Starting phenix.real_space_refine on Thu Jul 2 21:52:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7plt_13501/07_2026/7plt_13501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plt_13501/07_2026/7plt_13501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7plt_13501/07_2026/7plt_13501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plt_13501/07_2026/7plt_13501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7plt_13501/07_2026/7plt_13501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plt_13501/07_2026/7plt_13501.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7plt_13501/07_2026/7plt_13501.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7plt_13501/07_2026/7plt_13501.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6467 2.51 5 N 1723 2.21 5 O 1892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 10148 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.23, per 1000 atoms: 0.22 Number of scatterers: 10148 At special positions: 0 Unit cell: (103.88, 133.56, 150.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 2 15.00 Mg 1 11.99 O 1892 8.00 N 1723 7.00 C 6467 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 334.3 milliseconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 14 sheets defined 56.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.190A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.698A pdb=" N MET A 135 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.594A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.810A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.236A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.645A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 292 removed outlier: 4.094A pdb=" N GLY A 291 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 4.435A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.571A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 removed outlier: 4.076A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.577A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 515 removed outlier: 3.822A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.543A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.619A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.059A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.776A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.666A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.793A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.277A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.873A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.633A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 4.371A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.649A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.715A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.659A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.379A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 355 removed outlier: 6.013A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.670A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.937A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.199A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.570A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.606A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY A 227 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.532A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.580A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.622A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.371A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 528 hydrogen bonds defined for protein. 1437 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: 1.78 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1698 1.31 - 1.44: 2744 1.44 - 1.56: 5816 1.56 - 1.69: 3 1.69 - 1.81: 102 Bond restraints: 10363 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.439 0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.190 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " ideal model delta sigma weight residual 1.409 1.353 0.056 1.70e-02 3.46e+03 1.10e+01 bond pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 1.530 1.465 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.458 0.067 2.10e-02 2.27e+03 1.03e+01 ... (remaining 10358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 13450 2.63 - 5.25: 479 5.25 - 7.88: 53 7.88 - 10.51: 10 10.51 - 13.14: 2 Bond angle restraints: 13994 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.20 10.50 1.80e+00 3.09e-01 3.40e+01 angle pdb=" N PHE A 564 " pdb=" CA PHE A 564 " pdb=" CB PHE A 564 " ideal model delta sigma weight residual 110.16 118.59 -8.43 1.48e+00 4.57e-01 3.24e+01 angle pdb=" N ASN C 296 " pdb=" CA ASN C 296 " pdb=" C ASN C 296 " ideal model delta sigma weight residual 110.68 118.03 -7.35 1.39e+00 5.18e-01 2.79e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 100.47 9.63 1.90e+00 2.77e-01 2.57e+01 angle pdb=" C GLY A 563 " pdb=" N PHE A 564 " pdb=" CA PHE A 564 " ideal model delta sigma weight residual 120.29 113.34 6.95 1.42e+00 4.96e-01 2.40e+01 ... (remaining 13989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.12: 6103 32.12 - 64.24: 113 64.24 - 96.36: 31 96.36 - 128.48: 1 128.48 - 160.60: 2 Dihedral angle restraints: 6250 sinusoidal: 2557 harmonic: 3693 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 100.59 -160.60 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 164.34 135.66 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 56.94 -116.94 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 6247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.028: 1527 1.028 - 2.056: 0 2.056 - 3.084: 0 3.084 - 4.113: 0 4.113 - 5.141: 2 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.59 5.14 2.00e-01 2.50e+01 6.61e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.34 4.86 2.00e-01 2.50e+01 5.92e+02 chirality pdb=" CA PHE A 564 " pdb=" N PHE A 564 " pdb=" C PHE A 564 " pdb=" CB PHE A 564 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1526 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 564 " -0.058 2.00e-02 2.50e+03 5.41e-02 5.12e+01 pdb=" CG PHE A 564 " 0.125 2.00e-02 2.50e+03 pdb=" CD1 PHE A 564 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 564 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 564 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 564 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 564 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " -0.089 9.50e-02 1.11e+02 5.27e-02 1.57e+01 pdb=" NE ARG A 213 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.095 9.50e-02 1.11e+02 5.44e-02 1.55e+01 pdb=" NE ARG A 278 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.018 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 14 2.36 - 3.00: 5719 3.00 - 3.63: 14612 3.63 - 4.27: 22564 4.27 - 4.90: 38412 Nonbonded interactions: 81321 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.727 3.620 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.098 2.170 nonbonded pdb=" OE1 GLU A 144 " pdb=" OH TYR A 179 " model vdw 2.142 3.040 nonbonded pdb=" OE2 GLU A 476 " pdb=" NH1 ARG A 701 " model vdw 2.160 3.120 nonbonded pdb=" O TRP H 1 " pdb=" O1 EEP H 2 " model vdw 2.191 3.040 ... (remaining 81316 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.790 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 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 : 0.014 0.133 10365 Z= 0.609 Angle : 1.149 13.135 14000 Z= 0.654 Chirality : 0.193 5.141 1529 Planarity : 0.008 0.095 1791 Dihedral : 14.560 160.598 3864 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.08 % 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: -1.61 (0.21), residues: 1237 helix: -1.68 (0.17), residues: 615 sheet: 0.00 (0.36), residues: 172 loop : -0.22 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.066 0.010 ARG A 213 TYR 0.031 0.006 TYR A 439 PHE 0.125 0.004 PHE A 564 TRP 0.044 0.006 TRP C 356 HIS 0.016 0.003 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.01437 / 0.61 (10363) covalent geometry : angle 1.14503 / 0.65 (13994) hydrogen bonds : bond 0.15376 / 9.68 ( 526) hydrogen bonds : angle 6.75776 / 4.54 ( 1437) link_TRANS : bond 0.02040 / 1.01 ( 2) link_TRANS : angle 4.84086 / 2.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 MET cc_start: 0.8375 (mmm) cc_final: 0.8171 (mmt) REVERT: C 360 GLN cc_start: 0.7925 (tp40) cc_final: 0.7191 (tp40) REVERT: B 66 ASP cc_start: 0.9237 (p0) cc_final: 0.8896 (p0) REVERT: B 93 PHE cc_start: 0.9258 (m-80) cc_final: 0.8850 (m-80) REVERT: B 110 ARG cc_start: 0.9019 (mtt-85) cc_final: 0.8733 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1381 time to fit residues: 22.2308 Evaluate side-chains 69 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 0.0170 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN A 264 GLN A 398 ASN A 410 ASN A 463 GLN A 464 GLN A 481 GLN A 497 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 121 GLN C 296 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 147 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.073163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.049703 restraints weight = 31492.311| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.45 r_work: 0.2678 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10365 Z= 0.143 Angle : 0.631 8.882 14000 Z= 0.335 Chirality : 0.043 0.167 1529 Planarity : 0.005 0.054 1791 Dihedral : 8.329 165.104 1387 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.83 % Allowed : 4.16 % Favored : 95.01 % Cbeta Deviations : 0.08 % 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: 0.66 (0.23), residues: 1237 helix: 0.51 (0.20), residues: 614 sheet: 0.44 (0.38), residues: 161 loop : 0.63 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 41 TYR 0.017 0.001 TYR B 29 PHE 0.041 0.002 PHE A 564 TRP 0.024 0.002 TRP A 523 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10363) covalent geometry : angle 0.63100 / 0.33 (13994) hydrogen bonds : bond 0.04338 / 2.73 ( 526) hydrogen bonds : angle 4.72198 / 3.17 ( 1437) link_TRANS : bond 0.00386 / 0.19 ( 2) link_TRANS : angle 1.20674 / 0.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8809 (tptt) cc_final: 0.8567 (tptp) REVERT: A 305 MET cc_start: 0.9122 (tpp) cc_final: 0.8810 (tpp) REVERT: A 717 GLN cc_start: 0.8656 (tp-100) cc_final: 0.8435 (tp-100) REVERT: C 123 MET cc_start: 0.9348 (mmm) cc_final: 0.9092 (mmm) REVERT: B 36 MET cc_start: 0.8846 (mmt) cc_final: 0.8625 (mmt) REVERT: B 93 PHE cc_start: 0.9451 (m-80) cc_final: 0.8957 (m-80) REVERT: B 110 ARG cc_start: 0.9173 (mtt-85) cc_final: 0.8826 (ttm-80) outliers start: 9 outliers final: 4 residues processed: 87 average time/residue: 0.1105 time to fit residues: 13.7397 Evaluate side-chains 73 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 147 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 225 ASN B 8 GLN ** B 42 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 = 0.3370 r_free = 0.3370 target = 0.071232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.047697 restraints weight = 31872.997| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.38 r_work: 0.2622 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10365 Z= 0.263 Angle : 0.640 7.209 14000 Z= 0.334 Chirality : 0.045 0.222 1529 Planarity : 0.004 0.051 1791 Dihedral : 8.138 176.105 1387 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.48 % Allowed : 5.54 % Favored : 92.98 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1237 helix: 1.00 (0.21), residues: 618 sheet: 0.30 (0.39), residues: 161 loop : 0.50 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 41 TYR 0.015 0.001 TYR A 259 PHE 0.044 0.002 PHE B 12 TRP 0.015 0.002 TRP C 79 HIS 0.009 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.26 (10363) covalent geometry : angle 0.64017 / 0.33 (13994) hydrogen bonds : bond 0.04232 / 2.64 ( 526) hydrogen bonds : angle 4.62286 / 3.12 ( 1437) link_TRANS : bond 0.00314 / 0.15 ( 2) link_TRANS : angle 0.79707 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8846 (tptt) cc_final: 0.8534 (tptp) REVERT: A 135 MET cc_start: 0.9163 (mmm) cc_final: 0.8872 (mmm) REVERT: A 305 MET cc_start: 0.9087 (tpp) cc_final: 0.8828 (tpp) REVERT: A 364 MET cc_start: 0.9551 (mmp) cc_final: 0.9331 (mmt) REVERT: A 717 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8405 (tp-100) REVERT: B 93 PHE cc_start: 0.9492 (m-80) cc_final: 0.9007 (m-80) REVERT: B 110 ARG cc_start: 0.9107 (mtt-85) cc_final: 0.8833 (ttm-80) outliers start: 16 outliers final: 6 residues processed: 83 average time/residue: 0.0911 time to fit residues: 11.3249 Evaluate side-chains 74 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 GLN C 225 ASN B 8 GLN B 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.048434 restraints weight = 32045.303| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.42 r_work: 0.2646 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10365 Z= 0.126 Angle : 0.546 7.317 14000 Z= 0.281 Chirality : 0.041 0.170 1529 Planarity : 0.004 0.047 1791 Dihedral : 7.320 159.016 1387 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.29 % Allowed : 6.56 % Favored : 92.15 % Cbeta Deviations : 0.08 % 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: 1.37 (0.24), residues: 1237 helix: 1.48 (0.21), residues: 612 sheet: 0.13 (0.38), residues: 160 loop : 0.63 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.009 0.001 TYR A 259 PHE 0.044 0.001 PHE B 12 TRP 0.013 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10363) covalent geometry : angle 0.54618 / 0.28 (13994) hydrogen bonds : bond 0.03471 / 2.19 ( 526) hydrogen bonds : angle 4.31741 / 2.92 ( 1437) link_TRANS : bond 0.00081 / 0.04 ( 2) link_TRANS : angle 0.51893 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8892 (tptt) cc_final: 0.8549 (tptp) REVERT: A 135 MET cc_start: 0.9184 (mmm) cc_final: 0.8905 (mmm) REVERT: A 211 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8815 (t) REVERT: A 717 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8398 (tp-100) REVERT: C 123 MET cc_start: 0.9098 (mmm) cc_final: 0.8732 (mmm) REVERT: B 42 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7159 (t0) REVERT: B 70 PHE cc_start: 0.7171 (t80) cc_final: 0.6954 (t80) REVERT: B 93 PHE cc_start: 0.9478 (m-80) cc_final: 0.8986 (m-80) REVERT: B 110 ARG cc_start: 0.9115 (mtt-85) cc_final: 0.8801 (ttm-80) outliers start: 14 outliers final: 8 residues processed: 86 average time/residue: 0.0986 time to fit residues: 12.4943 Evaluate side-chains 80 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047373 restraints weight = 32332.094| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.38 r_work: 0.2617 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10365 Z= 0.201 Angle : 0.585 8.944 14000 Z= 0.299 Chirality : 0.043 0.188 1529 Planarity : 0.004 0.046 1791 Dihedral : 6.882 144.349 1387 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.29 % Allowed : 7.39 % Favored : 91.32 % Cbeta Deviations : 0.08 % 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: 1.39 (0.24), residues: 1237 helix: 1.55 (0.21), residues: 616 sheet: 0.17 (0.40), residues: 159 loop : 0.51 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 256 TYR 0.013 0.001 TYR A 259 PHE 0.044 0.002 PHE B 12 TRP 0.026 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (10363) covalent geometry : angle 0.58461 / 0.30 (13994) hydrogen bonds : bond 0.03617 / 2.27 ( 526) hydrogen bonds : angle 4.31040 / 2.92 ( 1437) link_TRANS : bond 0.00287 / 0.14 ( 2) link_TRANS : angle 0.41254 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8929 (tptt) cc_final: 0.8610 (tppt) REVERT: A 135 MET cc_start: 0.9177 (mmm) cc_final: 0.8893 (mmm) REVERT: A 211 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.9003 (t) REVERT: A 594 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: A 717 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8395 (tp-100) REVERT: C 123 MET cc_start: 0.9169 (mmm) cc_final: 0.8952 (mmm) REVERT: B 93 PHE cc_start: 0.9490 (m-80) cc_final: 0.9000 (m-80) REVERT: B 110 ARG cc_start: 0.9071 (mtt-85) cc_final: 0.8763 (ttm-80) outliers start: 14 outliers final: 7 residues processed: 83 average time/residue: 0.0974 time to fit residues: 11.6959 Evaluate side-chains 79 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 62 optimal weight: 0.0060 chunk 101 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.048296 restraints weight = 32280.790| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.43 r_work: 0.2644 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10365 Z= 0.131 Angle : 0.543 9.736 14000 Z= 0.276 Chirality : 0.041 0.176 1529 Planarity : 0.004 0.048 1791 Dihedral : 6.269 124.724 1387 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.48 % Allowed : 7.57 % Favored : 90.95 % Cbeta Deviations : 0.08 % 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: 1.55 (0.24), residues: 1237 helix: 1.76 (0.22), residues: 616 sheet: 0.16 (0.40), residues: 159 loop : 0.51 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.010 0.001 TYR A 259 PHE 0.043 0.001 PHE B 12 TRP 0.040 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10363) covalent geometry : angle 0.54281 / 0.28 (13994) hydrogen bonds : bond 0.03264 / 2.07 ( 526) hydrogen bonds : angle 4.18022 / 2.84 ( 1437) link_TRANS : bond 0.00135 / 0.07 ( 2) link_TRANS : angle 0.30206 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8947 (tptt) cc_final: 0.8637 (tppt) REVERT: A 135 MET cc_start: 0.9189 (mmm) cc_final: 0.8905 (mmm) REVERT: A 211 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.9008 (t) REVERT: A 594 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: A 717 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8377 (tp-100) REVERT: C 64 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9170 (tt) REVERT: B 36 MET cc_start: 0.8761 (mmt) cc_final: 0.8536 (mmm) REVERT: B 93 PHE cc_start: 0.9475 (m-80) cc_final: 0.8987 (m-80) outliers start: 16 outliers final: 9 residues processed: 86 average time/residue: 0.0945 time to fit residues: 11.8194 Evaluate side-chains 80 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 100 optimal weight: 0.0030 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.048131 restraints weight = 32287.159| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.40 r_work: 0.2640 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10365 Z= 0.148 Angle : 0.554 8.360 14000 Z= 0.281 Chirality : 0.042 0.182 1529 Planarity : 0.004 0.047 1791 Dihedral : 6.038 115.178 1387 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.57 % Allowed : 7.85 % Favored : 90.58 % Cbeta Deviations : 0.08 % 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: 1.53 (0.25), residues: 1237 helix: 1.72 (0.22), residues: 623 sheet: 0.15 (0.40), residues: 159 loop : 0.50 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.011 0.001 TYR A 259 PHE 0.050 0.002 PHE B 12 TRP 0.012 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10363) covalent geometry : angle 0.55388 / 0.28 (13994) hydrogen bonds : bond 0.03291 / 2.09 ( 526) hydrogen bonds : angle 4.18785 / 2.84 ( 1437) link_TRANS : bond 0.00170 / 0.08 ( 2) link_TRANS : angle 0.28061 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9006 (tptt) cc_final: 0.8704 (tppt) REVERT: A 135 MET cc_start: 0.9192 (mmm) cc_final: 0.8891 (mmm) REVERT: A 211 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9044 (t) REVERT: A 594 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: A 717 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8340 (tp-100) REVERT: A 788 MET cc_start: 0.9424 (mmt) cc_final: 0.9051 (tpp) REVERT: C 44 MET cc_start: 0.9052 (mtp) cc_final: 0.8821 (ttm) REVERT: C 123 MET cc_start: 0.9452 (mmm) cc_final: 0.9241 (mmm) REVERT: B 93 PHE cc_start: 0.9481 (m-80) cc_final: 0.9002 (m-80) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 0.0893 time to fit residues: 11.0910 Evaluate side-chains 83 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 33 optimal weight: 0.0060 chunk 119 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.047253 restraints weight = 32355.901| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.40 r_work: 0.2616 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10365 Z= 0.197 Angle : 0.591 12.132 14000 Z= 0.300 Chirality : 0.043 0.188 1529 Planarity : 0.004 0.047 1791 Dihedral : 6.012 111.848 1387 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.94 % Allowed : 8.13 % Favored : 89.94 % Cbeta Deviations : 0.08 % 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: 1.50 (0.24), residues: 1237 helix: 1.77 (0.22), residues: 617 sheet: 0.07 (0.40), residues: 159 loop : 0.43 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.013 0.001 TYR A 259 PHE 0.050 0.002 PHE B 12 TRP 0.012 0.001 TRP C 79 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (10363) covalent geometry : angle 0.59147 / 0.30 (13994) hydrogen bonds : bond 0.03495 / 2.20 ( 526) hydrogen bonds : angle 4.23757 / 2.87 ( 1437) link_TRANS : bond 0.00284 / 0.14 ( 2) link_TRANS : angle 0.39797 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9067 (tptt) cc_final: 0.8757 (tppt) REVERT: A 135 MET cc_start: 0.9200 (mmm) cc_final: 0.8894 (tpp) REVERT: A 211 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9057 (t) REVERT: A 594 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: A 717 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8432 (tp-100) REVERT: A 788 MET cc_start: 0.9499 (mmt) cc_final: 0.9165 (tpp) REVERT: C 44 MET cc_start: 0.9198 (mtp) cc_final: 0.8859 (ttm) REVERT: C 64 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9123 (tt) REVERT: C 167 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8501 (mp0) REVERT: B 93 PHE cc_start: 0.9479 (m-80) cc_final: 0.8997 (m-80) outliers start: 21 outliers final: 13 residues processed: 90 average time/residue: 0.1022 time to fit residues: 13.1632 Evaluate side-chains 89 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.0270 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.072264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049269 restraints weight = 31941.667| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.43 r_work: 0.2673 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10365 Z= 0.103 Angle : 0.552 11.599 14000 Z= 0.277 Chirality : 0.041 0.180 1529 Planarity : 0.004 0.049 1791 Dihedral : 5.725 104.007 1387 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.11 % Allowed : 9.33 % Favored : 89.57 % Cbeta Deviations : 0.08 % 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: 1.73 (0.25), residues: 1237 helix: 1.90 (0.22), residues: 618 sheet: 0.12 (0.40), residues: 160 loop : 0.66 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.008 0.001 TYR A 259 PHE 0.052 0.001 PHE B 12 TRP 0.011 0.001 TRP C 79 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (10363) covalent geometry : angle 0.55219 / 0.28 (13994) hydrogen bonds : bond 0.03028 / 1.92 ( 526) hydrogen bonds : angle 4.11094 / 2.79 ( 1437) link_TRANS : bond 0.00022 / 0.01 ( 2) link_TRANS : angle 0.25910 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8981 (tptt) cc_final: 0.8661 (tppt) REVERT: A 135 MET cc_start: 0.9184 (mmm) cc_final: 0.8963 (tpp) REVERT: A 211 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9042 (t) REVERT: A 594 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: A 717 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8417 (tp-100) REVERT: A 788 MET cc_start: 0.9532 (mmt) cc_final: 0.9222 (tpp) REVERT: C 64 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9144 (tt) REVERT: B 93 PHE cc_start: 0.9446 (m-80) cc_final: 0.8969 (m-80) REVERT: B 120 MET cc_start: 0.6700 (mmt) cc_final: 0.6482 (mmt) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.1026 time to fit residues: 12.2622 Evaluate side-chains 85 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 ASN B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.048050 restraints weight = 32233.712| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.43 r_work: 0.2638 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10365 Z= 0.161 Angle : 0.588 11.600 14000 Z= 0.292 Chirality : 0.042 0.186 1529 Planarity : 0.004 0.047 1791 Dihedral : 5.774 105.957 1387 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.29 % Allowed : 9.23 % Favored : 89.47 % Cbeta Deviations : 0.08 % 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: 1.62 (0.25), residues: 1237 helix: 1.82 (0.22), residues: 626 sheet: 0.16 (0.41), residues: 159 loop : 0.50 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.012 0.001 TYR A 259 PHE 0.055 0.001 PHE B 12 TRP 0.010 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (10363) covalent geometry : angle 0.58762 / 0.29 (13994) hydrogen bonds : bond 0.03216 / 2.03 ( 526) hydrogen bonds : angle 4.14485 / 2.81 ( 1437) link_TRANS : bond 0.00204 / 0.10 ( 2) link_TRANS : angle 0.32379 / 0.15 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.9216 (mmm) cc_final: 0.8906 (tpp) REVERT: A 211 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9049 (t) REVERT: A 594 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: A 717 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8510 (tp-100) REVERT: A 788 MET cc_start: 0.9539 (mmt) cc_final: 0.9240 (tpp) REVERT: C 47 MET cc_start: 0.7996 (ppp) cc_final: 0.7470 (ppp) REVERT: C 64 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9132 (tt) REVERT: C 167 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8576 (mp0) REVERT: B 93 PHE cc_start: 0.9439 (m-80) cc_final: 0.8957 (m-80) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.0938 time to fit residues: 11.3097 Evaluate side-chains 82 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 0.0000 chunk 118 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.048781 restraints weight = 31950.333| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.39 r_work: 0.2660 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10365 Z= 0.118 Angle : 0.562 10.060 14000 Z= 0.280 Chirality : 0.041 0.184 1529 Planarity : 0.004 0.048 1791 Dihedral : 5.687 103.551 1387 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.39 % Allowed : 9.33 % Favored : 89.29 % Cbeta Deviations : 0.08 % 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: 1.77 (0.25), residues: 1237 helix: 1.94 (0.22), residues: 619 sheet: 0.27 (0.41), residues: 157 loop : 0.60 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.009 0.001 TYR A 259 PHE 0.056 0.001 PHE B 12 TRP 0.010 0.001 TRP C 79 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10363) covalent geometry : angle 0.56172 / 0.28 (13994) hydrogen bonds : bond 0.03038 / 1.92 ( 526) hydrogen bonds : angle 4.07577 / 2.77 ( 1437) link_TRANS : bond 0.00095 / 0.05 ( 2) link_TRANS : angle 0.20776 / 0.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2242.72 seconds wall clock time: 39 minutes 17.50 seconds (2357.50 seconds total)