (p) REVERT: A 603 MET cc_start: 0.7414 (tmm) cc_final: 0.7115 (tmm) REVERT: B 353 LYS cc_start: 0.7268 (tttm) cc_final: 0.6990 (ptmt) REVERT: B 403 GLU cc_start: 0.7362 (tp30) cc_final: 0.7150 (tp30) REVERT: B 483 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8513 (tm-30) REVERT: B 491 MET cc_start: 0.7442 (tpp) cc_final: 0.7187 (mmt) REVERT: B 547 TYR cc_start: 0.6182 (m-80) cc_final: 0.5966 (m-80) REVERT: C 353 LYS cc_start: 0.7204 (tttm) cc_final: 0.6872 (ptmt) REVERT: C 403 GLU cc_start: 0.7546 (tp30) cc_final: 0.7323 (tp30) REVERT: C 466 MET cc_start: 0.8460 (mmp) cc_final: 0.8166 (mmt) REVERT: C 483 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8410 (tm-30) REVERT: C 547 TYR cc_start: 0.6392 (m-80) cc_final: 0.6192 (m-80) REVERT: C 601 THR cc_start: 0.7341 (m) cc_final: 0.5890 (p) REVERT: D 38 MET cc_start: 0.8055 (mmm) cc_final: 0.7764 (tpt) REVERT: D 466 MET cc_start: 0.8562 (mmp) cc_final: 0.8246 (mmt) REVERT: D 483 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8512 (tm-30) REVERT: D 601 THR cc_start: 0.7108 (m) cc_final: 0.5560 (p) outliers start: 80 outliers final: 61 residues processed: 349 average time/residue: 0.1149 time to fit residues: 65.3150 Evaluate side-chains 338 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 277 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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 542 ASP 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 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 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 408 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 465 VAL 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 252 ASN 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 602 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 136 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 227 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 55 optimal weight: 0.2980 chunk 158 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3727 r_free = 0.3727 target = 0.155154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130825 restraints weight = 23675.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130107 restraints weight = 22694.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131641 restraints weight = 22842.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131683 restraints weight = 18627.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131850 restraints weight = 17091.422| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2119 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= 0.138 Angle : 0.578 10.199 27084 Z= 0.285 Chirality : 0.040 0.118 3048 Planarity : 0.004 0.041 3416 Dihedral : 11.216 172.358 2748 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.36 % Allowed : 19.31 % Favored : 76.32 % 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: -1.75 (0.17), residues: 2400 helix: 0.19 (0.14), residues: 1484 sheet: -4.11 (0.33), residues: 64 loop : -3.43 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 628 TYR 0.013 0.001 TYR D 216 PHE 0.023 0.001 PHE A 611 TRP 0.011 0.001 TRP D 629 HIS 0.004 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00325 (19928) covalent geometry : angle 0.57811 (27084) hydrogen bonds : bond 0.03961 ( 1004) hydrogen bonds : angle 4.13754 ( 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 379 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 290 time to evaluate : 0.503 Fit side-chains REVERT: A 146 ARG cc_start: 0.7627 (mtp180) cc_final: 0.7384 (ttm170) REVERT: A 353 LYS cc_start: 0.7250 (tttm) cc_final: 0.6879 (ptmt) REVERT: A 403 GLU cc_start: 0.7582 (tp30) cc_final: 0.7357 (tp30) REVERT: A 483 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 547 TYR cc_start: 0.6325 (m-80) cc_final: 0.6074 (m-80) REVERT: A 601 THR cc_start: 0.6994 (m) cc_final: 0.5517 (p) REVERT: B 353 LYS cc_start: 0.7278 (tttm) cc_final: 0.7054 (ptmt) REVERT: B 403 GLU cc_start: 0.7395 (tp30) cc_final: 0.7175 (tp30) REVERT: B 483 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8507 (tm-30) REVERT: B 601 THR cc_start: 0.7137 (m) cc_final: 0.5661 (p) REVERT: C 466 MET cc_start: 0.8500 (mmp) cc_final: 0.8176 (mmt) REVERT: C 483 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8311 (tm-30) REVERT: C 601 THR cc_start: 0.7002 (m) cc_final: 0.5440 (p) REVERT: D 38 MET cc_start: 0.8151 (mmm) cc_final: 0.7849 (tpt) REVERT: D 483 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8519 (tm-30) REVERT: D 601 THR cc_start: 0.6900 (m) cc_final: 0.5297 (p) outliers start: 89 outliers final: 80 residues processed: 354 average time/residue: 0.1064 time to fit residues: 63.1039 Evaluate side-chains 350 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 270 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 499 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 565 ILE 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 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 499 VAL 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 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 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 499 VAL 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 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 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 565 ILE 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: 4.9990 chunk 131 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 146 optimal weight: 0.0050 chunk 125 optimal weight: 9.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 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 = 0.3693 r_free = 0.3693 target = 0.151773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126896 restraints weight = 24058.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127637 restraints weight = 18483.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127913 restraints weight = 15154.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127931 restraints weight = 14174.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128020 restraints weight = 14345.873| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19928 Z= 0.184 Angle : 0.640 9.641 27084 Z= 0.316 Chirality : 0.042 0.231 3048 Planarity : 0.004 0.041 3416 Dihedral : 10.859 179.993 2748 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 5.54 % Allowed : 20.49 % Favored : 73.97 % 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: -1.67 (0.17), residues: 2400 helix: 0.24 (0.14), residues: 1460 sheet: -3.97 (0.36), residues: 64 loop : -3.30 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 628 TYR 0.010 0.001 TYR B 222 PHE 0.021 0.001 PHE A 611 TRP 0.011 0.001 TRP D 629 HIS 0.004 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00445 (19928) covalent geometry : angle 0.63982 (27084) hydrogen bonds : bond 0.04680 ( 1004) hydrogen bonds : angle 4.33269 ( 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 383 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 270 time to evaluate : 0.572 Fit side-chains REVERT: A 146 ARG cc_start: 0.7815 (mtp180) cc_final: 0.7374 (ttm170) REVERT: A 353 LYS cc_start: 0.7279 (tttm) cc_final: 0.6948 (ptmt) REVERT: A 483 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 547 TYR cc_start: 0.6397 (m-80) cc_final: 0.6117 (m-80) REVERT: B 353 LYS cc_start: 0.7204 (tttm) cc_final: 0.6908 (ptmt) REVERT: B 629 TRP cc_start: 0.9163 (m100) cc_final: 0.8924 (m100) REVERT: C 483 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8426 (tm-30) REVERT: C 601 THR cc_start: 0.7223 (m) cc_final: 0.5642 (p) REVERT: D 38 MET cc_start: 0.8190 (mmm) cc_final: 0.7929 (tpt) outliers start: 113 outliers final: 87 residues processed: 350 average time/residue: 0.1057 time to fit residues: 61.9935 Evaluate side-chains 350 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 263 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 429 ILE Chi-restraints excluded: chain A residue 436 VAL 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 565 ILE 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 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 565 ILE Chi-restraints excluded: chain B residue 597 VAL 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 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 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 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 162 TYR 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 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: 1.9990 chunk 239 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 152 optimal weight: 0.0770 chunk 18 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.156183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132584 restraints weight = 23656.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131684 restraints weight = 24679.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.132326 restraints weight = 24558.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132737 restraints weight = 21039.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132950 restraints weight = 18793.516| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2452 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= 0.105 Angle : 0.565 9.522 27084 Z= 0.271 Chirality : 0.039 0.284 3048 Planarity : 0.004 0.038 3416 Dihedral : 10.399 171.010 2748 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.82 % Allowed : 23.73 % Favored : 72.45 % 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: -1.19 (0.17), residues: 2400 helix: 0.63 (0.14), residues: 1464 sheet: -3.67 (0.39), residues: 64 loop : -3.13 (0.18), residues: 872 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 0.022 0.001 PHE A 611 TRP 0.007 0.001 TRP C 286 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00234 (19928) covalent geometry : angle 0.56539 (27084) hydrogen bonds : bond 0.03431 ( 1004) hydrogen bonds : angle 4.06433 ( 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 384 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7733 (mtp180) cc_final: 0.7364 (ttm170) REVERT: A 341 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7958 (tp) REVERT: A 353 LYS cc_start: 0.7206 (tttm) cc_final: 0.6973 (ptmt) REVERT: A 466 MET cc_start: 0.8523 (mmp) cc_final: 0.8295 (mmt) REVERT: A 483 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8596 (tm-30) REVERT: A 547 TYR cc_start: 0.6269 (m-80) cc_final: 0.6030 (m-80) REVERT: A 603 MET cc_start: 0.7471 (tmm) cc_final: 0.7267 (tmm) REVERT: B 483 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8544 (tm-30) REVERT: B 629 TRP cc_start: 0.9176 (m100) cc_final: 0.8910 (m100) REVERT: C 483 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8393 (tm-30) REVERT: D 38 MET cc_start: 0.8085 (mmm) cc_final: 0.7809 (tpt) REVERT: D 483 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8561 (tm-30) REVERT: D 515 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7383 (mm-30) outliers start: 78 outliers final: 68 residues processed: 361 average time/residue: 0.1071 time to fit residues: 63.8009 Evaluate side-chains 357 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 288 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 454 LEU 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 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 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 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 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 397 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 429 ILE 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 528 THR 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 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 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 528 THR Chi-restraints excluded: chain D residue 565 ILE 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: 7.9990 chunk 6 optimal weight: 5.9990 chunk 233 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 168 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130310 restraints weight = 23827.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129596 restraints weight = 22689.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130501 restraints weight = 23945.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131300 restraints weight = 19013.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131222 restraints weight = 16932.364| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2523 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= 0.138 Angle : 0.592 8.175 27084 Z= 0.290 Chirality : 0.040 0.281 3048 Planarity : 0.004 0.038 3416 Dihedral : 10.001 160.730 2748 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.95 % Allowed : 22.94 % Favored : 72.11 % 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: -1.12 (0.17), residues: 2400 helix: 0.66 (0.14), residues: 1464 sheet: -3.53 (0.41), residues: 64 loop : -3.08 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.019 0.001 TYR C 216 PHE 0.020 0.001 PHE A 611 TRP 0.005 0.001 TRP A 583 HIS 0.003 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00326 (19928) covalent geometry : angle 0.59159 (27084) hydrogen bonds : bond 0.03893 ( 1004) hydrogen bonds : angle 4.11595 ( 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 381 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 280 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7841 (mtp180) cc_final: 0.7428 (ttm170) REVERT: A 215 MET cc_start: 0.7031 (tpp) cc_final: 0.6770 (tpp) REVERT: A 341 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7907 (tp) REVERT: A 353 LYS cc_start: 0.7121 (tttm) cc_final: 0.6918 (ptmt) REVERT: A 466 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8283 (mmm) REVERT: A 483 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8632 (tm-30) REVERT: A 547 TYR cc_start: 0.6402 (m-80) cc_final: 0.6197 (m-80) REVERT: A 554 MET cc_start: 0.7159 (tpp) cc_final: 0.6954 (tpp) REVERT: A 601 THR cc_start: 0.6953 (m) cc_final: 0.5406 (p) REVERT: A 603 MET cc_start: 0.7495 (tmm) cc_final: 0.7224 (tmm) REVERT: B 466 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8230 (mmm) REVERT: B 483 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8588 (tm-30) REVERT: B 554 MET cc_start: 0.7194 (tpp) cc_final: 0.6990 (tpp) REVERT: B 601 THR cc_start: 0.6944 (m) cc_final: 0.5451 (p) REVERT: B 629 TRP cc_start: 0.9160 (m100) cc_final: 0.8899 (m100) REVERT: C 483 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8429 (tm-30) REVERT: D 38 MET cc_start: 0.8156 (mmm) cc_final: 0.7877 (tpt) REVERT: D 601 THR cc_start: 0.6917 (m) cc_final: 0.5404 (p) outliers start: 101 outliers final: 87 residues processed: 350 average time/residue: 0.1039 time to fit residues: 60.9011 Evaluate side-chains 364 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 274 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 397 VAL Chi-restraints excluded: chain A residue 408 PHE 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 466 MET 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 A residue 578 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 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 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 369 GLN 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 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 481 MET 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 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 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 528 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 597 VAL 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 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 205 LEU 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 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 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: 9.9990 chunk 194 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3667 r_free = 0.3667 target = 0.149222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124774 restraints weight = 24268.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125628 restraints weight = 17824.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125635 restraints weight = 14772.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125672 restraints weight = 14080.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125701 restraints weight = 14280.102| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2611 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 : 0.702 8.085 27084 Z= 0.347 Chirality : 0.044 0.231 3048 Planarity : 0.004 0.042 3416 Dihedral : 9.715 155.406 2748 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.83 % Allowed : 22.35 % Favored : 71.81 % 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: -1.42 (0.17), residues: 2400 helix: 0.38 (0.14), residues: 1464 sheet: -3.49 (0.42), residues: 64 loop : -3.12 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.011 0.002 TYR D 547 PHE 0.019 0.002 PHE A 611 TRP 0.007 0.001 TRP A 583 HIS 0.005 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00552 (19928) covalent geometry : angle 0.70240 (27084) hydrogen bonds : bond 0.05105 ( 1004) hydrogen bonds : angle 4.46843 ( 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 390 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 271 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.7175 (tttm) cc_final: 0.6925 (ptmt) REVERT: A 466 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8303 (mmm) REVERT: A 547 TYR cc_start: 0.6407 (m-80) cc_final: 0.6184 (m-80) REVERT: A 554 MET cc_start: 0.7210 (tpp) cc_final: 0.6943 (tpp) REVERT: A 603 MET cc_start: 0.7600 (tmm) cc_final: 0.7268 (tmm) REVERT: B 341 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7919 (tp) REVERT: B 554 MET cc_start: 0.7310 (tpp) cc_final: 0.7051 (tpp) REVERT: D 38 MET cc_start: 0.8239 (mmm) cc_final: 0.7993 (tpt) REVERT: D 341 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7970 (tp) REVERT: D 466 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8231 (mmt) REVERT: D 554 MET cc_start: 0.7223 (tpp) cc_final: 0.7010 (tpp) REVERT: D 570 MET cc_start: 0.6936 (tpp) cc_final: 0.6630 (tpp) outliers start: 119 outliers final: 88 residues processed: 357 average time/residue: 0.1150 time to fit residues: 67.6156 Evaluate side-chains 351 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 259 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR 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 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 565 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 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 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 394 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 439 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 465 VAL 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 597 VAL 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 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 397 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 436 VAL 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 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 162 TYR 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 317 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 397 VAL 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 466 MET 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: 0.6980 chunk 232 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.155484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149692 restraints weight = 23455.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.146893 restraints weight = 33492.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.145801 restraints weight = 54889.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.138130 restraints weight = 53226.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137529 restraints weight = 43031.194| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2744 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= 0.106 Angle : 0.589 12.672 27084 Z= 0.282 Chirality : 0.039 0.179 3048 Planarity : 0.004 0.039 3416 Dihedral : 8.894 135.540 2748 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.82 % Allowed : 25.29 % Favored : 70.88 % 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: -0.93 (0.18), residues: 2400 helix: 0.80 (0.14), residues: 1464 sheet: -3.37 (0.43), residues: 64 loop : -2.98 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.015 0.001 TYR D 216 PHE 0.014 0.001 PHE A 611 TRP 0.008 0.001 TRP B 613 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00233 (19928) covalent geometry : angle 0.58919 (27084) hydrogen bonds : bond 0.03369 ( 1004) hydrogen bonds : angle 4.06637 ( 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 387 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 309 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8663 (tm-30) REVERT: A 603 MET cc_start: 0.7409 (tmm) cc_final: 0.7202 (tmm) REVERT: B 286 TRP cc_start: 0.5310 (t60) cc_final: 0.4513 (t60) REVERT: B 483 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8620 (tm-30) REVERT: C 483 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8450 (tm-30) REVERT: D 38 MET cc_start: 0.7848 (mmm) cc_final: 0.7623 (tpt) REVERT: D 483 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8639 (tm-30) REVERT: D 515 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7334 (mm-30) outliers start: 78 outliers final: 71 residues processed: 367 average time/residue: 0.1161 time to fit residues: 69.0379 Evaluate side-chains 363 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 292 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 454 LEU 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 436 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 440 MET 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 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 215 MET 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 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 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: 0.9980 chunk 185 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 178 optimal weight: 0.0030 chunk 69 optimal weight: 3.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.156935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.151191 restraints weight = 23494.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.150173 restraints weight = 35805.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.149395 restraints weight = 37344.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148021 restraints weight = 37793.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146947 restraints weight = 47359.511| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2912 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= 0.103 Angle : 0.582 12.126 27084 Z= 0.276 Chirality : 0.039 0.159 3048 Planarity : 0.004 0.037 3416 Dihedral : 8.377 122.445 2748 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.48 % Allowed : 25.64 % Favored : 70.88 % 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: -0.69 (0.18), residues: 2400 helix: 1.00 (0.14), residues: 1468 sheet: -3.12 (0.46), residues: 64 loop : -2.92 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.022 0.001 TYR B 216 PHE 0.017 0.001 PHE A 611 TRP 0.010 0.001 TRP B 629 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00226 (19928) covalent geometry : angle 0.58165 (27084) hydrogen bonds : bond 0.03254 ( 1004) hydrogen bonds : angle 3.93981 ( 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 374 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 303 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 MET cc_start: 0.8627 (mmp) cc_final: 0.8305 (mmt) REVERT: A 483 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8605 (tm-30) REVERT: A 603 MET cc_start: 0.7354 (tmm) cc_final: 0.7124 (tmm) REVERT: B 286 TRP cc_start: 0.5191 (t60) cc_final: 0.4519 (t60) REVERT: B 483 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8558 (tm-30) REVERT: C 483 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8410 (tm-30) REVERT: D 286 TRP cc_start: 0.5377 (t60) cc_final: 0.4689 (t60) REVERT: D 466 MET cc_start: 0.8587 (mmp) cc_final: 0.8311 (mmt) REVERT: D 483 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8607 (tm-30) REVERT: D 515 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7198 (mm-30) outliers start: 71 outliers final: 68 residues processed: 356 average time/residue: 0.1034 time to fit residues: 60.5559 Evaluate side-chains 364 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 296 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 565 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 152 PHE 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 439 THR Chi-restraints excluded: chain B residue 440 MET 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 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 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 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 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: 1.9990 chunk 3 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 230 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** 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 = 0.3661 r_free = 0.3661 target = 0.151171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142288 restraints weight = 23961.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140434 restraints weight = 42316.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139487 restraints weight = 48567.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138560 restraints weight = 45012.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137728 restraints weight = 48599.664| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19928 Z= 0.167 Angle : 0.647 12.381 27084 Z= 0.312 Chirality : 0.042 0.265 3048 Planarity : 0.004 0.040 3416 Dihedral : 8.539 128.312 2748 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.02 % Allowed : 25.93 % Favored : 70.05 % 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: -0.97 (0.17), residues: 2400 helix: 0.74 (0.14), residues: 1460 sheet: -3.14 (0.47), residues: 64 loop : -2.94 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.021 0.001 TYR B 216 PHE 0.017 0.001 PHE A 611 TRP 0.028 0.001 TRP B 629 HIS 0.003 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00402 (19928) covalent geometry : angle 0.64693 (27084) hydrogen bonds : bond 0.04316 ( 1004) hydrogen bonds : angle 4.18144 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2562.05 seconds wall clock time: 45 minutes 44.15 seconds (2744.15 seconds total)