Starting phenix.real_space_refine on Thu Jul 2 15:23:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iol_60744/07_2026/9iol_60744.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iol_60744/07_2026/9iol_60744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iol_60744/07_2026/9iol_60744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iol_60744/07_2026/9iol_60744.map" model { file = "/net/cci-nas-00/data/ceres_data/9iol_60744/07_2026/9iol_60744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iol_60744/07_2026/9iol_60744.cif" } resolution = 3.46 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 40 5.16 5 C 5631 2.51 5 N 1530 2.21 5 O 1789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4104 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 23, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3970 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 466} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 404 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 416 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "M" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 101 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'2OP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'2OP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.65, per 1000 atoms: 0.18 Number of scatterers: 9036 At special positions: 0 Unit cell: (95.57, 92.7029, 141.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 46 15.00 O 1789 8.00 N 1530 7.00 C 5631 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 204.7 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 39.7% alpha, 20.9% beta 12 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 29 through 48 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 106 through 123 removed outlier: 3.676A pdb=" N ILE A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 198 through 222 removed outlier: 9.357A pdb=" N GLU A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ASP A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 299 through 303 removed outlier: 4.543A pdb=" N THR A 303 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.829A pdb=" N LEU A 430 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 461 removed outlier: 3.582A pdb=" N ASP A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.574A pdb=" N ILE A 482 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 500 removed outlier: 3.702A pdb=" N GLN A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 58 through 78 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 136 Processing helix chain 'B' and resid 142 through 156 Processing helix chain 'B' and resid 179 through 196 Processing helix chain 'B' and resid 238 through 251 removed outlier: 3.935A pdb=" N THR B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.788A pdb=" N LYS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 377 through 393 removed outlier: 3.538A pdb=" N LEU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 474 through 478 removed outlier: 4.159A pdb=" N PHE B 478 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 removed outlier: 3.537A pdb=" N ARG B 488 " --> pdb=" O GLN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 519 Processing helix chain 'B' and resid 520 through 530 Processing helix chain 'M' and resid 9 through 13 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84 removed outlier: 5.194A pdb=" N VAL A 79 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 58 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU A 83 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 54 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ALA A 55 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 10 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL A 57 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU A 12 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N PHE A 59 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N MET A 14 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG A 130 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLN A 162 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 132 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 164 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 134 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A 225 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 165 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 253 removed outlier: 6.913A pdb=" N VAL A 361 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU A 268 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N ASN A 359 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN A 359 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 11.930A pdb=" N TYR A 421 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N VAL A 361 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N LEU A 419 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N LYS A 363 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 10.850A pdb=" N GLU A 417 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N MET A 389 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 344 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG A 394 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL A 342 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA A 396 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE A 340 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE A 340 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 280 Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 297 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA7, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 109 removed outlier: 7.161A pdb=" N LEU B 105 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N PHE B 87 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU B 107 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL B 85 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 43 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262 removed outlier: 7.825A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 395 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE B 350 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 397 " --> pdb=" O MET B 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 419 through 420 removed outlier: 6.882A pdb=" N GLU B 419 " --> pdb=" O VAL B 427 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1428 1.29 - 1.42: 2464 1.42 - 1.55: 5244 1.55 - 1.69: 89 1.69 - 1.82: 67 Bond restraints: 9292 Sorted by residual: bond pdb=" CB GLN B 320 " pdb=" CG GLN B 320 " ideal model delta sigma weight residual 1.520 1.340 0.180 3.00e-02 1.11e+03 3.59e+01 bond pdb=" CZ ARG B 318 " pdb=" NH2 ARG B 318 " ideal model delta sigma weight residual 1.330 1.259 0.071 1.30e-02 5.92e+03 3.00e+01 bond pdb=" O14 IHP B 801 " pdb=" P4 IHP B 801 " ideal model delta sigma weight residual 1.671 1.571 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C5' DC C 1 " pdb=" C4' DC C 1 " ideal model delta sigma weight residual 1.512 1.544 -0.032 7.00e-03 2.04e+04 2.15e+01 bond pdb=" C4 DC D 13 " pdb=" N4 DC D 13 " ideal model delta sigma weight residual 1.335 1.293 0.042 9.00e-03 1.23e+04 2.15e+01 ... (remaining 9287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 12387 4.09 - 8.18: 310 8.18 - 12.27: 10 12.27 - 16.36: 1 16.36 - 20.45: 1 Bond angle restraints: 12709 Sorted by residual: angle pdb=" CB GLN B 320 " pdb=" CG GLN B 320 " pdb=" CD GLN B 320 " ideal model delta sigma weight residual 112.60 133.05 -20.45 1.70e+00 3.46e-01 1.45e+02 angle pdb=" O2 DT C 14 " pdb=" C2 DT C 14 " pdb=" N3 DT C 14 " ideal model delta sigma weight residual 122.30 117.00 5.30 6.00e-01 2.78e+00 7.81e+01 angle pdb=" C5 DA D 7 " pdb=" C6 DA D 7 " pdb=" N1 DA D 7 " ideal model delta sigma weight residual 117.70 121.92 -4.22 5.00e-01 4.00e+00 7.12e+01 angle pdb=" C5 DA C 17 " pdb=" C6 DA C 17 " pdb=" N1 DA C 17 " ideal model delta sigma weight residual 117.70 121.87 -4.17 5.00e-01 4.00e+00 6.97e+01 angle pdb=" N6 DA D 1 " pdb=" C6 DA D 1 " pdb=" N1 DA D 1 " ideal model delta sigma weight residual 118.60 113.76 4.84 6.00e-01 2.78e+00 6.52e+01 ... (remaining 12704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.39: 5110 23.39 - 46.77: 372 46.77 - 70.15: 121 70.15 - 93.54: 14 93.54 - 116.92: 4 Dihedral angle restraints: 5621 sinusoidal: 2627 harmonic: 2994 Sorted by residual: dihedral pdb=" C LEU A 108 " pdb=" N LEU A 108 " pdb=" CA LEU A 108 " pdb=" CB LEU A 108 " ideal model delta harmonic sigma weight residual -122.60 -137.02 14.42 0 2.50e+00 1.60e-01 3.33e+01 dihedral pdb=" CA LYS A 413 " pdb=" C LYS A 413 " pdb=" N HIS A 414 " pdb=" CA HIS A 414 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLU B 91 " pdb=" C GLU B 91 " pdb=" N LYS B 92 " pdb=" CA LYS B 92 " ideal model delta harmonic sigma weight residual 180.00 154.09 25.91 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 5618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1154 0.107 - 0.215: 241 0.215 - 0.322: 31 0.322 - 0.429: 2 0.429 - 0.536: 2 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA LEU A 108 " pdb=" N LEU A 108 " pdb=" C LEU A 108 " pdb=" CB LEU A 108 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" CA PHE B 159 " pdb=" N PHE B 159 " pdb=" C PHE B 159 " pdb=" CB PHE B 159 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CG LEU B 57 " pdb=" CB LEU B 57 " pdb=" CD1 LEU B 57 " pdb=" CD2 LEU B 57 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 1427 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA D 1 " 0.355 2.00e-02 2.50e+03 1.51e-01 6.30e+02 pdb=" N9 DA D 1 " -0.069 2.00e-02 2.50e+03 pdb=" C8 DA D 1 " -0.095 2.00e-02 2.50e+03 pdb=" N7 DA D 1 " -0.097 2.00e-02 2.50e+03 pdb=" C5 DA D 1 " -0.093 2.00e-02 2.50e+03 pdb=" C6 DA D 1 " 0.028 2.00e-02 2.50e+03 pdb=" N6 DA D 1 " 0.242 2.00e-02 2.50e+03 pdb=" N1 DA D 1 " 0.030 2.00e-02 2.50e+03 pdb=" C2 DA D 1 " -0.053 2.00e-02 2.50e+03 pdb=" N3 DA D 1 " -0.114 2.00e-02 2.50e+03 pdb=" C4 DA D 1 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 14 " -0.188 2.00e-02 2.50e+03 1.22e-01 3.72e+02 pdb=" N1 DT C 14 " 0.121 2.00e-02 2.50e+03 pdb=" C2 DT C 14 " 0.141 2.00e-02 2.50e+03 pdb=" O2 DT C 14 " -0.141 2.00e-02 2.50e+03 pdb=" N3 DT C 14 " 0.128 2.00e-02 2.50e+03 pdb=" C4 DT C 14 " 0.022 2.00e-02 2.50e+03 pdb=" O4 DT C 14 " -0.155 2.00e-02 2.50e+03 pdb=" C5 DT C 14 " 0.035 2.00e-02 2.50e+03 pdb=" C7 DT C 14 " -0.073 2.00e-02 2.50e+03 pdb=" C6 DT C 14 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC C 7 " -0.155 2.00e-02 2.50e+03 8.46e-02 1.61e+02 pdb=" N1 DC C 7 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DC C 7 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DC C 7 " 0.119 2.00e-02 2.50e+03 pdb=" N3 DC C 7 " -0.036 2.00e-02 2.50e+03 pdb=" C4 DC C 7 " -0.028 2.00e-02 2.50e+03 pdb=" N4 DC C 7 " -0.081 2.00e-02 2.50e+03 pdb=" C5 DC C 7 " 0.077 2.00e-02 2.50e+03 pdb=" C6 DC C 7 " 0.109 2.00e-02 2.50e+03 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1288 2.79 - 3.31: 9097 3.31 - 3.84: 14986 3.84 - 4.37: 17397 4.37 - 4.90: 28012 Nonbonded interactions: 70780 Sorted by model distance: nonbonded pdb=" OG SER A 324 " pdb=" OD2 ASP A 327 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR A 61 " pdb=" O GLY A 63 " model vdw 2.265 3.040 nonbonded pdb=" O LYS B 265 " pdb=" NZ LYS B 265 " model vdw 2.293 3.120 nonbonded pdb=" O GLY A 17 " pdb=" OG SER A 21 " model vdw 2.335 3.040 nonbonded pdb=" O ILE A 197 " pdb=" NZ LYS A 202 " model vdw 2.345 3.120 ... (remaining 70775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.012 0.180 9293 Z= 0.789 Angle : 1.676 20.454 12709 Z= 1.255 Chirality : 0.087 0.536 1430 Planarity : 0.017 0.173 1482 Dihedral : 18.011 116.920 3667 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.87 % Allowed : 7.85 % Favored : 91.28 % Cbeta Deviations : 0.20 % 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: -0.52 (0.24), residues: 1007 helix: -0.29 (0.25), residues: 354 sheet: 0.52 (0.38), residues: 156 loop : -0.57 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 165 TYR 0.111 0.015 TYR B 217 PHE 0.060 0.010 PHE A 409 TRP 0.077 0.016 TRP A 276 HIS 0.014 0.003 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.01179 / 0.79 ( 9292) covalent geometry : angle 1.67611 / 1.26 (12709) hydrogen bonds : bond 0.15671 / 10.71 ( 403) hydrogen bonds : angle 7.91297 / 5.55 ( 1092) Misc. bond : bond 0.01948 / 1.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9320 (mmt) cc_final: 0.8968 (mmm) REVERT: A 208 VAL cc_start: 0.9637 (t) cc_final: 0.9428 (t) REVERT: A 292 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: A 427 MET cc_start: 0.9567 (tmm) cc_final: 0.9040 (tmm) REVERT: A 461 MET cc_start: 0.9015 (mpp) cc_final: 0.8790 (mmp) REVERT: B 41 LEU cc_start: 0.9299 (mm) cc_final: 0.9076 (mm) REVERT: B 62 MET cc_start: 0.9120 (tpp) cc_final: 0.8805 (tpp) REVERT: B 68 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9225 (mm-40) REVERT: B 287 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8898 (mmmt) REVERT: B 488 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8961 (tpp80) REVERT: B 514 MET cc_start: 0.9705 (mtp) cc_final: 0.9173 (mtp) REVERT: B 518 LEU cc_start: 0.9683 (mt) cc_final: 0.9448 (mt) outliers start: 8 outliers final: 2 residues processed: 90 average time/residue: 0.0820 time to fit residues: 10.3811 Evaluate side-chains 69 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 488 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 432 GLN A 517 ASN B 68 GLN B 152 ASN B 176 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.058759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.040394 restraints weight = 43400.253| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 4.94 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9293 Z= 0.196 Angle : 0.735 7.074 12709 Z= 0.397 Chirality : 0.045 0.178 1430 Planarity : 0.004 0.054 1482 Dihedral : 19.656 103.788 1568 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.64 % Allowed : 9.71 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1007 helix: 0.58 (0.27), residues: 356 sheet: 0.20 (0.37), residues: 166 loop : -0.49 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 9 TYR 0.022 0.002 TYR A 264 PHE 0.017 0.002 PHE A 31 TRP 0.019 0.002 TRP A 247 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 ( 9292) covalent geometry : angle 0.73494 / 0.40 (12709) hydrogen bonds : bond 0.06838 / 4.95 ( 403) hydrogen bonds : angle 6.11424 / 4.30 ( 1092) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9380 (mmt) cc_final: 0.9070 (mmm) REVERT: A 115 MET cc_start: 0.9741 (tpp) cc_final: 0.9514 (tmm) REVERT: A 427 MET cc_start: 0.9609 (tmm) cc_final: 0.9068 (tmm) REVERT: A 461 MET cc_start: 0.9108 (mpp) cc_final: 0.8846 (mmp) REVERT: B 62 MET cc_start: 0.9159 (tpp) cc_final: 0.8719 (tpp) REVERT: B 68 GLN cc_start: 0.9561 (OUTLIER) cc_final: 0.9315 (mm-40) REVERT: B 287 LYS cc_start: 0.9273 (mmmt) cc_final: 0.8911 (mmmt) REVERT: B 518 LEU cc_start: 0.9708 (mt) cc_final: 0.9479 (mt) outliers start: 15 outliers final: 4 residues processed: 77 average time/residue: 0.0734 time to fit residues: 8.0992 Evaluate side-chains 68 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 84 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 HIS A 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.059017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.040593 restraints weight = 43744.663| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.87 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9293 Z= 0.156 Angle : 0.650 7.050 12709 Z= 0.348 Chirality : 0.043 0.160 1430 Planarity : 0.004 0.047 1482 Dihedral : 19.433 103.222 1557 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.09 % Allowed : 11.23 % Favored : 87.68 % 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: 0.20 (0.25), residues: 1007 helix: 0.95 (0.27), residues: 355 sheet: 0.20 (0.38), residues: 165 loop : -0.44 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 399 TYR 0.016 0.001 TYR A 264 PHE 0.019 0.002 PHE A 31 TRP 0.011 0.001 TRP A 247 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 9292) covalent geometry : angle 0.64998 / 0.35 (12709) hydrogen bonds : bond 0.05720 / 4.11 ( 403) hydrogen bonds : angle 5.61099 / 3.95 ( 1092) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.9643 (tmm) cc_final: 0.9093 (tmm) REVERT: A 461 MET cc_start: 0.9156 (mpp) cc_final: 0.8789 (mmp) REVERT: B 62 MET cc_start: 0.9181 (tpp) cc_final: 0.8878 (tpp) REVERT: B 203 MET cc_start: 0.9447 (mmp) cc_final: 0.8819 (mmp) REVERT: B 287 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8850 (mmmt) REVERT: B 518 LEU cc_start: 0.9673 (mt) cc_final: 0.9431 (mt) REVERT: M 9 ARG cc_start: 0.8340 (ptm-80) cc_final: 0.8138 (ptm-80) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.0639 time to fit residues: 6.7847 Evaluate side-chains 72 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 307 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 87 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.058109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.039609 restraints weight = 44836.929| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 4.94 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9293 Z= 0.211 Angle : 0.660 8.813 12709 Z= 0.350 Chirality : 0.043 0.176 1430 Planarity : 0.004 0.051 1482 Dihedral : 19.370 101.445 1554 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.64 % Allowed : 11.67 % Favored : 86.70 % 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: 0.28 (0.26), residues: 1007 helix: 1.10 (0.27), residues: 355 sheet: 0.19 (0.38), residues: 166 loop : -0.43 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 517 TYR 0.015 0.001 TYR A 264 PHE 0.014 0.002 PHE B 487 TRP 0.007 0.001 TRP A 247 HIS 0.004 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 ( 9292) covalent geometry : angle 0.66028 / 0.35 (12709) hydrogen bonds : bond 0.05551 / 3.97 ( 403) hydrogen bonds : angle 5.47346 / 3.88 ( 1092) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.9530 (tpp) cc_final: 0.9183 (tpp) REVERT: A 427 MET cc_start: 0.9668 (tmm) cc_final: 0.9140 (tmm) REVERT: A 461 MET cc_start: 0.9183 (mpp) cc_final: 0.8963 (mmp) REVERT: B 62 MET cc_start: 0.9184 (tpp) cc_final: 0.8804 (tpp) REVERT: B 518 LEU cc_start: 0.9664 (mt) cc_final: 0.9431 (mt) outliers start: 15 outliers final: 11 residues processed: 78 average time/residue: 0.0697 time to fit residues: 8.1039 Evaluate side-chains 76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 307 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 92 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 79 optimal weight: 0.0270 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.058555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.040324 restraints weight = 43804.629| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 4.85 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9293 Z= 0.150 Angle : 0.630 9.918 12709 Z= 0.330 Chirality : 0.042 0.172 1430 Planarity : 0.003 0.049 1482 Dihedral : 19.271 98.743 1554 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.85 % Allowed : 12.21 % Favored : 85.93 % 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: 0.44 (0.26), residues: 1007 helix: 1.26 (0.28), residues: 355 sheet: 0.26 (0.39), residues: 165 loop : -0.37 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 9 TYR 0.013 0.001 TYR A 264 PHE 0.018 0.001 PHE A 31 TRP 0.006 0.001 TRP A 247 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 9292) covalent geometry : angle 0.62993 / 0.33 (12709) hydrogen bonds : bond 0.05152 / 3.68 ( 403) hydrogen bonds : angle 5.21803 / 3.70 ( 1092) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 VAL cc_start: 0.9666 (t) cc_final: 0.9365 (t) REVERT: A 427 MET cc_start: 0.9655 (tmm) cc_final: 0.9161 (tmm) REVERT: A 461 MET cc_start: 0.9176 (tpp) cc_final: 0.8747 (mmp) REVERT: B 62 MET cc_start: 0.9160 (tpp) cc_final: 0.8748 (tpp) REVERT: B 203 MET cc_start: 0.9464 (mmp) cc_final: 0.8921 (mmp) REVERT: B 497 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8983 (pp) REVERT: B 518 LEU cc_start: 0.9653 (mt) cc_final: 0.9427 (mt) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 0.0707 time to fit residues: 8.6191 Evaluate side-chains 79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 6 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.058873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.040382 restraints weight = 44060.188| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 4.93 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9293 Z= 0.136 Angle : 0.636 10.136 12709 Z= 0.329 Chirality : 0.041 0.180 1430 Planarity : 0.003 0.048 1482 Dihedral : 19.199 97.067 1554 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.18 % Allowed : 12.10 % Favored : 85.71 % 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: 0.61 (0.26), residues: 1007 helix: 1.47 (0.28), residues: 354 sheet: 0.42 (0.39), residues: 164 loop : -0.35 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 9 TYR 0.012 0.001 TYR A 264 PHE 0.018 0.001 PHE A 31 TRP 0.006 0.001 TRP A 247 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 9292) covalent geometry : angle 0.63587 / 0.33 (12709) hydrogen bonds : bond 0.05041 / 3.59 ( 403) hydrogen bonds : angle 5.08744 / 3.60 ( 1092) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.9589 (tpp) cc_final: 0.9230 (tpp) REVERT: A 427 MET cc_start: 0.9657 (tmm) cc_final: 0.9172 (tmm) REVERT: A 461 MET cc_start: 0.9175 (tpp) cc_final: 0.8727 (mmp) REVERT: B 62 MET cc_start: 0.9107 (tpp) cc_final: 0.8664 (tpp) REVERT: B 203 MET cc_start: 0.9506 (mmp) cc_final: 0.8985 (mmp) REVERT: B 497 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9032 (pp) REVERT: B 518 LEU cc_start: 0.9643 (mt) cc_final: 0.9422 (mt) outliers start: 20 outliers final: 15 residues processed: 80 average time/residue: 0.0733 time to fit residues: 9.0328 Evaluate side-chains 81 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.058240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.039872 restraints weight = 44524.448| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 4.93 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9293 Z= 0.175 Angle : 0.659 12.966 12709 Z= 0.338 Chirality : 0.043 0.224 1430 Planarity : 0.003 0.049 1482 Dihedral : 19.119 95.041 1554 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.07 % Allowed : 12.98 % Favored : 84.95 % 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: 0.58 (0.26), residues: 1007 helix: 1.43 (0.28), residues: 355 sheet: 0.38 (0.39), residues: 164 loop : -0.34 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 9 TYR 0.011 0.001 TYR A 264 PHE 0.023 0.001 PHE A 227 TRP 0.005 0.001 TRP A 247 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 9292) covalent geometry : angle 0.65858 / 0.34 (12709) hydrogen bonds : bond 0.05014 / 3.56 ( 403) hydrogen bonds : angle 5.13036 / 3.64 ( 1092) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 CYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8479 (t) REVERT: A 14 MET cc_start: 0.9531 (tpp) cc_final: 0.9228 (tpp) REVERT: A 427 MET cc_start: 0.9665 (tmm) cc_final: 0.9171 (tmm) REVERT: A 461 MET cc_start: 0.9186 (tpp) cc_final: 0.8919 (mmp) REVERT: B 203 MET cc_start: 0.9532 (mmp) cc_final: 0.9154 (mmp) REVERT: B 518 LEU cc_start: 0.9640 (mt) cc_final: 0.9409 (mt) outliers start: 19 outliers final: 14 residues processed: 78 average time/residue: 0.0690 time to fit residues: 8.2828 Evaluate side-chains 80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 498 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.058802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.040356 restraints weight = 44413.304| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 4.95 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 0.028 9293 Z= 0.135 Angle : 0.647 11.335 12709 Z= 0.328 Chirality : 0.042 0.213 1430 Planarity : 0.003 0.049 1482 Dihedral : 19.024 92.748 1554 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.85 % Allowed : 13.30 % Favored : 84.84 % 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: 0.60 (0.26), residues: 1007 helix: 1.44 (0.28), residues: 355 sheet: 0.43 (0.39), residues: 164 loop : -0.33 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 9 TYR 0.011 0.001 TYR B 217 PHE 0.029 0.001 PHE A 31 TRP 0.005 0.001 TRP A 247 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 9292) covalent geometry : angle 0.64683 / 0.33 (12709) hydrogen bonds : bond 0.04748 / 3.37 ( 403) hydrogen bonds : angle 5.02132 / 3.56 ( 1092) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 CYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8466 (t) REVERT: A 14 MET cc_start: 0.9515 (tpp) cc_final: 0.9307 (tpp) REVERT: A 212 MET cc_start: 0.9085 (ptp) cc_final: 0.8882 (tpp) REVERT: A 427 MET cc_start: 0.9655 (tmm) cc_final: 0.9206 (tmm) REVERT: A 461 MET cc_start: 0.9188 (tpp) cc_final: 0.8732 (mmp) REVERT: B 203 MET cc_start: 0.9541 (mmp) cc_final: 0.9156 (mmp) REVERT: B 518 LEU cc_start: 0.9614 (mt) cc_final: 0.9382 (mt) outliers start: 17 outliers final: 14 residues processed: 78 average time/residue: 0.0791 time to fit residues: 9.0440 Evaluate side-chains 79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 498 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 36 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.058953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.040415 restraints weight = 43784.158| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 4.92 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9293 Z= 0.136 Angle : 0.647 12.916 12709 Z= 0.326 Chirality : 0.042 0.230 1430 Planarity : 0.003 0.049 1482 Dihedral : 18.916 90.158 1554 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.85 % Allowed : 13.20 % Favored : 84.95 % 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: 0.62 (0.26), residues: 1007 helix: 1.47 (0.28), residues: 355 sheet: 0.39 (0.40), residues: 160 loop : -0.32 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 9 TYR 0.010 0.001 TYR B 217 PHE 0.026 0.001 PHE A 227 TRP 0.005 0.001 TRP A 247 HIS 0.003 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 9292) covalent geometry : angle 0.64738 / 0.33 (12709) hydrogen bonds : bond 0.04633 / 3.28 ( 403) hydrogen bonds : angle 4.95829 / 3.53 ( 1092) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 CYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8454 (t) REVERT: A 427 MET cc_start: 0.9665 (tmm) cc_final: 0.9230 (tmm) REVERT: A 461 MET cc_start: 0.9177 (tpp) cc_final: 0.8721 (mmp) REVERT: B 62 MET cc_start: 0.9058 (ttt) cc_final: 0.8502 (tpp) REVERT: B 203 MET cc_start: 0.9540 (mmp) cc_final: 0.9112 (mmm) REVERT: B 518 LEU cc_start: 0.9622 (mt) cc_final: 0.9392 (mt) REVERT: M 9 ARG cc_start: 0.8867 (ptm-80) cc_final: 0.8584 (ptm-80) outliers start: 17 outliers final: 15 residues processed: 76 average time/residue: 0.0776 time to fit residues: 8.8677 Evaluate side-chains 79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 498 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 55 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 0.0170 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 0.0000 chunk 102 optimal weight: 20.0000 chunk 89 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 511 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.059997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.041480 restraints weight = 43415.074| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 4.95 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9293 Z= 0.113 Angle : 0.656 9.365 12709 Z= 0.325 Chirality : 0.042 0.247 1430 Planarity : 0.003 0.052 1482 Dihedral : 18.811 86.798 1554 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.53 % Allowed : 13.85 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1007 helix: 1.40 (0.28), residues: 354 sheet: 0.48 (0.41), residues: 155 loop : -0.27 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 318 TYR 0.010 0.001 TYR B 217 PHE 0.020 0.001 PHE A 31 TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 9292) covalent geometry : angle 0.65593 / 0.33 (12709) hydrogen bonds : bond 0.04329 / 3.08 ( 403) hydrogen bonds : angle 4.89154 / 3.47 ( 1092) Misc. bond : bond 0.00004 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 CYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8415 (t) REVERT: A 14 MET cc_start: 0.9446 (tpp) cc_final: 0.9245 (tpp) REVERT: A 427 MET cc_start: 0.9649 (tmm) cc_final: 0.9242 (tmm) REVERT: A 461 MET cc_start: 0.9085 (tpp) cc_final: 0.8817 (mmp) REVERT: B 203 MET cc_start: 0.9542 (mmp) cc_final: 0.9145 (mmm) REVERT: B 336 GLU cc_start: 0.9545 (tt0) cc_final: 0.9334 (tm-30) REVERT: B 348 MET cc_start: 0.9049 (mmm) cc_final: 0.8718 (mmm) REVERT: B 518 LEU cc_start: 0.9605 (mt) cc_final: 0.9256 (pp) REVERT: M 9 ARG cc_start: 0.8853 (ptm-80) cc_final: 0.8581 (ptm-80) outliers start: 14 outliers final: 12 residues processed: 78 average time/residue: 0.0775 time to fit residues: 9.1723 Evaluate side-chains 80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 498 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.058820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.040433 restraints weight = 43485.082| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 4.87 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9293 Z= 0.169 Angle : 0.651 9.868 12709 Z= 0.331 Chirality : 0.042 0.245 1430 Planarity : 0.003 0.051 1482 Dihedral : 18.745 84.961 1554 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.53 % Allowed : 13.96 % Favored : 84.51 % 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: 0.64 (0.26), residues: 1007 helix: 1.42 (0.28), residues: 354 sheet: 0.44 (0.40), residues: 163 loop : -0.26 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 9 TYR 0.010 0.001 TYR B 217 PHE 0.018 0.001 PHE A 31 TRP 0.004 0.001 TRP A 247 HIS 0.003 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 9292) covalent geometry : angle 0.65116 / 0.33 (12709) hydrogen bonds : bond 0.04543 / 3.16 ( 403) hydrogen bonds : angle 4.93043 / 3.51 ( 1092) Misc. bond : bond 0.00021 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1438.59 seconds wall clock time: 25 minutes 30.59 seconds (1530.59 seconds total)