Starting phenix.real_space_refine on Thu Mar 13 18:30:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zwa_14995/03_2025/7zwa_14995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zwa_14995/03_2025/7zwa_14995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zwa_14995/03_2025/7zwa_14995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zwa_14995/03_2025/7zwa_14995.map" model { file = "/net/cci-nas-00/data/ceres_data/7zwa_14995/03_2025/7zwa_14995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zwa_14995/03_2025/7zwa_14995.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.012 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 42 5.16 5 C 5678 2.51 5 N 1532 2.21 5 O 1754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9038 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4009 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 27, 'TRANS': 475} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4222 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 165 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 304 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.07, per 1000 atoms: 0.78 Number of scatterers: 9038 At special positions: 0 Unit cell: (92.95, 87.75, 141.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 32 15.00 O 1754 8.00 N 1532 7.00 C 5678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 983.1 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 37.5% alpha, 20.9% beta 6 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.801A pdb=" N GLU A 50 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 78 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.974A pdb=" N GLY A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 removed outlier: 4.074A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.613A pdb=" N GLY A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.586A pdb=" N LYS A 443 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 106 through 123 removed outlier: 4.041A pdb=" N ILE B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.755A pdb=" N LEU B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 233 No H-bonds generated for 'chain 'B' and resid 232 through 233' Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.013A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.555A pdb=" N LEU B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.902A pdb=" N ARG A 35 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS A 164 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N SER A 37 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 166 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 39 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU A 168 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 41 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR A 170 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASP A 43 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 168 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.689A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR A 401 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU A 345 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 304 removed outlier: 3.797A pdb=" N PHE A 303 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 290 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA7, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.652A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.339A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 247 through 253 removed outlier: 3.554A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU B 268 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N ASN B 359 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 466 367 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2463 1.33 - 1.45: 1551 1.45 - 1.57: 5139 1.57 - 1.69: 60 1.69 - 1.81: 70 Bond restraints: 9283 Sorted by residual: bond pdb=" O3 PO4 A 701 " pdb=" P PO4 A 701 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" O4 PO4 A 701 " pdb=" P PO4 A 701 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" O2 PO4 A 701 " pdb=" P PO4 A 701 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" O1 PO4 A 701 " pdb=" P PO4 A 701 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" C3' DT E 4 " pdb=" O3' DT E 4 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.27e+00 ... (remaining 9278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 12338 1.37 - 2.73: 262 2.73 - 4.10: 47 4.10 - 5.47: 12 5.47 - 6.84: 1 Bond angle restraints: 12660 Sorted by residual: angle pdb=" N GLY A 127 " pdb=" CA GLY A 127 " pdb=" C GLY A 127 " ideal model delta sigma weight residual 112.77 108.96 3.81 1.28e+00 6.10e-01 8.85e+00 angle pdb=" C LEU B 215 " pdb=" N GLU B 216 " pdb=" CA GLU B 216 " ideal model delta sigma weight residual 122.79 117.67 5.12 1.78e+00 3.16e-01 8.27e+00 angle pdb=" C GLN A 125 " pdb=" N GLN A 126 " pdb=" CA GLN A 126 " ideal model delta sigma weight residual 121.54 126.57 -5.03 1.91e+00 2.74e-01 6.95e+00 angle pdb=" C ASN B 514 " pdb=" N MET B 515 " pdb=" CA MET B 515 " ideal model delta sigma weight residual 120.31 117.13 3.18 1.52e+00 4.33e-01 4.37e+00 angle pdb=" N PHE B 107 " pdb=" CA PHE B 107 " pdb=" C PHE B 107 " ideal model delta sigma weight residual 113.01 110.50 2.51 1.20e+00 6.94e-01 4.36e+00 ... (remaining 12655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 5407 35.58 - 71.16: 204 71.16 - 106.74: 9 106.74 - 142.32: 0 142.32 - 177.90: 1 Dihedral angle restraints: 5621 sinusoidal: 2533 harmonic: 3088 Sorted by residual: dihedral pdb=" C4' DT E 4 " pdb=" C3' DT E 4 " pdb=" O3' DT E 4 " pdb=" P DC E 5 " ideal model delta sinusoidal sigma weight residual 220.00 42.10 177.90 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ASP B 398 " pdb=" CB ASP B 398 " pdb=" CG ASP B 398 " pdb=" OD1 ASP B 398 " ideal model delta sinusoidal sigma weight residual -30.00 -88.85 58.85 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP B 72 " pdb=" C ASP B 72 " pdb=" N GLN B 73 " pdb=" CA GLN B 73 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 853 0.028 - 0.057: 358 0.057 - 0.085: 117 0.085 - 0.113: 77 0.113 - 0.141: 14 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CA GLU B 216 " pdb=" N GLU B 216 " pdb=" C GLU B 216 " pdb=" CB GLU B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE B 24 " pdb=" N ILE B 24 " pdb=" C ILE B 24 " pdb=" CB ILE B 24 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1416 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 126 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C GLN A 126 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 126 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 127 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 211 " 0.013 2.00e-02 2.50e+03 1.39e-02 3.37e+00 pdb=" CG PHE A 211 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 211 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 211 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 211 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 211 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 211 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 518 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO B 519 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 519 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 519 " 0.018 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1188 2.76 - 3.29: 8601 3.29 - 3.83: 15153 3.83 - 4.36: 17888 4.36 - 4.90: 30091 Nonbonded interactions: 72921 Sorted by model distance: nonbonded pdb=" OH TYR A 409 " pdb=" OE1 GLN B 269 " model vdw 2.220 3.040 nonbonded pdb=" ND2 ASN A 171 " pdb=" O LYS A 206 " model vdw 2.237 3.120 nonbonded pdb=" OG SER A 78 " pdb=" OD2 ASP A 81 " model vdw 2.245 3.040 nonbonded pdb=" OE1 GLU B 223 " pdb=" OH TYR B 225 " model vdw 2.247 3.040 nonbonded pdb=" O ILE B 118 " pdb=" OG1 THR B 122 " model vdw 2.254 3.040 ... (remaining 72916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.040 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.003 0.059 9283 Z= 0.166 Angle : 0.512 6.835 12660 Z= 0.280 Chirality : 0.040 0.141 1419 Planarity : 0.003 0.032 1523 Dihedral : 16.751 177.899 3611 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1047 helix: 1.93 (0.29), residues: 336 sheet: 0.39 (0.41), residues: 164 loop : -0.21 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.002 0.000 HIS A 176 PHE 0.032 0.001 PHE A 211 TYR 0.010 0.001 TYR A 103 ARG 0.002 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.110 Fit side-chains REVERT: A 128 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8299 (pm20) REVERT: A 129 LYS cc_start: 0.9077 (mppt) cc_final: 0.8755 (mptt) REVERT: A 216 PHE cc_start: 0.8415 (t80) cc_final: 0.8174 (t80) REVERT: A 265 LYS cc_start: 0.8929 (pttp) cc_final: 0.8656 (pptt) REVERT: C 184 SER cc_start: 0.9008 (t) cc_final: 0.8794 (t) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 1.4672 time to fit residues: 214.5164 Evaluate side-chains 91 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 304 ASN B 269 GLN B 312 GLN B 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.069742 restraints weight = 15264.476| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.07 r_work: 0.2628 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9283 Z= 0.288 Angle : 0.570 6.814 12660 Z= 0.297 Chirality : 0.042 0.142 1419 Planarity : 0.004 0.033 1523 Dihedral : 17.691 177.221 1467 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.39 % Allowed : 10.60 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1047 helix: 2.00 (0.29), residues: 336 sheet: 0.28 (0.40), residues: 159 loop : -0.13 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 148 HIS 0.003 0.001 HIS B 511 PHE 0.014 0.001 PHE B 18 TYR 0.013 0.001 TYR A 409 ARG 0.005 0.001 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.105 Fit side-chains REVERT: A 48 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: A 99 PHE cc_start: 0.7755 (m-10) cc_final: 0.7539 (m-10) REVERT: A 128 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8349 (pm20) REVERT: A 129 LYS cc_start: 0.9148 (mppt) cc_final: 0.8847 (mptt) REVERT: A 299 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8611 (mtmm) REVERT: B 270 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8643 (tt0) REVERT: B 310 ILE cc_start: 0.8955 (mt) cc_final: 0.8666 (mp) REVERT: C 184 SER cc_start: 0.8986 (t) cc_final: 0.8776 (t) outliers start: 13 outliers final: 5 residues processed: 114 average time/residue: 1.3965 time to fit residues: 169.9592 Evaluate side-chains 104 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 270 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.108935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.070315 restraints weight = 15458.396| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.09 r_work: 0.2646 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9283 Z= 0.198 Angle : 0.520 5.683 12660 Z= 0.274 Chirality : 0.041 0.138 1419 Planarity : 0.003 0.031 1523 Dihedral : 17.601 177.544 1467 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.39 % Allowed : 13.28 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1047 helix: 2.07 (0.29), residues: 336 sheet: 0.19 (0.41), residues: 155 loop : -0.13 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 247 HIS 0.003 0.000 HIS B 511 PHE 0.012 0.001 PHE B 18 TYR 0.014 0.001 TYR A 289 ARG 0.005 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8351 (mtp) REVERT: A 99 PHE cc_start: 0.7880 (m-10) cc_final: 0.7669 (m-80) REVERT: A 128 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8183 (pm20) REVERT: B 282 LYS cc_start: 0.9239 (mmmm) cc_final: 0.8976 (mmmm) REVERT: B 328 GLU cc_start: 0.9431 (OUTLIER) cc_final: 0.9230 (tt0) outliers start: 13 outliers final: 5 residues processed: 113 average time/residue: 1.2994 time to fit residues: 158.1888 Evaluate side-chains 103 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 0.0570 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.108808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.070109 restraints weight = 15216.440| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.09 r_work: 0.2604 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9283 Z= 0.256 Angle : 0.543 6.606 12660 Z= 0.282 Chirality : 0.041 0.137 1419 Planarity : 0.003 0.032 1523 Dihedral : 17.623 176.835 1467 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.71 % Allowed : 14.35 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1047 helix: 2.07 (0.29), residues: 335 sheet: 0.18 (0.39), residues: 159 loop : -0.13 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 276 HIS 0.003 0.001 HIS B 511 PHE 0.012 0.001 PHE B 18 TYR 0.008 0.001 TYR A 289 ARG 0.006 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8330 (mtp) REVERT: A 128 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8287 (pm20) REVERT: A 199 PHE cc_start: 0.8561 (t80) cc_final: 0.8336 (t80) REVERT: A 201 ASP cc_start: 0.8400 (m-30) cc_final: 0.8055 (m-30) REVERT: B 242 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7604 (ttm-80) REVERT: B 282 LYS cc_start: 0.9254 (mmmm) cc_final: 0.8937 (mmmm) outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 1.1441 time to fit residues: 138.2812 Evaluate side-chains 108 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.069668 restraints weight = 15359.066| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.10 r_work: 0.2623 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9283 Z= 0.267 Angle : 0.543 6.915 12660 Z= 0.283 Chirality : 0.041 0.149 1419 Planarity : 0.003 0.033 1523 Dihedral : 17.614 176.470 1467 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.36 % Allowed : 14.99 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1047 helix: 2.06 (0.29), residues: 335 sheet: 0.14 (0.39), residues: 159 loop : -0.12 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 247 HIS 0.003 0.001 HIS B 511 PHE 0.025 0.001 PHE A 216 TYR 0.008 0.001 TYR A 88 ARG 0.006 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8362 (mtp) REVERT: A 99 PHE cc_start: 0.8155 (m-80) cc_final: 0.7590 (m-10) REVERT: A 128 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8288 (pm20) REVERT: A 199 PHE cc_start: 0.8540 (t80) cc_final: 0.8302 (t80) REVERT: A 201 ASP cc_start: 0.8406 (m-30) cc_final: 0.8076 (m-30) REVERT: B 141 ARG cc_start: 0.7840 (tpm170) cc_final: 0.7639 (tpm170) REVERT: B 242 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7657 (ttm-80) REVERT: B 282 LYS cc_start: 0.9266 (mmmm) cc_final: 0.8954 (mmmm) REVERT: B 328 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9238 (tt0) REVERT: B 368 ARG cc_start: 0.8682 (mtm110) cc_final: 0.8437 (mtp85) outliers start: 22 outliers final: 9 residues processed: 116 average time/residue: 1.0860 time to fit residues: 136.0766 Evaluate side-chains 106 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.070302 restraints weight = 15170.525| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.13 r_work: 0.2641 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9283 Z= 0.206 Angle : 0.546 9.114 12660 Z= 0.284 Chirality : 0.040 0.142 1419 Planarity : 0.003 0.031 1523 Dihedral : 17.565 177.090 1467 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.14 % Allowed : 15.85 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1047 helix: 2.05 (0.29), residues: 335 sheet: 0.28 (0.41), residues: 150 loop : -0.16 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 247 HIS 0.003 0.000 HIS B 382 PHE 0.011 0.001 PHE B 59 TYR 0.008 0.001 TYR A 88 ARG 0.007 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8393 (mtp) REVERT: A 99 PHE cc_start: 0.8132 (m-80) cc_final: 0.7566 (m-10) REVERT: A 128 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8183 (pm20) REVERT: A 137 HIS cc_start: 0.8454 (p90) cc_final: 0.8229 (p-80) REVERT: A 199 PHE cc_start: 0.8533 (t80) cc_final: 0.8309 (t80) REVERT: A 201 ASP cc_start: 0.8407 (m-30) cc_final: 0.8097 (m-30) REVERT: B 148 ASP cc_start: 0.9267 (m-30) cc_final: 0.8936 (p0) REVERT: B 242 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7671 (ttm-80) REVERT: B 282 LYS cc_start: 0.9269 (mmmm) cc_final: 0.8962 (mmmm) REVERT: B 328 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9240 (tt0) REVERT: B 368 ARG cc_start: 0.8694 (mtm110) cc_final: 0.8434 (mtp85) outliers start: 20 outliers final: 9 residues processed: 116 average time/residue: 1.6663 time to fit residues: 208.3053 Evaluate side-chains 111 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.065960 restraints weight = 15508.272| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.11 r_work: 0.2562 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 9283 Z= 0.559 Angle : 0.679 11.898 12660 Z= 0.348 Chirality : 0.046 0.178 1419 Planarity : 0.004 0.037 1523 Dihedral : 17.807 173.456 1467 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.46 % Allowed : 16.81 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1047 helix: 1.70 (0.29), residues: 335 sheet: 0.09 (0.39), residues: 152 loop : -0.27 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 513 HIS 0.005 0.001 HIS B 511 PHE 0.028 0.002 PHE A 216 TYR 0.012 0.002 TYR A 409 ARG 0.007 0.001 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.099 Fit side-chains REVERT: A 48 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8511 (mtp) REVERT: A 99 PHE cc_start: 0.8266 (m-80) cc_final: 0.7741 (m-10) REVERT: A 128 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8266 (pm20) REVERT: A 129 LYS cc_start: 0.9185 (mppt) cc_final: 0.8636 (mptt) REVERT: A 199 PHE cc_start: 0.8466 (t80) cc_final: 0.8235 (t80) REVERT: A 201 ASP cc_start: 0.8478 (m-30) cc_final: 0.8141 (m-30) REVERT: A 250 GLU cc_start: 0.8687 (tp30) cc_final: 0.8182 (mm-30) REVERT: A 299 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8508 (mtmm) REVERT: B 242 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7666 (ttm-80) REVERT: B 270 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8673 (tt0) REVERT: B 282 LYS cc_start: 0.9274 (mmmm) cc_final: 0.9003 (mmmm) outliers start: 23 outliers final: 8 residues processed: 114 average time/residue: 1.3855 time to fit residues: 169.3194 Evaluate side-chains 106 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 310 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 46 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS B 43 GLN B 382 HIS B 432 GLN B 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.069975 restraints weight = 15522.508| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.15 r_work: 0.2632 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9283 Z= 0.201 Angle : 0.583 9.478 12660 Z= 0.302 Chirality : 0.041 0.151 1419 Planarity : 0.003 0.032 1523 Dihedral : 17.569 175.454 1467 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.28 % Allowed : 18.84 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1047 helix: 1.74 (0.29), residues: 342 sheet: 0.12 (0.40), residues: 150 loop : -0.21 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 247 HIS 0.003 0.000 HIS B 511 PHE 0.013 0.001 PHE B 59 TYR 0.010 0.001 TYR A 88 ARG 0.013 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.053 Fit side-chains REVERT: A 48 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8477 (mtp) REVERT: A 99 PHE cc_start: 0.8147 (m-80) cc_final: 0.7611 (m-10) REVERT: A 128 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8276 (pm20) REVERT: A 129 LYS cc_start: 0.9197 (mppt) cc_final: 0.8925 (mptt) REVERT: A 134 MET cc_start: 0.9265 (ttp) cc_final: 0.8887 (ttp) REVERT: A 135 MET cc_start: 0.8855 (mpp) cc_final: 0.8338 (mpt) REVERT: A 199 PHE cc_start: 0.8492 (t80) cc_final: 0.8249 (t80) REVERT: A 201 ASP cc_start: 0.8446 (m-30) cc_final: 0.8102 (m-30) REVERT: A 212 ASP cc_start: 0.8411 (t0) cc_final: 0.8196 (t0) REVERT: A 250 GLU cc_start: 0.8680 (tp30) cc_final: 0.7914 (tp30) REVERT: B 141 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7721 (tpm-80) REVERT: B 242 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7666 (ttm-80) REVERT: B 282 LYS cc_start: 0.9269 (mmmm) cc_final: 0.8983 (mmmm) REVERT: B 368 ARG cc_start: 0.8700 (mtm110) cc_final: 0.8464 (mtp85) outliers start: 12 outliers final: 7 residues processed: 109 average time/residue: 1.2779 time to fit residues: 149.6218 Evaluate side-chains 112 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 310 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 432 GLN B 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.067300 restraints weight = 15356.697| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.12 r_work: 0.2585 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9283 Z= 0.399 Angle : 0.623 8.891 12660 Z= 0.320 Chirality : 0.043 0.151 1419 Planarity : 0.004 0.048 1523 Dihedral : 17.723 174.327 1467 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.71 % Allowed : 18.95 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1047 helix: 1.69 (0.28), residues: 342 sheet: 0.09 (0.39), residues: 152 loop : -0.25 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.005 0.001 HIS A 176 PHE 0.029 0.002 PHE A 216 TYR 0.010 0.001 TYR A 289 ARG 0.013 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.098 Fit side-chains REVERT: A 48 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8557 (mtp) REVERT: A 99 PHE cc_start: 0.8189 (m-80) cc_final: 0.7706 (m-10) REVERT: A 128 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8271 (pm20) REVERT: A 129 LYS cc_start: 0.9200 (mppt) cc_final: 0.8926 (mptt) REVERT: A 134 MET cc_start: 0.9292 (ttp) cc_final: 0.8895 (ttp) REVERT: A 135 MET cc_start: 0.8855 (mpp) cc_final: 0.8268 (mpt) REVERT: A 199 PHE cc_start: 0.8489 (t80) cc_final: 0.8255 (t80) REVERT: A 201 ASP cc_start: 0.8500 (m-30) cc_final: 0.8164 (m-30) REVERT: A 212 ASP cc_start: 0.8448 (t0) cc_final: 0.8196 (t0) REVERT: A 250 GLU cc_start: 0.8717 (tp30) cc_final: 0.8161 (mm-30) REVERT: A 299 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8472 (mtmm) REVERT: B 242 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7654 (ttm-80) REVERT: B 282 LYS cc_start: 0.9270 (mmmm) cc_final: 0.9062 (mmmm) REVERT: B 368 ARG cc_start: 0.8750 (mtm110) cc_final: 0.8496 (mtp85) outliers start: 16 outliers final: 10 residues processed: 108 average time/residue: 1.1965 time to fit residues: 138.7316 Evaluate side-chains 111 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.0050 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.068223 restraints weight = 15385.338| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.13 r_work: 0.2604 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9283 Z= 0.295 Angle : 0.627 11.503 12660 Z= 0.320 Chirality : 0.042 0.162 1419 Planarity : 0.004 0.047 1523 Dihedral : 17.686 174.628 1467 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.61 % Allowed : 19.06 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1047 helix: 1.84 (0.28), residues: 335 sheet: 0.02 (0.39), residues: 152 loop : -0.24 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.003 0.001 HIS B 382 PHE 0.014 0.001 PHE B 59 TYR 0.010 0.001 TYR A 88 ARG 0.013 0.001 ARG A 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.998 Fit side-chains REVERT: A 48 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8474 (mtp) REVERT: A 99 PHE cc_start: 0.8190 (m-80) cc_final: 0.7693 (m-10) REVERT: A 128 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8262 (pm20) REVERT: A 129 LYS cc_start: 0.9188 (mppt) cc_final: 0.8976 (mptt) REVERT: A 134 MET cc_start: 0.9286 (ttp) cc_final: 0.9038 (ttp) REVERT: A 135 MET cc_start: 0.8809 (mpp) cc_final: 0.8400 (mpt) REVERT: A 199 PHE cc_start: 0.8486 (t80) cc_final: 0.8249 (t80) REVERT: A 201 ASP cc_start: 0.8492 (m-30) cc_final: 0.8145 (m-30) REVERT: A 212 ASP cc_start: 0.8437 (t0) cc_final: 0.8196 (t0) REVERT: A 250 GLU cc_start: 0.8755 (tp30) cc_final: 0.8075 (tm-30) REVERT: A 299 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8463 (mtmm) REVERT: B 368 ARG cc_start: 0.8753 (mtm110) cc_final: 0.8499 (mtp85) outliers start: 15 outliers final: 11 residues processed: 113 average time/residue: 1.0691 time to fit residues: 130.3915 Evaluate side-chains 114 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.068608 restraints weight = 15384.145| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.13 r_work: 0.2607 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9283 Z= 0.287 Angle : 0.618 10.813 12660 Z= 0.315 Chirality : 0.042 0.154 1419 Planarity : 0.004 0.048 1523 Dihedral : 17.699 174.861 1467 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.39 % Allowed : 19.38 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1047 helix: 1.73 (0.28), residues: 342 sheet: 0.14 (0.39), residues: 153 loop : -0.24 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.003 0.001 HIS B 511 PHE 0.029 0.001 PHE A 216 TYR 0.015 0.001 TYR A 103 ARG 0.013 0.001 ARG A 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6197.55 seconds wall clock time: 109 minutes 58.93 seconds (6598.93 seconds total)