Starting phenix.real_space_refine on Thu Feb 5 17:25:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6k_25717/02_2026/7t6k_25717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6k_25717/02_2026/7t6k_25717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6k_25717/02_2026/7t6k_25717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6k_25717/02_2026/7t6k_25717.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6k_25717/02_2026/7t6k_25717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6k_25717/02_2026/7t6k_25717.cif" } resolution = 3.0 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= 0.006 sd= 0.066 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 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 4.80, per 1000 atoms: 0.25 Number of scatterers: 19412 At special positions: 0 Unit cell: (130.38, 130.38, 120.84, 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 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 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: 1.75 Conformation dependent library (CDL) restraints added in 921.7 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 66.0% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.509A 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 103 through 108 removed outlier: 3.952A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.752A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.563A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.497A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 280 through 285 removed outlier: 4.019A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.831A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.826A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 379 through 410 removed outlier: 3.688A pdb=" N LEU A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.678A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.619A pdb=" N PHE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.641A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.961A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.468A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.575A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 605 removed outlier: 4.710A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.508A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.508A 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 103 through 108 removed outlier: 3.958A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.742A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.545A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 210 through 222 removed outlier: 4.494A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 280 through 285 removed outlier: 4.026A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.832A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 removed outlier: 3.907A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 379 through 410 removed outlier: 3.688A pdb=" N LEU B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.666A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.611A pdb=" N PHE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.594A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 489 through 512 removed outlier: 4.125A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.468A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.579A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 605 removed outlier: 4.810A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.507A 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 103 through 108 removed outlier: 3.950A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.768A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.610A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 213 through 220 removed outlier: 3.502A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 280 through 285 removed outlier: 4.027A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.830A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 removed outlier: 3.909A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 379 through 410 removed outlier: 3.686A pdb=" N LEU C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.661A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.613A pdb=" N PHE C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.563A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.978A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.465A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.576A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 605 removed outlier: 4.844A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.951A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.767A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.616A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 210 through 220 removed outlier: 4.507A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.026A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.834A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.911A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 379 through 410 removed outlier: 3.744A pdb=" N LEU D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.651A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.664A pdb=" N PHE D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.601A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 489 through 512 removed outlier: 4.154A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.468A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.578A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 605 removed outlier: 4.827A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 269 removed outlier: 7.006A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (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 264 through 269 removed outlier: 7.005A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (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 264 through 269 removed outlier: 7.005A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (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 264 through 269 removed outlier: 7.008A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1047 hydrogen bonds defined for protein. 3063 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: 3.49 Time building geometry restraints manager: 2.34 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: 5960 1.34 - 1.46: 3688 1.46 - 1.58: 9984 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C ARG D 326 " pdb=" N PRO D 327 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.74e+00 bond pdb=" C ARG A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.69e+00 bond pdb=" C ARG C 326 " pdb=" N PRO C 327 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.69e+00 bond pdb=" C ARG B 326 " pdb=" N PRO B 327 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.49e+00 bond pdb=" C THR C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.38e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 25584 2.06 - 4.12: 1041 4.12 - 6.18: 241 6.18 - 8.24: 66 8.24 - 10.30: 32 Bond angle restraints: 26964 Sorted by residual: angle pdb=" C ASP D 223 " pdb=" N GLU D 224 " pdb=" CA GLU D 224 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C ASP C 223 " pdb=" N GLU C 224 " pdb=" CA GLU C 224 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C ASP A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta sigma weight residual 121.54 131.25 -9.71 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C ASP B 223 " pdb=" N GLU B 224 " pdb=" CA GLU B 224 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLU A 605 " pdb=" N ARG A 606 " pdb=" CA ARG A 606 " ideal model delta sigma weight residual 123.91 131.48 -7.57 1.66e+00 3.63e-01 2.08e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10631 17.85 - 35.69: 953 35.69 - 53.54: 183 53.54 - 71.38: 36 71.38 - 89.23: 9 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA MET D 485 " pdb=" C MET D 485 " pdb=" N ILE D 486 " pdb=" CA ILE D 486 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA MET B 485 " pdb=" C MET B 485 " pdb=" N ILE B 486 " pdb=" CA ILE B 486 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA MET A 485 " pdb=" C MET A 485 " pdb=" N ILE A 486 " pdb=" CA ILE A 486 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2894 0.112 - 0.225: 164 0.225 - 0.337: 11 0.337 - 0.450: 0 0.450 - 0.562: 3 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB VAL B 585 " pdb=" CA VAL B 585 " pdb=" CG1 VAL B 585 " pdb=" CG2 VAL B 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" CB VAL D 585 " pdb=" CA VAL D 585 " pdb=" CG1 VAL D 585 " pdb=" CG2 VAL D 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CB VAL C 585 " pdb=" CA VAL C 585 " pdb=" CG1 VAL C 585 " pdb=" CG2 VAL C 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.67e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 456 " -0.026 2.00e-02 2.50e+03 1.98e-02 6.89e+00 pdb=" CG PHE C 456 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 456 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 456 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 456 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 456 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 456 " -0.026 2.00e-02 2.50e+03 1.96e-02 6.70e+00 pdb=" CG PHE B 456 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 456 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 456 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 456 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 456 " -0.026 2.00e-02 2.50e+03 1.95e-02 6.69e+00 pdb=" CG PHE D 456 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE D 456 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 456 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 456 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 456 " -0.011 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5830 2.83 - 3.35: 17302 3.35 - 3.87: 32794 3.87 - 4.38: 37888 4.38 - 4.90: 65135 Nonbonded interactions: 158949 Sorted by model distance: nonbonded pdb=" OD1 ASP B 525 " pdb=" OG1 THR B 528 " model vdw 2.313 3.040 nonbonded pdb=" OD1 ASP C 525 " pdb=" OG1 THR C 528 " model vdw 2.313 3.040 nonbonded pdb=" OD1 ASP D 525 " pdb=" OG1 THR D 528 " model vdw 2.313 3.040 nonbonded pdb=" OD1 ASP A 525 " pdb=" OG1 THR A 528 " model vdw 2.313 3.040 nonbonded pdb=" O THR A 479 " pdb=" NE2 GLN A 483 " model vdw 2.338 3.120 ... (remaining 158944 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: 0.04 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.560 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.005 0.062 19860 Z= 0.259 Angle : 1.050 10.300 26964 Z= 0.560 Chirality : 0.060 0.562 3072 Planarity : 0.008 0.062 3416 Dihedral : 14.248 89.227 7236 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.04 % 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: -3.51 (0.13), residues: 2408 helix: -2.28 (0.10), residues: 1452 sheet: -1.59 (0.49), residues: 88 loop : -2.20 (0.17), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 606 TYR 0.024 0.002 TYR A 339 PHE 0.044 0.003 PHE C 456 TRP 0.018 0.001 TRP D 593 HIS 0.009 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00510 (19860) covalent geometry : angle 1.05012 (26964) hydrogen bonds : bond 0.14238 ( 1047) hydrogen bonds : angle 7.14285 ( 3063) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 356 time to evaluate : 0.701 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.6349 time to fit residues: 255.8159 Evaluate side-chains 230 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 369 GLN A 374 GLN A 483 GLN A 636 HIS B 230 GLN B 369 GLN B 636 HIS C 230 GLN C 369 GLN C 636 HIS D 230 GLN D 369 GLN D 636 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116485 restraints weight = 24991.018| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.74 r_work: 0.3193 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19860 Z= 0.128 Angle : 0.604 9.748 26964 Z= 0.303 Chirality : 0.040 0.162 3072 Planarity : 0.005 0.039 3416 Dihedral : 4.566 21.662 2644 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.29 % Allowed : 9.11 % Favored : 88.60 % 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: -1.27 (0.16), residues: 2408 helix: -0.28 (0.13), residues: 1464 sheet: -1.70 (0.51), residues: 96 loop : -1.57 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.015 0.001 TYR B 222 PHE 0.021 0.001 PHE D 456 TRP 0.009 0.001 TRP D 462 HIS 0.004 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00292 (19860) covalent geometry : angle 0.60374 (26964) hydrogen bonds : bond 0.03959 ( 1047) hydrogen bonds : angle 4.56302 ( 3063) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8454 (t) cc_final: 0.8251 (t) REVERT: B 300 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8343 (mtmt) REVERT: B 486 ILE cc_start: 0.8361 (mm) cc_final: 0.8138 (mm) REVERT: B 495 TRP cc_start: 0.8257 (m100) cc_final: 0.7928 (m100) REVERT: C 487 PHE cc_start: 0.8068 (m-10) cc_final: 0.7828 (m-10) REVERT: D 300 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8396 (mtmt) REVERT: D 486 ILE cc_start: 0.8411 (mm) cc_final: 0.8184 (mm) outliers start: 48 outliers final: 13 residues processed: 280 average time/residue: 0.6699 time to fit residues: 210.5797 Evaluate side-chains 231 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 427 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 37 ASN A 230 GLN B 230 GLN C 37 ASN C 230 GLN D 37 ASN D 230 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105477 restraints weight = 25013.891| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.80 r_work: 0.3073 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19860 Z= 0.248 Angle : 0.671 6.606 26964 Z= 0.342 Chirality : 0.046 0.167 3072 Planarity : 0.005 0.043 3416 Dihedral : 4.638 23.410 2644 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.77 % Allowed : 13.17 % Favored : 83.06 % 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: -0.73 (0.16), residues: 2408 helix: 0.18 (0.13), residues: 1464 sheet: -1.34 (0.50), residues: 88 loop : -1.44 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.010 0.002 TYR B 222 PHE 0.014 0.002 PHE B 425 TRP 0.008 0.001 TRP B 593 HIS 0.007 0.002 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00607 (19860) covalent geometry : angle 0.67145 (26964) hydrogen bonds : bond 0.04530 ( 1047) hydrogen bonds : angle 4.41059 ( 3063) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 221 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 474 MET cc_start: 0.7766 (ttm) cc_final: 0.7528 (ttm) REVERT: B 403 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: B 495 TRP cc_start: 0.8324 (m100) cc_final: 0.7966 (m100) REVERT: C 30 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: C 176 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: C 403 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: C 495 TRP cc_start: 0.8335 (m100) cc_final: 0.7973 (m100) REVERT: D 176 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8296 (mt-10) REVERT: D 495 TRP cc_start: 0.8336 (m100) cc_final: 0.7978 (m100) outliers start: 79 outliers final: 28 residues processed: 270 average time/residue: 0.6671 time to fit residues: 202.3521 Evaluate side-chains 233 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 226 optimal weight: 0.7980 chunk 117 optimal weight: 0.0770 chunk 108 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 ASN A 230 GLN B 31 GLN B 230 GLN C 31 GLN C 37 ASN C 230 GLN D 31 GLN D 37 ASN D 230 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111392 restraints weight = 24767.884| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.73 r_work: 0.3151 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.119 Angle : 0.568 7.735 26964 Z= 0.290 Chirality : 0.040 0.247 3072 Planarity : 0.004 0.044 3416 Dihedral : 4.278 18.549 2644 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.91 % Allowed : 14.31 % Favored : 81.77 % 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: -0.08 (0.17), residues: 2408 helix: 0.71 (0.14), residues: 1464 sheet: -1.23 (0.52), residues: 96 loop : -1.18 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 180 TYR 0.010 0.001 TYR A 555 PHE 0.012 0.001 PHE A 456 TRP 0.009 0.001 TRP B 462 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00274 (19860) covalent geometry : angle 0.56833 (26964) hydrogen bonds : bond 0.03631 ( 1047) hydrogen bonds : angle 4.08524 ( 3063) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 229 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8440 (mtmt) REVERT: A 403 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: A 474 MET cc_start: 0.7650 (ttm) cc_final: 0.7426 (ttm) REVERT: B 38 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7031 (mmm) REVERT: B 300 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8394 (mtmt) REVERT: B 403 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: B 495 TRP cc_start: 0.8360 (m100) cc_final: 0.7967 (m100) REVERT: C 30 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: C 38 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7109 (mmm) REVERT: C 176 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8298 (mt-10) REVERT: C 300 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (mtmt) REVERT: C 403 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: C 495 TRP cc_start: 0.8356 (m100) cc_final: 0.7962 (m100) REVERT: D 38 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7095 (mmm) REVERT: D 176 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: D 300 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8421 (mtmt) REVERT: D 495 TRP cc_start: 0.8354 (m100) cc_final: 0.7983 (m100) outliers start: 82 outliers final: 31 residues processed: 276 average time/residue: 0.6080 time to fit residues: 188.4340 Evaluate side-chains 248 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 230 GLN Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 ASN A 230 GLN B 230 GLN C 31 GLN C 37 ASN C 230 GLN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 230 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110508 restraints weight = 24807.638| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.76 r_work: 0.3118 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19860 Z= 0.137 Angle : 0.566 7.143 26964 Z= 0.290 Chirality : 0.040 0.191 3072 Planarity : 0.004 0.044 3416 Dihedral : 4.177 17.018 2644 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.25 % Allowed : 14.84 % Favored : 80.92 % 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: 0.17 (0.17), residues: 2408 helix: 0.92 (0.14), residues: 1464 sheet: -1.11 (0.52), residues: 96 loop : -1.08 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 180 TYR 0.009 0.001 TYR C 216 PHE 0.011 0.001 PHE D 456 TRP 0.007 0.001 TRP B 462 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00327 (19860) covalent geometry : angle 0.56618 (26964) hydrogen bonds : bond 0.03664 ( 1047) hydrogen bonds : angle 4.00182 ( 3063) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 204 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8432 (mtmt) REVERT: A 403 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: A 474 MET cc_start: 0.7616 (ttm) cc_final: 0.7367 (ttm) REVERT: A 565 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 38 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7000 (mmm) REVERT: B 300 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8420 (mtmt) REVERT: B 403 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: B 495 TRP cc_start: 0.8369 (m100) cc_final: 0.7975 (m100) REVERT: B 565 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8428 (mp) REVERT: C 30 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: C 38 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7086 (mmm) REVERT: C 176 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: C 300 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8419 (mtmt) REVERT: C 403 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: C 495 TRP cc_start: 0.8369 (m100) cc_final: 0.7972 (m100) REVERT: C 565 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 585 VAL cc_start: 0.8732 (p) cc_final: 0.8520 (m) REVERT: D 38 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7030 (mmm) REVERT: D 176 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: D 300 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8429 (mtmt) REVERT: D 495 TRP cc_start: 0.8342 (m100) cc_final: 0.7967 (m100) REVERT: D 565 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8442 (mp) outliers start: 89 outliers final: 35 residues processed: 264 average time/residue: 0.6084 time to fit residues: 181.3307 Evaluate side-chains 252 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN C 230 GLN D 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109594 restraints weight = 24825.279| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.67 r_work: 0.3112 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19860 Z= 0.177 Angle : 0.602 7.625 26964 Z= 0.306 Chirality : 0.042 0.163 3072 Planarity : 0.004 0.045 3416 Dihedral : 4.235 20.201 2644 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.72 % Allowed : 15.98 % Favored : 80.30 % 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: 0.16 (0.17), residues: 2408 helix: 0.90 (0.14), residues: 1468 sheet: -1.21 (0.51), residues: 96 loop : -1.06 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 180 TYR 0.008 0.001 TYR C 216 PHE 0.010 0.001 PHE D 425 TRP 0.007 0.001 TRP A 495 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00434 (19860) covalent geometry : angle 0.60210 (26964) hydrogen bonds : bond 0.03928 ( 1047) hydrogen bonds : angle 4.03337 ( 3063) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 203 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7870 (pm20) cc_final: 0.7197 (tm-30) REVERT: A 300 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8440 (mtmt) REVERT: A 403 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 474 MET cc_start: 0.7711 (ttm) cc_final: 0.7433 (ttm) REVERT: B 38 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7066 (mmm) REVERT: B 300 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8424 (mtmt) REVERT: B 403 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: B 495 TRP cc_start: 0.8339 (m100) cc_final: 0.7954 (m100) REVERT: C 30 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: C 176 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8435 (mt-10) REVERT: C 300 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8424 (mtmt) REVERT: C 403 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: C 485 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7957 (mmt) REVERT: C 495 TRP cc_start: 0.8350 (m100) cc_final: 0.7958 (m100) REVERT: D 176 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: D 300 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8419 (mtmt) REVERT: D 495 TRP cc_start: 0.8325 (m100) cc_final: 0.7948 (m100) REVERT: D 570 MET cc_start: 0.8723 (mtp) cc_final: 0.8407 (mtm) outliers start: 78 outliers final: 42 residues processed: 261 average time/residue: 0.6458 time to fit residues: 190.0005 Evaluate side-chains 243 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 230 GLN Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 175 optimal weight: 0.5980 chunk 203 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 190 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110885 restraints weight = 24754.769| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.72 r_work: 0.3142 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19860 Z= 0.122 Angle : 0.571 8.045 26964 Z= 0.292 Chirality : 0.040 0.165 3072 Planarity : 0.004 0.062 3416 Dihedral : 4.103 18.334 2644 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.72 % Allowed : 16.51 % Favored : 79.77 % 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: 0.38 (0.17), residues: 2408 helix: 1.09 (0.14), residues: 1464 sheet: -0.69 (0.52), residues: 88 loop : -1.05 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 180 TYR 0.010 0.001 TYR D 555 PHE 0.014 0.001 PHE C 456 TRP 0.008 0.001 TRP C 462 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00286 (19860) covalent geometry : angle 0.57112 (26964) hydrogen bonds : bond 0.03553 ( 1047) hydrogen bonds : angle 3.91094 ( 3063) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 208 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8451 (mtmt) REVERT: A 403 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: A 474 MET cc_start: 0.7685 (ttm) cc_final: 0.7448 (ttm) REVERT: A 487 PHE cc_start: 0.8265 (m-10) cc_final: 0.8054 (m-10) REVERT: B 38 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7096 (mmm) REVERT: B 104 GLU cc_start: 0.7863 (pm20) cc_final: 0.7002 (tm-30) REVERT: B 300 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8445 (mtmt) REVERT: B 403 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: B 495 TRP cc_start: 0.8315 (m100) cc_final: 0.7978 (m100) REVERT: C 30 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: C 38 MET cc_start: 0.7615 (ttt) cc_final: 0.7087 (mmm) REVERT: C 104 GLU cc_start: 0.7842 (pm20) cc_final: 0.7180 (tm-30) REVERT: C 176 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8439 (mt-10) REVERT: C 300 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (mtmt) REVERT: C 403 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: C 485 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7915 (mmt) REVERT: C 487 PHE cc_start: 0.8244 (m-10) cc_final: 0.8031 (m-10) REVERT: C 495 TRP cc_start: 0.8336 (m100) cc_final: 0.7988 (m100) REVERT: D 38 MET cc_start: 0.7620 (ttt) cc_final: 0.7099 (mmm) REVERT: D 104 GLU cc_start: 0.7847 (pm20) cc_final: 0.7194 (tm-30) REVERT: D 113 GLU cc_start: 0.7545 (tp30) cc_final: 0.7273 (tp30) REVERT: D 176 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8324 (mt-10) REVERT: D 300 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8440 (mtmt) REVERT: D 487 PHE cc_start: 0.8275 (m-10) cc_final: 0.8069 (m-10) REVERT: D 495 TRP cc_start: 0.8289 (m100) cc_final: 0.7968 (m100) REVERT: D 565 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8501 (mp) outliers start: 78 outliers final: 36 residues processed: 265 average time/residue: 0.6005 time to fit residues: 180.3681 Evaluate side-chains 247 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 230 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN C 206 GLN C 230 GLN D 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104015 restraints weight = 25123.282| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.80 r_work: 0.3061 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19860 Z= 0.232 Angle : 0.654 8.768 26964 Z= 0.333 Chirality : 0.045 0.178 3072 Planarity : 0.005 0.060 3416 Dihedral : 4.356 21.816 2644 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.86 % Allowed : 16.75 % Favored : 79.39 % 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: 0.12 (0.17), residues: 2408 helix: 0.83 (0.14), residues: 1476 sheet: -1.33 (0.50), residues: 96 loop : -0.99 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 180 TYR 0.010 0.002 TYR B 547 PHE 0.013 0.002 PHE B 425 TRP 0.009 0.001 TRP A 495 HIS 0.006 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00571 (19860) covalent geometry : angle 0.65379 (26964) hydrogen bonds : bond 0.04230 ( 1047) hydrogen bonds : angle 4.09785 ( 3063) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 203 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7928 (pm20) cc_final: 0.7044 (tm-30) REVERT: A 300 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8483 (mtmt) REVERT: A 403 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: A 474 MET cc_start: 0.7730 (ttm) cc_final: 0.7454 (ttm) REVERT: B 38 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7112 (mmm) REVERT: B 180 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7855 (mtt-85) REVERT: B 300 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8476 (mtmt) REVERT: B 403 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 495 TRP cc_start: 0.8361 (m100) cc_final: 0.7977 (m100) REVERT: C 30 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: C 176 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8434 (mt-10) REVERT: C 300 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8474 (mtmt) REVERT: C 403 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: C 485 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8019 (mmt) REVERT: C 495 TRP cc_start: 0.8358 (m100) cc_final: 0.8010 (m100) REVERT: C 565 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8627 (mm) REVERT: C 570 MET cc_start: 0.8690 (mtp) cc_final: 0.8365 (ttm) REVERT: D 113 GLU cc_start: 0.7631 (tp30) cc_final: 0.7224 (tp30) REVERT: D 176 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: D 300 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8480 (mtmt) REVERT: D 495 TRP cc_start: 0.8317 (m100) cc_final: 0.7949 (m100) REVERT: D 570 MET cc_start: 0.8733 (mtp) cc_final: 0.8398 (ttm) outliers start: 81 outliers final: 39 residues processed: 269 average time/residue: 0.5637 time to fit residues: 172.1393 Evaluate side-chains 252 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 637 HIS C 230 GLN C 637 HIS D 637 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109592 restraints weight = 24728.555| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.77 r_work: 0.3113 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19860 Z= 0.132 Angle : 0.601 8.352 26964 Z= 0.306 Chirality : 0.040 0.198 3072 Planarity : 0.004 0.048 3416 Dihedral : 4.190 17.546 2644 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.91 % Allowed : 18.42 % Favored : 78.67 % 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: 0.35 (0.17), residues: 2408 helix: 1.03 (0.14), residues: 1472 sheet: -1.24 (0.50), residues: 96 loop : -0.94 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 180 TYR 0.011 0.001 TYR D 555 PHE 0.013 0.001 PHE C 456 TRP 0.008 0.001 TRP D 462 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00314 (19860) covalent geometry : angle 0.60130 (26964) hydrogen bonds : bond 0.03636 ( 1047) hydrogen bonds : angle 3.95700 ( 3063) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7564 (ttt) cc_final: 0.7097 (mmm) REVERT: A 104 GLU cc_start: 0.7914 (pm20) cc_final: 0.6995 (tm-30) REVERT: A 113 GLU cc_start: 0.7241 (tp30) cc_final: 0.5787 (tt0) REVERT: A 300 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8457 (mtmt) REVERT: A 403 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: B 38 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6957 (mmm) REVERT: B 104 GLU cc_start: 0.7906 (pm20) cc_final: 0.6939 (tm-30) REVERT: B 180 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7786 (mtt-85) REVERT: B 300 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8463 (mtmt) REVERT: B 403 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: B 495 TRP cc_start: 0.8361 (m100) cc_final: 0.7974 (m100) REVERT: B 580 ASP cc_start: 0.8067 (t70) cc_final: 0.7361 (m-30) REVERT: C 30 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: C 38 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7057 (mmm) REVERT: C 104 GLU cc_start: 0.7910 (pm20) cc_final: 0.6993 (tm-30) REVERT: C 176 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8450 (mt-10) REVERT: C 300 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8463 (mtmt) REVERT: C 403 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: C 485 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7963 (mmt) REVERT: C 495 TRP cc_start: 0.8386 (m100) cc_final: 0.8030 (m100) REVERT: C 565 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8615 (mm) REVERT: C 580 ASP cc_start: 0.8087 (t70) cc_final: 0.7358 (m-30) REVERT: D 38 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7042 (mmm) REVERT: D 104 GLU cc_start: 0.7911 (pm20) cc_final: 0.7651 (pm20) REVERT: D 176 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: D 300 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8459 (mtmt) REVERT: D 495 TRP cc_start: 0.8308 (m100) cc_final: 0.7945 (m100) REVERT: D 580 ASP cc_start: 0.8075 (t70) cc_final: 0.7372 (m-30) outliers start: 61 outliers final: 36 residues processed: 251 average time/residue: 0.6062 time to fit residues: 171.6928 Evaluate side-chains 248 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 GLN A 637 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 637 HIS C 637 HIS ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108050 restraints weight = 25040.548| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.88 r_work: 0.3117 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19860 Z= 0.127 Angle : 0.597 9.950 26964 Z= 0.301 Chirality : 0.041 0.405 3072 Planarity : 0.004 0.045 3416 Dihedral : 4.094 17.354 2644 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.91 % Allowed : 18.46 % Favored : 78.63 % 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: 0.40 (0.17), residues: 2408 helix: 1.10 (0.14), residues: 1472 sheet: -1.18 (0.51), residues: 96 loop : -0.98 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 180 TYR 0.010 0.001 TYR A 555 PHE 0.019 0.001 PHE D 456 TRP 0.008 0.001 TRP A 495 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00299 (19860) covalent geometry : angle 0.59700 (26964) hydrogen bonds : bond 0.03562 ( 1047) hydrogen bonds : angle 3.90412 ( 3063) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7566 (ttt) cc_final: 0.7021 (mmm) REVERT: A 113 GLU cc_start: 0.7160 (tp30) cc_final: 0.5757 (tt0) REVERT: A 300 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8444 (mtmt) REVERT: A 403 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: A 487 PHE cc_start: 0.8230 (m-10) cc_final: 0.8025 (m-10) REVERT: B 38 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7021 (mmm) REVERT: B 104 GLU cc_start: 0.7892 (pm20) cc_final: 0.7656 (pm20) REVERT: B 300 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8440 (mtmt) REVERT: B 403 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: B 495 TRP cc_start: 0.8343 (m100) cc_final: 0.7993 (m100) REVERT: B 580 ASP cc_start: 0.8015 (t70) cc_final: 0.7319 (m-30) REVERT: C 30 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: C 38 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7012 (mmm) REVERT: C 104 GLU cc_start: 0.7905 (pm20) cc_final: 0.7668 (pm20) REVERT: C 176 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8440 (mt-10) REVERT: C 300 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8456 (mtmt) REVERT: C 403 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: C 485 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7742 (mmt) REVERT: C 495 TRP cc_start: 0.8376 (m100) cc_final: 0.8043 (m100) REVERT: C 565 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8598 (mm) REVERT: D 38 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6998 (mmm) REVERT: D 104 GLU cc_start: 0.7908 (pm20) cc_final: 0.7675 (pm20) REVERT: D 176 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: D 300 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8446 (mtmt) REVERT: D 495 TRP cc_start: 0.8301 (m100) cc_final: 0.7968 (m100) REVERT: D 580 ASP cc_start: 0.8023 (t70) cc_final: 0.7345 (m-30) outliers start: 61 outliers final: 35 residues processed: 245 average time/residue: 0.5867 time to fit residues: 161.6539 Evaluate side-chains 249 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 16 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN A 637 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 637 HIS C 637 HIS D 483 GLN D 637 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.138251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109973 restraints weight = 24968.280| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.74 r_work: 0.3108 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.251 19860 Z= 0.217 Angle : 0.787 59.170 26964 Z= 0.430 Chirality : 0.041 0.424 3072 Planarity : 0.004 0.044 3416 Dihedral : 4.086 17.190 2644 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.53 % Allowed : 18.65 % Favored : 78.82 % Cbeta Deviations : 0.04 % 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: 0.40 (0.17), residues: 2408 helix: 1.10 (0.14), residues: 1472 sheet: -1.17 (0.51), residues: 96 loop : -0.98 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 305 TYR 0.010 0.001 TYR C 555 PHE 0.018 0.001 PHE D 456 TRP 0.007 0.001 TRP C 462 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00480 (19860) covalent geometry : angle 0.78714 (26964) hydrogen bonds : bond 0.03578 ( 1047) hydrogen bonds : angle 3.90441 ( 3063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6188.20 seconds wall clock time: 106 minutes 16.80 seconds (6376.80 seconds total)