Starting phenix.real_space_refine on Thu Mar 5 05:04:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6l_25718/03_2026/7t6l_25718.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6l_25718/03_2026/7t6l_25718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t6l_25718/03_2026/7t6l_25718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6l_25718/03_2026/7t6l_25718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t6l_25718/03_2026/7t6l_25718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6l_25718/03_2026/7t6l_25718.map" } resolution = 3.7 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= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.42, per 1000 atoms: 0.23 Number of scatterers: 19412 At special positions: 0 Unit cell: (141.93, 141.93, 121.18, 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: 1.57 Conformation dependent library (CDL) restraints added in 800.9 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: 109 helices and 8 sheets defined 64.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.720A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.587A pdb=" N GLN A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 67 removed outlier: 3.679A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.731A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.610A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.989A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.737A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 264 removed outlier: 4.078A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.895A pdb=" N ILE A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.918A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.451A 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: 3.629A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.640A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.942A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 4.098A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 513 removed outlier: 3.641A pdb=" N LEU A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.518A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.725A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 605 removed outlier: 3.940A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.717A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.586A pdb=" N GLN B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 removed outlier: 3.679A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.735A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.612A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.991A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.733A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.708A pdb=" N GLY B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 4.078A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.857A pdb=" N ILE B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.908A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.421A 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: 3.613A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.631A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.992A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.787A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 513 removed outlier: 3.641A pdb=" N LEU B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.520A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.767A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 605 removed outlier: 3.914A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.715A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.590A pdb=" N GLN C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 67 removed outlier: 3.680A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.732A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.610A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.990A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.732A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 174 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 222 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 264 removed outlier: 4.082A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.895A pdb=" N ILE C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 310 through 324 removed outlier: 3.912A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.444A 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: 3.615A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.630A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 4.343A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.847A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 513 removed outlier: 3.697A pdb=" N LEU C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.504A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.688A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 605 removed outlier: 3.917A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.715A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.586A pdb=" N GLN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 67 removed outlier: 3.680A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.722A pdb=" N TYR D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.622A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.990A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.750A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 213 through 222 Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.743A pdb=" N GLY D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 4.080A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.865A pdb=" N ILE D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.907A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.439A 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: 3.615A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.614A 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 removed outlier: 4.344A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.780A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 513 removed outlier: 3.604A pdb=" N LEU D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 493 " --> pdb=" O ASP D 489 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.518A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.742A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 605 removed outlier: 3.861A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 279 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 273 through 279 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 273 through 279 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 273 through 279 Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1025 hydrogen bonds defined for protein. 3033 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: 3.11 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5942 1.34 - 1.46: 3808 1.46 - 1.58: 9882 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" CB PHE D 574 " pdb=" CG PHE D 574 " ideal model delta sigma weight residual 1.502 1.409 0.093 2.30e-02 1.89e+03 1.65e+01 bond pdb=" CB PHE B 574 " pdb=" CG PHE B 574 " ideal model delta sigma weight residual 1.502 1.410 0.092 2.30e-02 1.89e+03 1.58e+01 bond pdb=" CB PHE C 574 " pdb=" CG PHE C 574 " ideal model delta sigma weight residual 1.502 1.416 0.086 2.30e-02 1.89e+03 1.41e+01 bond pdb=" CB PHE A 574 " pdb=" CG PHE A 574 " ideal model delta sigma weight residual 1.502 1.417 0.085 2.30e-02 1.89e+03 1.37e+01 bond pdb=" CD2 PHE A 574 " pdb=" CE2 PHE A 574 " ideal model delta sigma weight residual 1.382 1.287 0.095 3.00e-02 1.11e+03 1.00e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 26416 3.51 - 7.02: 441 7.02 - 10.53: 100 10.53 - 14.04: 3 14.04 - 17.54: 4 Bond angle restraints: 26964 Sorted by residual: angle pdb=" N ILE D 367 " pdb=" CA ILE D 367 " pdb=" C ILE D 367 " ideal model delta sigma weight residual 113.53 108.25 5.28 9.80e-01 1.04e+00 2.90e+01 angle pdb=" CA LEU C 98 " pdb=" CB LEU C 98 " pdb=" CG LEU C 98 " ideal model delta sigma weight residual 116.30 133.84 -17.54 3.50e+00 8.16e-02 2.51e+01 angle pdb=" C ASP A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.49e+01 angle pdb=" CA LEU A 98 " pdb=" CB LEU A 98 " pdb=" CG LEU A 98 " ideal model delta sigma weight residual 116.30 133.78 -17.48 3.50e+00 8.16e-02 2.49e+01 angle pdb=" C ASP D 223 " pdb=" N GLU D 224 " pdb=" CA GLU D 224 " ideal model delta sigma weight residual 121.54 131.05 -9.51 1.91e+00 2.74e-01 2.48e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 10323 16.60 - 33.21: 1198 33.21 - 49.81: 212 49.81 - 66.41: 48 66.41 - 83.02: 31 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA PHE D 493 " pdb=" C PHE D 493 " pdb=" N CYS D 494 " pdb=" CA CYS D 494 " ideal model delta harmonic sigma weight residual 180.00 148.24 31.76 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CA PHE C 493 " pdb=" C PHE C 493 " pdb=" N CYS C 494 " pdb=" CA CYS C 494 " ideal model delta harmonic sigma weight residual 180.00 148.63 31.37 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA PHE B 493 " pdb=" C PHE B 493 " pdb=" N CYS B 494 " pdb=" CA CYS B 494 " ideal model delta harmonic sigma weight residual 180.00 149.54 30.46 0 5.00e+00 4.00e-02 3.71e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2773 0.106 - 0.211: 261 0.211 - 0.317: 34 0.317 - 0.422: 0 0.422 - 0.528: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB ILE A 575 " pdb=" CA ILE A 575 " pdb=" CG1 ILE A 575 " pdb=" CG2 ILE A 575 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CB ILE D 575 " pdb=" CA ILE D 575 " pdb=" CG1 ILE D 575 " pdb=" CG2 ILE D 575 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CB ILE C 575 " pdb=" CA ILE C 575 " pdb=" CG1 ILE C 575 " pdb=" CG2 ILE C 575 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 493 " -0.054 2.00e-02 2.50e+03 5.06e-02 4.49e+01 pdb=" CG PHE C 493 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE C 493 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 493 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE C 493 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE C 493 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 493 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 493 " -0.057 2.00e-02 2.50e+03 5.01e-02 4.40e+01 pdb=" CG PHE A 493 " 0.114 2.00e-02 2.50e+03 pdb=" CD1 PHE A 493 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 493 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 493 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 493 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 493 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 493 " 0.053 2.00e-02 2.50e+03 4.94e-02 4.27e+01 pdb=" CG PHE D 493 " -0.112 2.00e-02 2.50e+03 pdb=" CD1 PHE D 493 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 493 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE D 493 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE D 493 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE D 493 " 0.006 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3971 2.78 - 3.31: 17949 3.31 - 3.84: 32596 3.84 - 4.37: 36435 4.37 - 4.90: 62630 Nonbonded interactions: 153581 Sorted by model distance: nonbonded pdb=" OE2 GLU B 522 " pdb=" OG SER B 532 " model vdw 2.245 3.040 nonbonded pdb=" OE1 GLN C 267 " pdb=" OG SER C 275 " model vdw 2.313 3.040 nonbonded pdb=" OE1 GLN B 267 " pdb=" OG SER B 275 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLN A 267 " pdb=" OG SER A 275 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLN D 267 " pdb=" OG SER D 275 " model vdw 2.314 3.040 ... (remaining 153576 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.680 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.660 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.007 0.095 19860 Z= 0.298 Angle : 1.179 17.544 26964 Z= 0.613 Chirality : 0.066 0.528 3072 Planarity : 0.009 0.092 3416 Dihedral : 15.114 83.018 7236 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.03 (0.12), residues: 2408 helix: -2.53 (0.10), residues: 1460 sheet: -3.06 (0.46), residues: 76 loop : -2.60 (0.16), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 154 TYR 0.030 0.002 TYR A 467 PHE 0.116 0.005 PHE C 493 TRP 0.012 0.001 TRP D 613 HIS 0.006 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00655 (19860) covalent geometry : angle 1.17916 (26964) hydrogen bonds : bond 0.13968 ( 1025) hydrogen bonds : angle 7.05671 ( 3033) *********************** 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 342 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8303 (tp30) cc_final: 0.8044 (tp30) REVERT: A 447 MET cc_start: 0.6885 (ppp) cc_final: 0.6550 (ppp) REVERT: A 472 PHE cc_start: 0.7893 (m-80) cc_final: 0.7682 (m-10) REVERT: A 570 MET cc_start: 0.8428 (mmm) cc_final: 0.8207 (mmm) REVERT: B 447 MET cc_start: 0.6883 (ppp) cc_final: 0.6515 (ppp) REVERT: B 481 MET cc_start: 0.7975 (mmm) cc_final: 0.7713 (tpt) REVERT: B 553 PHE cc_start: 0.8179 (t80) cc_final: 0.7673 (p90) REVERT: B 570 MET cc_start: 0.8425 (mmm) cc_final: 0.8014 (mmm) REVERT: C 447 MET cc_start: 0.6894 (ppp) cc_final: 0.6532 (ppp) REVERT: C 570 MET cc_start: 0.8326 (mmm) cc_final: 0.7992 (mmm) REVERT: D 447 MET cc_start: 0.6900 (ppp) cc_final: 0.6529 (ppp) REVERT: D 481 MET cc_start: 0.7907 (mmm) cc_final: 0.7564 (tpt) REVERT: D 570 MET cc_start: 0.8315 (mmm) cc_final: 0.8035 (mmm) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1239 time to fit residues: 69.7564 Evaluate side-chains 254 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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: 1.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN A 306 GLN A 582 HIS ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN C 306 GLN D 208 ASN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.116978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095239 restraints weight = 42923.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098229 restraints weight = 22864.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100214 restraints weight = 15457.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.101542 restraints weight = 12049.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102411 restraints weight = 10222.871| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19860 Z= 0.139 Angle : 0.608 7.167 26964 Z= 0.312 Chirality : 0.039 0.198 3072 Planarity : 0.005 0.041 3416 Dihedral : 4.842 27.317 2644 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.48 % Allowed : 9.49 % Favored : 89.03 % 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: -1.81 (0.16), residues: 2408 helix: -0.48 (0.13), residues: 1460 sheet: -2.46 (0.47), residues: 84 loop : -2.21 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 302 TYR 0.013 0.001 TYR C 467 PHE 0.040 0.001 PHE A 493 TRP 0.009 0.001 TRP C 495 HIS 0.010 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00313 (19860) covalent geometry : angle 0.60809 (26964) hydrogen bonds : bond 0.03900 ( 1025) hydrogen bonds : angle 4.51612 ( 3033) *********************** 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 330 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.7841 (ptp) cc_final: 0.7540 (ptp) REVERT: A 447 MET cc_start: 0.6845 (ppp) cc_final: 0.6310 (ppp) REVERT: A 472 PHE cc_start: 0.8017 (m-80) cc_final: 0.7769 (m-10) REVERT: A 582 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6637 (t70) REVERT: B 447 MET cc_start: 0.6862 (ppp) cc_final: 0.6321 (ppp) REVERT: B 554 MET cc_start: 0.6865 (tpp) cc_final: 0.6648 (tpp) REVERT: B 570 MET cc_start: 0.8354 (mmm) cc_final: 0.8139 (mmm) REVERT: C 447 MET cc_start: 0.6876 (ppp) cc_final: 0.6357 (ppp) REVERT: C 554 MET cc_start: 0.7776 (tpp) cc_final: 0.7535 (tpp) REVERT: D 306 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: D 340 MET cc_start: 0.9377 (mmt) cc_final: 0.9024 (mmt) REVERT: D 447 MET cc_start: 0.6860 (ppp) cc_final: 0.6357 (ppp) REVERT: D 554 MET cc_start: 0.6865 (tpp) cc_final: 0.6652 (tpp) outliers start: 31 outliers final: 23 residues processed: 316 average time/residue: 0.1177 time to fit residues: 62.0844 Evaluate side-chains 292 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 76 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 145 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 582 HIS D 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095428 restraints weight = 42914.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098417 restraints weight = 22735.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100409 restraints weight = 15300.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101742 restraints weight = 11898.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102596 restraints weight = 10091.126| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19860 Z= 0.115 Angle : 0.573 6.832 26964 Z= 0.287 Chirality : 0.038 0.156 3072 Planarity : 0.004 0.038 3416 Dihedral : 4.399 18.854 2644 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.72 % Allowed : 12.79 % Favored : 85.50 % 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: -0.89 (0.17), residues: 2408 helix: 0.26 (0.13), residues: 1464 sheet: -2.15 (0.49), residues: 84 loop : -1.85 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 584 TYR 0.013 0.001 TYR C 467 PHE 0.031 0.001 PHE A 493 TRP 0.009 0.001 TRP A 495 HIS 0.011 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00253 (19860) covalent geometry : angle 0.57336 (26964) hydrogen bonds : bond 0.03423 ( 1025) hydrogen bonds : angle 4.11026 ( 3033) *********************** 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 316 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 442 MET cc_start: 0.7811 (ptp) cc_final: 0.7477 (ptp) REVERT: A 447 MET cc_start: 0.6821 (ppp) cc_final: 0.6345 (ppp) REVERT: A 574 PHE cc_start: 0.8190 (m-10) cc_final: 0.7922 (m-10) REVERT: B 447 MET cc_start: 0.6834 (ppp) cc_final: 0.6319 (ppp) REVERT: B 554 MET cc_start: 0.6888 (tpp) cc_final: 0.6673 (tpp) REVERT: B 570 MET cc_start: 0.8353 (mmm) cc_final: 0.8148 (mmm) REVERT: C 447 MET cc_start: 0.6821 (ppp) cc_final: 0.6346 (ppp) REVERT: D 306 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: D 447 MET cc_start: 0.6811 (ppp) cc_final: 0.6338 (ppp) outliers start: 36 outliers final: 18 residues processed: 306 average time/residue: 0.1182 time to fit residues: 60.5370 Evaluate side-chains 274 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 255 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 306 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 226 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN C 582 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.116453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094787 restraints weight = 42508.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097743 restraints weight = 22562.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099748 restraints weight = 15216.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101065 restraints weight = 11817.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101932 restraints weight = 10013.177| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19860 Z= 0.117 Angle : 0.565 8.129 26964 Z= 0.280 Chirality : 0.038 0.159 3072 Planarity : 0.004 0.036 3416 Dihedral : 4.227 15.149 2644 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.38 % Allowed : 14.27 % Favored : 84.35 % 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: -0.47 (0.17), residues: 2408 helix: 0.63 (0.14), residues: 1468 sheet: -1.92 (0.52), residues: 84 loop : -1.77 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 302 TYR 0.009 0.001 TYR C 467 PHE 0.022 0.001 PHE C 574 TRP 0.008 0.001 TRP C 495 HIS 0.007 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00262 (19860) covalent geometry : angle 0.56520 (26964) hydrogen bonds : bond 0.03292 ( 1025) hydrogen bonds : angle 4.00840 ( 3033) *********************** 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 292 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 263 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 447 MET cc_start: 0.6792 (ppp) cc_final: 0.6341 (ppp) REVERT: B 447 MET cc_start: 0.6805 (ppp) cc_final: 0.6321 (ppp) REVERT: B 570 MET cc_start: 0.8399 (mmm) cc_final: 0.8113 (mmm) REVERT: C 447 MET cc_start: 0.6802 (ppp) cc_final: 0.6332 (ppp) REVERT: C 493 PHE cc_start: 0.5481 (t80) cc_final: 0.4700 (t80) REVERT: C 554 MET cc_start: 0.7412 (tpp) cc_final: 0.7124 (tpp) REVERT: D 447 MET cc_start: 0.6782 (ppp) cc_final: 0.6314 (ppp) outliers start: 29 outliers final: 21 residues processed: 285 average time/residue: 0.1168 time to fit residues: 55.3095 Evaluate side-chains 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 214 optimal weight: 0.0030 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 208 ASN B 37 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 208 ASN C 582 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094984 restraints weight = 42417.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097847 restraints weight = 23070.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099775 restraints weight = 15775.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101025 restraints weight = 12358.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.101866 restraints weight = 10553.908| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19860 Z= 0.118 Angle : 0.553 8.439 26964 Z= 0.276 Chirality : 0.038 0.161 3072 Planarity : 0.004 0.035 3416 Dihedral : 4.115 15.022 2644 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.19 % Allowed : 14.98 % Favored : 82.82 % 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: -0.19 (0.17), residues: 2408 helix: 0.87 (0.14), residues: 1460 sheet: -1.75 (0.56), residues: 84 loop : -1.66 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 584 TYR 0.009 0.001 TYR A 467 PHE 0.025 0.001 PHE C 574 TRP 0.008 0.001 TRP C 495 HIS 0.014 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00271 (19860) covalent geometry : angle 0.55258 (26964) hydrogen bonds : bond 0.03173 ( 1025) hydrogen bonds : angle 3.90717 ( 3033) *********************** 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 313 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.7973 (t0) REVERT: A 447 MET cc_start: 0.6850 (ppp) cc_final: 0.6374 (ppp) REVERT: A 536 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8080 (tt) REVERT: B 37 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.7965 (t0) REVERT: B 430 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7830 (mm) REVERT: B 447 MET cc_start: 0.6850 (ppp) cc_final: 0.6376 (ppp) REVERT: B 536 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8086 (tt) REVERT: C 37 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.7958 (t0) REVERT: C 447 MET cc_start: 0.6841 (ppp) cc_final: 0.6375 (ppp) REVERT: C 536 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8049 (tt) REVERT: D 447 MET cc_start: 0.6835 (ppp) cc_final: 0.6371 (ppp) REVERT: D 536 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8084 (tt) REVERT: D 554 MET cc_start: 0.6988 (tpp) cc_final: 0.6782 (tpp) outliers start: 46 outliers final: 24 residues processed: 301 average time/residue: 0.1193 time to fit residues: 59.8290 Evaluate side-chains 281 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 91 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090647 restraints weight = 43036.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093512 restraints weight = 23039.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.095436 restraints weight = 15659.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096694 restraints weight = 12260.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097501 restraints weight = 10472.702| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19860 Z= 0.159 Angle : 0.594 10.802 26964 Z= 0.296 Chirality : 0.040 0.339 3072 Planarity : 0.004 0.032 3416 Dihedral : 4.143 16.871 2644 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.43 % Allowed : 16.13 % Favored : 81.44 % 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: -0.03 (0.17), residues: 2408 helix: 0.92 (0.14), residues: 1472 sheet: -1.80 (0.58), residues: 84 loop : -1.45 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 584 TYR 0.009 0.001 TYR A 467 PHE 0.035 0.001 PHE C 574 TRP 0.010 0.001 TRP C 495 HIS 0.009 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00373 (19860) covalent geometry : angle 0.59368 (26964) hydrogen bonds : bond 0.03344 ( 1025) hydrogen bonds : angle 3.95025 ( 3033) *********************** 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 315 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.6915 (ppp) cc_final: 0.6449 (ppp) REVERT: B 340 MET cc_start: 0.9169 (tpp) cc_final: 0.8858 (tpt) REVERT: B 447 MET cc_start: 0.6893 (ppp) cc_final: 0.6420 (ppp) REVERT: C 402 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8672 (tt) REVERT: C 447 MET cc_start: 0.6898 (ppp) cc_final: 0.6471 (ppp) REVERT: C 554 MET cc_start: 0.7436 (tpp) cc_final: 0.7153 (tpp) REVERT: D 37 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.7826 (t0) REVERT: D 447 MET cc_start: 0.6880 (ppp) cc_final: 0.6456 (ppp) REVERT: D 554 MET cc_start: 0.7067 (tpp) cc_final: 0.6837 (tpp) outliers start: 51 outliers final: 35 residues processed: 299 average time/residue: 0.1216 time to fit residues: 60.3599 Evaluate side-chains 281 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 234 optimal weight: 0.5980 chunk 201 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.089453 restraints weight = 43040.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092166 restraints weight = 24205.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093972 restraints weight = 16879.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.095171 restraints weight = 13420.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095954 restraints weight = 11544.574| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19860 Z= 0.158 Angle : 0.614 13.234 26964 Z= 0.305 Chirality : 0.041 0.325 3072 Planarity : 0.004 0.031 3416 Dihedral : 4.188 17.140 2644 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.39 % Allowed : 18.13 % Favored : 79.48 % 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: 0.04 (0.18), residues: 2408 helix: 0.95 (0.14), residues: 1464 sheet: -1.85 (0.57), residues: 84 loop : -1.34 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 615 TYR 0.009 0.001 TYR A 467 PHE 0.037 0.001 PHE A 493 TRP 0.009 0.001 TRP C 495 HIS 0.011 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00373 (19860) covalent geometry : angle 0.61445 (26964) hydrogen bonds : bond 0.03413 ( 1025) hydrogen bonds : angle 3.99112 ( 3033) *********************** 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 298 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.6973 (ppp) cc_final: 0.6485 (ppp) REVERT: A 554 MET cc_start: 0.7058 (tpp) cc_final: 0.6830 (tpp) REVERT: A 584 ARG cc_start: 0.7730 (mtm180) cc_final: 0.7526 (mtm110) REVERT: B 447 MET cc_start: 0.6962 (ppp) cc_final: 0.6457 (ppp) REVERT: C 402 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8648 (tt) REVERT: C 447 MET cc_start: 0.6979 (ppp) cc_final: 0.6516 (ppp) REVERT: C 554 MET cc_start: 0.7341 (tpp) cc_final: 0.7095 (tpp) REVERT: C 584 ARG cc_start: 0.7406 (mtm180) cc_final: 0.7144 (mtm180) REVERT: D 37 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.7742 (t0) REVERT: D 447 MET cc_start: 0.6914 (ppp) cc_final: 0.6474 (ppp) REVERT: D 474 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7550 (ttp) REVERT: D 554 MET cc_start: 0.7007 (tpp) cc_final: 0.6785 (tpp) outliers start: 50 outliers final: 36 residues processed: 281 average time/residue: 0.1187 time to fit residues: 55.9472 Evaluate side-chains 273 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.092209 restraints weight = 42923.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.095015 restraints weight = 23902.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096884 restraints weight = 16565.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098108 restraints weight = 13092.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098893 restraints weight = 11228.603| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19860 Z= 0.116 Angle : 0.575 9.273 26964 Z= 0.286 Chirality : 0.038 0.222 3072 Planarity : 0.004 0.032 3416 Dihedral : 4.137 19.397 2644 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.29 % Allowed : 17.99 % Favored : 79.72 % 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: 0.11 (0.18), residues: 2408 helix: 1.09 (0.14), residues: 1444 sheet: -1.80 (0.56), residues: 84 loop : -1.45 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 584 TYR 0.009 0.001 TYR A 467 PHE 0.024 0.001 PHE C 574 TRP 0.010 0.001 TRP C 495 HIS 0.010 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00265 (19860) covalent geometry : angle 0.57511 (26964) hydrogen bonds : bond 0.03215 ( 1025) hydrogen bonds : angle 3.91269 ( 3033) *********************** 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 312 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7693 (t0) REVERT: A 447 MET cc_start: 0.6920 (ppp) cc_final: 0.6426 (ppp) REVERT: A 554 MET cc_start: 0.7100 (tpp) cc_final: 0.6762 (tpp) REVERT: A 584 ARG cc_start: 0.7807 (mtm180) cc_final: 0.7572 (mtm110) REVERT: B 37 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.7703 (t0) REVERT: B 447 MET cc_start: 0.6911 (ppp) cc_final: 0.6415 (ppp) REVERT: B 568 LEU cc_start: 0.8013 (tp) cc_final: 0.7753 (tt) REVERT: B 570 MET cc_start: 0.8144 (mmm) cc_final: 0.7712 (mmm) REVERT: C 37 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.7696 (t0) REVERT: C 402 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8642 (tt) REVERT: C 447 MET cc_start: 0.6920 (ppp) cc_final: 0.6447 (ppp) REVERT: C 554 MET cc_start: 0.7245 (tpp) cc_final: 0.7000 (tpp) REVERT: C 584 ARG cc_start: 0.7454 (mtm180) cc_final: 0.7179 (ptt-90) REVERT: D 37 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.7726 (t0) REVERT: D 447 MET cc_start: 0.6890 (ppp) cc_final: 0.6426 (ppp) REVERT: D 474 MET cc_start: 0.7807 (ttp) cc_final: 0.7489 (ttp) REVERT: D 493 PHE cc_start: 0.6096 (t80) cc_final: 0.5010 (t80) REVERT: D 554 MET cc_start: 0.6918 (tpp) cc_final: 0.6658 (tpp) REVERT: D 584 ARG cc_start: 0.7346 (mtm180) cc_final: 0.7143 (mtm180) outliers start: 48 outliers final: 33 residues processed: 293 average time/residue: 0.1172 time to fit residues: 57.3556 Evaluate side-chains 287 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 195 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 91 ASN B 118 GLN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.091486 restraints weight = 42824.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094260 restraints weight = 24274.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096119 restraints weight = 16968.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097305 restraints weight = 13479.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098115 restraints weight = 11634.695| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2726 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= 0.131 Angle : 0.593 12.577 26964 Z= 0.294 Chirality : 0.039 0.305 3072 Planarity : 0.004 0.031 3416 Dihedral : 4.137 26.107 2644 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.39 % Allowed : 18.32 % Favored : 79.29 % 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: 0.09 (0.18), residues: 2408 helix: 1.07 (0.14), residues: 1444 sheet: -1.85 (0.56), residues: 84 loop : -1.42 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 584 TYR 0.009 0.001 TYR A 467 PHE 0.031 0.001 PHE C 493 TRP 0.008 0.001 TRP C 495 HIS 0.010 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00310 (19860) covalent geometry : angle 0.59329 (26964) hydrogen bonds : bond 0.03249 ( 1025) hydrogen bonds : angle 3.95629 ( 3033) *********************** 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 309 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.7731 (t0) REVERT: A 447 MET cc_start: 0.6941 (ppp) cc_final: 0.6453 (ppp) REVERT: A 554 MET cc_start: 0.7056 (tpp) cc_final: 0.6694 (tpp) REVERT: B 37 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.7735 (t0) REVERT: B 447 MET cc_start: 0.6940 (ppp) cc_final: 0.6446 (ppp) REVERT: B 474 MET cc_start: 0.7807 (ttp) cc_final: 0.7569 (ttp) REVERT: B 568 LEU cc_start: 0.8019 (tp) cc_final: 0.7735 (tt) REVERT: B 570 MET cc_start: 0.8144 (mmm) cc_final: 0.7793 (mmm) REVERT: C 37 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7721 (t0) REVERT: C 402 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8641 (tt) REVERT: C 447 MET cc_start: 0.6921 (ppp) cc_final: 0.6444 (ppp) REVERT: C 554 MET cc_start: 0.7259 (tpp) cc_final: 0.6986 (tpp) REVERT: C 577 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7331 (ptt) REVERT: D 37 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.7760 (t0) REVERT: D 307 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8348 (mt) REVERT: D 447 MET cc_start: 0.6906 (ppp) cc_final: 0.6435 (ppp) REVERT: D 474 MET cc_start: 0.7850 (ttp) cc_final: 0.7546 (ttp) REVERT: D 493 PHE cc_start: 0.5826 (t80) cc_final: 0.4993 (t80) REVERT: D 497 MET cc_start: 0.7313 (mmt) cc_final: 0.6665 (mmt) REVERT: D 554 MET cc_start: 0.6905 (tpp) cc_final: 0.6647 (tpp) REVERT: D 584 ARG cc_start: 0.7367 (mtm180) cc_final: 0.7104 (mtm180) outliers start: 50 outliers final: 30 residues processed: 293 average time/residue: 0.1111 time to fit residues: 54.5394 Evaluate side-chains 283 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 0.2980 chunk 104 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 91 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.091061 restraints weight = 43062.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093800 restraints weight = 24324.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095618 restraints weight = 16964.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096862 restraints weight = 13476.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097658 restraints weight = 11549.422| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2818 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= 0.142 Angle : 0.639 13.356 26964 Z= 0.312 Chirality : 0.040 0.229 3072 Planarity : 0.004 0.031 3416 Dihedral : 4.172 25.842 2644 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.34 % Allowed : 18.89 % Favored : 78.77 % 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: 0.03 (0.17), residues: 2408 helix: 0.96 (0.14), residues: 1448 sheet: -1.80 (0.55), residues: 84 loop : -1.36 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 492 TYR 0.024 0.001 TYR B 415 PHE 0.030 0.001 PHE C 493 TRP 0.012 0.001 TRP C 495 HIS 0.011 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00335 (19860) covalent geometry : angle 0.63923 (26964) hydrogen bonds : bond 0.03395 ( 1025) hydrogen bonds : angle 4.06812 ( 3033) ********************** 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 304 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.7748 (t0) REVERT: A 447 MET cc_start: 0.6947 (ppp) cc_final: 0.6463 (ppp) REVERT: A 474 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7737 (ttp) REVERT: A 554 MET cc_start: 0.7067 (tpp) cc_final: 0.6688 (tpp) REVERT: B 37 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.7742 (t0) REVERT: B 447 MET cc_start: 0.6956 (ppp) cc_final: 0.6473 (ppp) REVERT: B 497 MET cc_start: 0.7207 (tpp) cc_final: 0.6530 (mpp) REVERT: B 570 MET cc_start: 0.8259 (mmm) cc_final: 0.7691 (mmm) REVERT: C 37 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.7738 (t0) REVERT: C 402 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8570 (tt) REVERT: C 447 MET cc_start: 0.6947 (ppp) cc_final: 0.6497 (ppp) REVERT: C 554 MET cc_start: 0.7275 (tpp) cc_final: 0.7055 (tpp) REVERT: C 570 MET cc_start: 0.8203 (mmm) cc_final: 0.7996 (mmm) REVERT: C 584 ARG cc_start: 0.7389 (mtm180) cc_final: 0.7119 (mtm180) REVERT: D 37 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.7773 (t0) REVERT: D 307 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8412 (mt) REVERT: D 447 MET cc_start: 0.6916 (ppp) cc_final: 0.6444 (ppp) REVERT: D 493 PHE cc_start: 0.5886 (t80) cc_final: 0.4948 (t80) REVERT: D 497 MET cc_start: 0.7321 (mmt) cc_final: 0.6560 (mmt) REVERT: D 554 MET cc_start: 0.6907 (tpp) cc_final: 0.6656 (tpp) REVERT: D 584 ARG cc_start: 0.7571 (mtm180) cc_final: 0.7366 (mtm180) outliers start: 49 outliers final: 30 residues processed: 289 average time/residue: 0.1195 time to fit residues: 57.5217 Evaluate side-chains 278 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 16 optimal weight: 0.1980 chunk 129 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 306 GLN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.092950 restraints weight = 42903.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095730 restraints weight = 24183.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097578 restraints weight = 16833.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098814 restraints weight = 13328.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099627 restraints weight = 11432.309| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19860 Z= 0.120 Angle : 0.618 14.687 26964 Z= 0.301 Chirality : 0.039 0.211 3072 Planarity : 0.004 0.045 3416 Dihedral : 4.128 24.758 2644 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.05 % Allowed : 19.47 % Favored : 78.48 % 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: 0.05 (0.17), residues: 2408 helix: 1.00 (0.14), residues: 1440 sheet: -1.62 (0.56), residues: 84 loop : -1.39 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 584 TYR 0.022 0.001 TYR B 415 PHE 0.023 0.001 PHE C 493 TRP 0.012 0.001 TRP C 495 HIS 0.012 0.001 HIS B 582 Details of bonding type rmsd covalent geometry : bond 0.00275 (19860) covalent geometry : angle 0.61761 (26964) hydrogen bonds : bond 0.03252 ( 1025) hydrogen bonds : angle 4.02280 ( 3033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.54 seconds wall clock time: 53 minutes 58.22 seconds (3238.22 seconds total)