Starting phenix.real_space_refine on Thu Jul 2 21:34:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pm9_13525/07_2026/7pm9_13525.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm9_13525/07_2026/7pm9_13525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pm9_13525/07_2026/7pm9_13525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm9_13525/07_2026/7pm9_13525.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pm9_13525/07_2026/7pm9_13525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm9_13525/07_2026/7pm9_13525.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pm9_13525/07_2026/7pm9_13525.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pm9_13525/07_2026/7pm9_13525.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 4 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 6422 2.51 5 N 1713 2.21 5 O 1883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 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: 10086 Number of models: 1 Model: "" Number of chains: 7 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: "A" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 6007 Classifications: {'peptide': 735} Link IDs: {'PTRANS': 27, 'TRANS': 707} Chain breaks: 6 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: "A" 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} 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: 1.87, per 1000 atoms: 0.19 Number of scatterers: 10086 At special positions: 0 Unit cell: (109.18, 137.8, 149.46, 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 62 16.00 P 4 15.00 Mg 2 11.99 O 1883 8.00 N 1713 7.00 C 6422 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: 0.78 Conformation dependent library (CDL) restraints added in 238.4 milliseconds 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 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: 2358 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 55.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.174A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.580A 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 helix chain 'A' and resid 65 through 70 removed outlier: 3.742A pdb=" N GLY A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 4.139A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.621A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.571A 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 249 removed outlier: 3.684A pdb=" N ARG A 248 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.386A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.166A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.679A pdb=" N GLU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.530A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.527A pdb=" N THR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.526A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.769A pdb=" N ASP A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.968A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.938A pdb=" N LYS A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.587A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.350A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.521A pdb=" N ALA A 678 " --> pdb=" O ASP A 674 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 removed outlier: 3.976A pdb=" N GLY A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 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 removed outlier: 3.793A pdb=" N ARG A 784 " --> pdb=" O GLY A 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.856A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.568A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.576A 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 196 removed outlier: 3.926A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.859A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.770A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.196A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.658A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.773A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.828A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 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 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.755A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.671A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.580A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103 removed outlier: 7.783A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 3.603A pdb=" N ARG A 343 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 378 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.637A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.852A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.526A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 514 hydrogen bonds defined for protein. 1443 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: 1.61 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1676 1.32 - 1.44: 2734 1.44 - 1.56: 5784 1.56 - 1.69: 6 1.69 - 1.81: 100 Bond restraints: 10300 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.201 0.062 2.00e-02 2.50e+03 9.49e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.71e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.40e-02 5.10e+03 8.43e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 ... (remaining 10295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13503 2.38 - 4.75: 349 4.75 - 7.13: 50 7.13 - 9.51: 8 9.51 - 11.88: 4 Bond angle restraints: 13914 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 121.70 109.82 11.88 1.80e+00 3.09e-01 4.36e+01 angle pdb=" N LEU A 782 " pdb=" CA LEU A 782 " pdb=" C LEU A 782 " ideal model delta sigma weight residual 111.14 117.11 -5.97 1.08e+00 8.57e-01 3.05e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.77 -4.77 1.10e+00 8.26e-01 1.88e+01 angle pdb=" CA TYR A 787 " pdb=" CB TYR A 787 " pdb=" CG TYR A 787 " ideal model delta sigma weight residual 113.90 121.55 -7.65 1.80e+00 3.09e-01 1.81e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.08 8.02 1.90e+00 2.77e-01 1.78e+01 ... (remaining 13909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 6064 34.88 - 69.76: 100 69.76 - 104.64: 31 104.64 - 139.53: 4 139.53 - 174.41: 1 Dihedral angle restraints: 6200 sinusoidal: 2543 harmonic: 3657 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 -60.00 114.40 -174.41 1 2.00e+01 2.50e-03 4.79e+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 72.24 -132.24 1 2.00e+01 2.50e-03 4.01e+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 300.00 172.66 127.34 1 2.00e+01 2.50e-03 3.86e+01 ... (remaining 6197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 1518 1.020 - 2.040: 0 2.040 - 3.061: 0 3.061 - 4.081: 0 4.081 - 5.101: 2 Chirality restraints: 1520 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 -2.55 5.10 2.00e-01 2.50e+01 6.51e+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 -2.39 4.92 2.00e-01 2.50e+01 6.05e+02 chirality pdb=" CA MET A 648 " pdb=" N MET A 648 " pdb=" C MET A 648 " pdb=" CB MET A 648 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1517 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 116 " 0.138 9.50e-02 1.11e+02 7.90e-02 3.26e+01 pdb=" NE ARG C 116 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG C 116 " 0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG C 116 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG C 116 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.003 2.00e-02 2.50e+03 3.90e-02 3.04e+01 pdb=" CG TYR C 306 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.058 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 231 " 0.121 9.50e-02 1.11e+02 7.00e-02 2.64e+01 pdb=" NE ARG A 231 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 231 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG A 231 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A 231 " -0.024 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 26 2.37 - 3.00: 5491 3.00 - 3.63: 15183 3.63 - 4.27: 22416 4.27 - 4.90: 37848 Nonbonded interactions: 80964 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.157 2.170 nonbonded pdb=" OH TYR A 100 " pdb=" OH TYR A 119 " model vdw 2.170 3.040 nonbonded pdb=" OG SER A 165 " pdb=" O ASN A 216 " model vdw 2.175 3.040 nonbonded pdb=" NZ LYS A 633 " pdb=" O GLY C 23 " model vdw 2.182 3.120 ... (remaining 80959 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 8.820 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 10302 Z= 0.225 Angle : 0.931 11.883 13920 Z= 0.543 Chirality : 0.189 5.101 1520 Planarity : 0.008 0.085 1774 Dihedral : 16.042 174.408 3836 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.81 % 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: -1.87 (0.20), residues: 1221 helix: -1.55 (0.16), residues: 614 sheet: 0.01 (0.41), residues: 141 loop : -0.92 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.095 0.012 ARG C 116 TYR 0.059 0.007 TYR C 306 PHE 0.028 0.003 PHE C 266 TRP 0.029 0.003 TRP C 356 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (10300) covalent geometry : angle 0.92723 / 0.54 (13914) hydrogen bonds : bond 0.15774 / 10.41 ( 512) hydrogen bonds : angle 6.99107 / 4.89 ( 1443) link_TRANS : bond 0.00930 / 0.49 ( 2) link_TRANS : angle 4.22393 / 2.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.261 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: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8173 (p0) cc_final: 0.7937 (t70) REVERT: A 759 LEU cc_start: 0.9142 (mt) cc_final: 0.8774 (tt) REVERT: C 80 ASP cc_start: 0.7890 (p0) cc_final: 0.7686 (p0) outliers start: 1 outliers final: 1 residues processed: 178 average time/residue: 0.0871 time to fit residues: 21.5057 Evaluate side-chains 101 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 0.0170 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 75 GLN A 72 ASN A 156 ASN A 264 GLN A 395 HIS C 12 ASN C 41 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 280 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.066044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048194 restraints weight = 48300.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.049944 restraints weight = 23890.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051128 restraints weight = 14759.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051892 restraints weight = 10460.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.052400 restraints weight = 8190.677| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10302 Z= 0.160 Angle : 0.695 10.703 13920 Z= 0.362 Chirality : 0.045 0.212 1520 Planarity : 0.004 0.047 1774 Dihedral : 10.040 167.879 1385 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.58 % Allowed : 6.33 % Favored : 92.09 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.26 (0.22), residues: 1221 helix: 0.42 (0.20), residues: 619 sheet: 0.50 (0.38), residues: 168 loop : -0.09 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 155 TYR 0.031 0.002 TYR A 787 PHE 0.017 0.002 PHE A 564 TRP 0.018 0.002 TRP A 484 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (10300) covalent geometry : angle 0.69454 / 0.36 (13914) hydrogen bonds : bond 0.04272 / 2.81 ( 512) hydrogen bonds : angle 5.16944 / 3.57 ( 1443) link_TRANS : bond 0.00210 / 0.10 ( 2) link_TRANS : angle 0.73394 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.266 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: symmetry clash REVERT: B 66 ASP cc_start: 0.8102 (p0) cc_final: 0.7894 (t70) REVERT: A 135 MET cc_start: 0.9125 (tpp) cc_final: 0.8906 (tpt) REVERT: A 305 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8769 (tmm) REVERT: A 363 LEU cc_start: 0.9316 (mt) cc_final: 0.9049 (tp) REVERT: A 507 ASP cc_start: 0.8224 (t0) cc_final: 0.7964 (t0) REVERT: A 744 PHE cc_start: 0.8623 (m-80) cc_final: 0.8019 (m-80) REVERT: A 759 LEU cc_start: 0.9189 (mt) cc_final: 0.8882 (pp) REVERT: C 57 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8816 (tp30) REVERT: C 355 MET cc_start: 0.8916 (mmm) cc_final: 0.8591 (mmm) outliers start: 17 outliers final: 7 residues processed: 126 average time/residue: 0.0695 time to fit residues: 13.1424 Evaluate side-chains 102 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS A 252 GLN A 418 HIS A 430 HIS A 525 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.063602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046054 restraints weight = 49229.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.047666 restraints weight = 25127.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048729 restraints weight = 15880.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049391 restraints weight = 11450.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049906 restraints weight = 9135.810| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10302 Z= 0.206 Angle : 0.660 12.536 13920 Z= 0.340 Chirality : 0.044 0.197 1520 Planarity : 0.004 0.043 1774 Dihedral : 8.689 130.703 1384 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.58 % Allowed : 8.29 % Favored : 90.13 % 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: 0.65 (0.23), residues: 1221 helix: 0.96 (0.21), residues: 617 sheet: 0.38 (0.38), residues: 166 loop : -0.15 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 155 TYR 0.027 0.002 TYR A 787 PHE 0.015 0.002 PHE C 255 TRP 0.016 0.002 TRP A 484 HIS 0.006 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (10300) covalent geometry : angle 0.66044 / 0.34 (13914) hydrogen bonds : bond 0.04152 / 2.76 ( 512) hydrogen bonds : angle 4.95374 / 3.42 ( 1443) link_TRANS : bond 0.00289 / 0.15 ( 2) link_TRANS : angle 0.26455 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8056 (p0) cc_final: 0.7850 (t70) REVERT: A 305 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8736 (tmm) REVERT: A 478 MET cc_start: 0.8533 (mmm) cc_final: 0.8277 (mmm) REVERT: A 744 PHE cc_start: 0.8485 (m-80) cc_final: 0.8004 (m-80) REVERT: A 759 LEU cc_start: 0.9197 (mt) cc_final: 0.8910 (pp) REVERT: A 767 LEU cc_start: 0.8722 (pp) cc_final: 0.8387 (tt) REVERT: C 47 MET cc_start: 0.7988 (ppp) cc_final: 0.7729 (ppp) outliers start: 17 outliers final: 11 residues processed: 108 average time/residue: 0.0664 time to fit residues: 11.1531 Evaluate side-chains 97 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 737 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 0.0170 chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 115 optimal weight: 0.0270 chunk 4 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.065221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.047553 restraints weight = 49075.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049207 restraints weight = 24918.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.050319 restraints weight = 15714.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.051027 restraints weight = 11303.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.051520 restraints weight = 8961.974| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10302 Z= 0.114 Angle : 0.598 11.977 13920 Z= 0.300 Chirality : 0.041 0.191 1520 Planarity : 0.004 0.042 1774 Dihedral : 7.279 104.824 1384 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.40 % Allowed : 10.06 % Favored : 88.55 % 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: 0.98 (0.24), residues: 1221 helix: 1.31 (0.21), residues: 616 sheet: 0.44 (0.38), residues: 167 loop : -0.08 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 327 TYR 0.023 0.001 TYR A 787 PHE 0.011 0.001 PHE C 255 TRP 0.010 0.001 TRP A 484 HIS 0.011 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10300) covalent geometry : angle 0.59766 / 0.30 (13914) hydrogen bonds : bond 0.03497 / 2.32 ( 512) hydrogen bonds : angle 4.70917 / 3.22 ( 1443) link_TRANS : bond 0.00093 / 0.05 ( 2) link_TRANS : angle 0.11561 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8616 (ttp) cc_final: 0.8371 (ttp) REVERT: A 239 MET cc_start: 0.8114 (tpp) cc_final: 0.7859 (tmm) REVERT: A 305 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8691 (tmm) REVERT: A 671 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7626 (t80) REVERT: A 744 PHE cc_start: 0.8446 (m-80) cc_final: 0.7988 (m-80) REVERT: A 759 LEU cc_start: 0.9187 (mt) cc_final: 0.8897 (pp) REVERT: C 47 MET cc_start: 0.8039 (ppp) cc_final: 0.7837 (ppp) outliers start: 15 outliers final: 7 residues processed: 113 average time/residue: 0.0703 time to fit residues: 12.2965 Evaluate side-chains 92 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 0.0040 chunk 18 optimal weight: 0.4980 chunk 91 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS A 88 ASN A 463 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.065191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.047802 restraints weight = 48708.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.049438 restraints weight = 24873.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050539 restraints weight = 15745.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051254 restraints weight = 11308.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.051705 restraints weight = 8926.737| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10302 Z= 0.112 Angle : 0.588 11.414 13920 Z= 0.292 Chirality : 0.041 0.185 1520 Planarity : 0.004 0.039 1774 Dihedral : 6.379 82.031 1384 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.14 % Allowed : 11.64 % Favored : 86.22 % 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: 1.08 (0.24), residues: 1221 helix: 1.40 (0.21), residues: 617 sheet: 0.51 (0.38), residues: 159 loop : -0.05 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.022 0.001 TYR A 787 PHE 0.010 0.001 PHE A 262 TRP 0.012 0.001 TRP A 484 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10300) covalent geometry : angle 0.58780 / 0.29 (13914) hydrogen bonds : bond 0.03307 / 2.20 ( 512) hydrogen bonds : angle 4.57244 / 3.13 ( 1443) link_TRANS : bond 0.00103 / 0.05 ( 2) link_TRANS : angle 0.10442 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7977 (tpt) cc_final: 0.7294 (tpt) REVERT: A 305 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8650 (tmm) REVERT: A 478 MET cc_start: 0.8856 (mmm) cc_final: 0.8619 (tpt) REVERT: A 512 GLU cc_start: 0.8188 (tp30) cc_final: 0.7878 (tp30) REVERT: A 671 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7488 (t80) REVERT: A 744 PHE cc_start: 0.8397 (m-80) cc_final: 0.7970 (m-80) REVERT: A 759 LEU cc_start: 0.9181 (mt) cc_final: 0.8897 (pp) REVERT: A 783 MET cc_start: 0.4892 (mpp) cc_final: 0.4652 (mpp) REVERT: C 47 MET cc_start: 0.8032 (ppp) cc_final: 0.7810 (ppp) REVERT: C 117 GLU cc_start: 0.8387 (mp0) cc_final: 0.8014 (mm-30) outliers start: 23 outliers final: 11 residues processed: 108 average time/residue: 0.0661 time to fit residues: 10.9094 Evaluate side-chains 97 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 100 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.064496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047058 restraints weight = 48888.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.048669 restraints weight = 24930.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.049748 restraints weight = 15808.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050439 restraints weight = 11386.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.050926 restraints weight = 9025.501| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10302 Z= 0.140 Angle : 0.592 8.943 13920 Z= 0.293 Chirality : 0.041 0.185 1520 Planarity : 0.004 0.039 1774 Dihedral : 6.422 79.679 1384 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.49 % Allowed : 11.73 % Favored : 86.78 % 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: 1.10 (0.24), residues: 1221 helix: 1.43 (0.21), residues: 618 sheet: 0.42 (0.39), residues: 159 loop : -0.02 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.021 0.001 TYR A 787 PHE 0.011 0.001 PHE C 255 TRP 0.010 0.001 TRP C 79 HIS 0.009 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10300) covalent geometry : angle 0.59256 / 0.29 (13914) hydrogen bonds : bond 0.03340 / 2.21 ( 512) hydrogen bonds : angle 4.60476 / 3.16 ( 1443) link_TRANS : bond 0.00165 / 0.09 ( 2) link_TRANS : angle 0.11379 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7635 (tpt) cc_final: 0.6975 (tpt) REVERT: A 305 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8679 (tmm) REVERT: A 478 MET cc_start: 0.8852 (mmm) cc_final: 0.8601 (tpt) REVERT: A 671 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7476 (t80) REVERT: A 744 PHE cc_start: 0.8425 (m-80) cc_final: 0.8033 (m-80) REVERT: A 759 LEU cc_start: 0.9184 (mt) cc_final: 0.8907 (pp) REVERT: A 783 MET cc_start: 0.5062 (mpp) cc_final: 0.4815 (mpp) REVERT: C 47 MET cc_start: 0.8090 (ppp) cc_final: 0.7858 (ppp) REVERT: C 117 GLU cc_start: 0.8386 (mp0) cc_final: 0.8129 (mm-30) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.0729 time to fit residues: 10.7602 Evaluate side-chains 99 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 300 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 68 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.065083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.047438 restraints weight = 49106.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049075 restraints weight = 25170.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.050132 restraints weight = 15954.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.050871 restraints weight = 11574.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.051298 restraints weight = 9148.292| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10302 Z= 0.111 Angle : 0.583 9.956 13920 Z= 0.288 Chirality : 0.041 0.192 1520 Planarity : 0.004 0.042 1774 Dihedral : 6.225 79.414 1384 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.68 % Allowed : 12.29 % Favored : 86.03 % 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: 1.14 (0.24), residues: 1221 helix: 1.47 (0.22), residues: 618 sheet: 0.40 (0.40), residues: 159 loop : 0.01 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 64 TYR 0.019 0.001 TYR A 787 PHE 0.012 0.001 PHE A 470 TRP 0.012 0.001 TRP A 374 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (10300) covalent geometry : angle 0.58354 / 0.29 (13914) hydrogen bonds : bond 0.03182 / 2.09 ( 512) hydrogen bonds : angle 4.52904 / 3.11 ( 1443) link_TRANS : bond 0.00107 / 0.05 ( 2) link_TRANS : angle 0.11792 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 LYS cc_start: 0.9517 (mmtt) cc_final: 0.9284 (mmtm) REVERT: B 120 MET cc_start: 0.7554 (tpt) cc_final: 0.7128 (tpt) REVERT: A 305 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8660 (tmm) REVERT: A 478 MET cc_start: 0.8803 (mmm) cc_final: 0.8594 (tpt) REVERT: A 671 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7225 (t80) REVERT: A 744 PHE cc_start: 0.8394 (m-80) cc_final: 0.8006 (m-80) REVERT: A 759 LEU cc_start: 0.9190 (mt) cc_final: 0.8917 (pp) REVERT: A 783 MET cc_start: 0.5145 (OUTLIER) cc_final: 0.4909 (mpp) REVERT: C 47 MET cc_start: 0.8087 (ppp) cc_final: 0.7843 (ppp) REVERT: C 117 GLU cc_start: 0.8358 (mp0) cc_final: 0.7944 (mm-30) REVERT: C 305 MET cc_start: 0.9271 (mmm) cc_final: 0.8975 (tpp) outliers start: 18 outliers final: 13 residues processed: 96 average time/residue: 0.0716 time to fit residues: 10.5643 Evaluate side-chains 97 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 300 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 123 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.064816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047174 restraints weight = 48731.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048786 restraints weight = 24983.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049872 restraints weight = 15896.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.050536 restraints weight = 11498.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.051018 restraints weight = 9196.677| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10302 Z= 0.123 Angle : 0.584 11.450 13920 Z= 0.287 Chirality : 0.041 0.183 1520 Planarity : 0.004 0.043 1774 Dihedral : 6.154 78.971 1384 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.05 % Allowed : 12.10 % Favored : 85.85 % 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: 1.16 (0.24), residues: 1221 helix: 1.50 (0.22), residues: 619 sheet: 0.38 (0.40), residues: 159 loop : 0.01 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.019 0.001 TYR A 787 PHE 0.013 0.001 PHE A 470 TRP 0.008 0.001 TRP C 79 HIS 0.009 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10300) covalent geometry : angle 0.58369 / 0.29 (13914) hydrogen bonds : bond 0.03176 / 2.11 ( 512) hydrogen bonds : angle 4.50563 / 3.09 ( 1443) link_TRANS : bond 0.00137 / 0.07 ( 2) link_TRANS : angle 0.11153 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7147 (p0) cc_final: 0.6455 (t0) REVERT: B 120 MET cc_start: 0.7544 (tpt) cc_final: 0.7074 (tpt) REVERT: A 305 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8672 (tmm) REVERT: A 478 MET cc_start: 0.8852 (mmm) cc_final: 0.8609 (tpt) REVERT: A 671 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.7234 (t80) REVERT: A 744 PHE cc_start: 0.8414 (m-80) cc_final: 0.8021 (m-80) REVERT: A 759 LEU cc_start: 0.9184 (mt) cc_final: 0.8912 (pp) REVERT: A 783 MET cc_start: 0.5293 (OUTLIER) cc_final: 0.5069 (mpp) REVERT: C 117 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8111 (mm-30) outliers start: 22 outliers final: 14 residues processed: 98 average time/residue: 0.0605 time to fit residues: 9.2525 Evaluate side-chains 98 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 300 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.064621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046982 restraints weight = 49193.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048594 restraints weight = 25349.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049666 restraints weight = 16115.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050408 restraints weight = 11662.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.050871 restraints weight = 9222.238| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10302 Z= 0.136 Angle : 0.628 11.514 13920 Z= 0.308 Chirality : 0.042 0.192 1520 Planarity : 0.004 0.041 1774 Dihedral : 6.159 78.877 1384 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.96 % Allowed : 12.85 % Favored : 85.20 % 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: 1.11 (0.24), residues: 1221 helix: 1.43 (0.22), residues: 620 sheet: 0.40 (0.40), residues: 159 loop : 0.00 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.019 0.001 TYR A 787 PHE 0.027 0.001 PHE B 12 TRP 0.008 0.001 TRP C 79 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10300) covalent geometry : angle 0.62843 / 0.31 (13914) hydrogen bonds : bond 0.03276 / 2.17 ( 512) hydrogen bonds : angle 4.55740 / 3.13 ( 1443) link_TRANS : bond 0.00152 / 0.08 ( 2) link_TRANS : angle 0.11295 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7455 (tpt) cc_final: 0.6640 (tpt) REVERT: A 305 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8675 (tmm) REVERT: A 478 MET cc_start: 0.8845 (mmm) cc_final: 0.8604 (tpt) REVERT: A 671 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7316 (t80) REVERT: A 689 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8513 (tm-30) REVERT: A 744 PHE cc_start: 0.8417 (m-80) cc_final: 0.8027 (m-80) REVERT: A 759 LEU cc_start: 0.9179 (mt) cc_final: 0.8907 (pp) REVERT: A 783 MET cc_start: 0.5209 (OUTLIER) cc_final: 0.4967 (mpp) REVERT: C 117 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7938 (mm-30) outliers start: 21 outliers final: 16 residues processed: 95 average time/residue: 0.0686 time to fit residues: 10.1738 Evaluate side-chains 101 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 88 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.064429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.046654 restraints weight = 48684.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048252 restraints weight = 25174.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049330 restraints weight = 16081.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050051 restraints weight = 11673.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050418 restraints weight = 9305.446| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10302 Z= 0.148 Angle : 0.624 11.831 13920 Z= 0.307 Chirality : 0.042 0.191 1520 Planarity : 0.004 0.042 1774 Dihedral : 6.192 78.803 1384 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.86 % Allowed : 12.94 % Favored : 85.20 % 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: 1.10 (0.24), residues: 1221 helix: 1.42 (0.22), residues: 626 sheet: 0.28 (0.41), residues: 161 loop : 0.03 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.018 0.001 TYR A 787 PHE 0.024 0.001 PHE B 12 TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (10300) covalent geometry : angle 0.62453 / 0.31 (13914) hydrogen bonds : bond 0.03329 / 2.20 ( 512) hydrogen bonds : angle 4.56828 / 3.14 ( 1443) link_TRANS : bond 0.00180 / 0.09 ( 2) link_TRANS : angle 0.12068 / 0.07 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7271 (tpt) cc_final: 0.6548 (tpt) REVERT: A 305 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8682 (tmm) REVERT: A 478 MET cc_start: 0.8863 (mmm) cc_final: 0.8616 (tpt) REVERT: A 671 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7472 (t80) REVERT: A 689 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: A 744 PHE cc_start: 0.8430 (m-80) cc_final: 0.8030 (m-80) REVERT: A 759 LEU cc_start: 0.9165 (mt) cc_final: 0.8891 (pp) REVERT: A 783 MET cc_start: 0.5177 (OUTLIER) cc_final: 0.4937 (mpp) REVERT: C 117 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7953 (mm-30) outliers start: 20 outliers final: 15 residues processed: 92 average time/residue: 0.0667 time to fit residues: 9.5534 Evaluate side-chains 100 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 chunk 43 optimal weight: 0.0070 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.065595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048049 restraints weight = 48254.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049694 restraints weight = 24841.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.050796 restraints weight = 15727.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051481 restraints weight = 11374.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.051988 restraints weight = 9053.255| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10302 Z= 0.106 Angle : 0.609 11.733 13920 Z= 0.297 Chirality : 0.041 0.223 1520 Planarity : 0.004 0.040 1774 Dihedral : 6.021 78.718 1384 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.86 % Allowed : 12.85 % Favored : 85.29 % 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: 1.21 (0.24), residues: 1221 helix: 1.50 (0.22), residues: 625 sheet: 0.43 (0.42), residues: 156 loop : 0.06 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 177 TYR 0.013 0.001 TYR A 787 PHE 0.022 0.001 PHE B 12 TRP 0.011 0.001 TRP C 86 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10300) covalent geometry : angle 0.60940 / 0.30 (13914) hydrogen bonds : bond 0.03130 / 2.08 ( 512) hydrogen bonds : angle 4.50293 / 3.10 ( 1443) link_TRANS : bond 0.00080 / 0.04 ( 2) link_TRANS : angle 0.13419 / 0.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1526.88 seconds wall clock time: 27 minutes 2.87 seconds (1622.87 seconds total)