Starting phenix.real_space_refine on Wed Feb 14 10:11:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwa_14995/02_2024/7zwa_14995.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwa_14995/02_2024/7zwa_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwa_14995/02_2024/7zwa_14995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwa_14995/02_2024/7zwa_14995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwa_14995/02_2024/7zwa_14995.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwa_14995/02_2024/7zwa_14995.pdb" } 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 Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "C ASP 200": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.55, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 2.87 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: 2.68 Time building geometry restraints manager: 4.12 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: 99.12 - 106.10: 409 106.10 - 113.07: 5034 113.07 - 120.05: 3165 120.05 - 127.02: 3896 127.02 - 134.00: 156 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 2.440 nonbonded pdb=" ND2 ASN A 171 " pdb=" O LYS A 206 " model vdw 2.237 2.520 nonbonded pdb=" OG SER A 78 " pdb=" OD2 ASP A 81 " model vdw 2.245 2.440 nonbonded pdb=" OE1 GLU B 223 " pdb=" OH TYR B 225 " model vdw 2.247 2.440 nonbonded pdb=" O ILE B 118 " pdb=" OG1 THR B 122 " model vdw 2.254 2.440 ... (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 ========== 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: 2.290 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: 11.860 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.130 Find NCS groups from input model: 0.280 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:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.320 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.071 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: 1.4080 time to fit residues: 205.9730 Evaluate side-chains 91 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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: 0.5980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 312 GLN B 440 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9283 Z= 0.259 Angle : 0.547 6.698 12660 Z= 0.284 Chirality : 0.041 0.136 1419 Planarity : 0.003 0.032 1523 Dihedral : 17.675 176.535 1467 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.39 % Allowed : 10.49 % Favored : 88.12 % 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: 2.06 (0.29), residues: 336 sheet: 0.32 (0.39), residues: 159 loop : -0.16 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 0.000 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 117 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.028 Fit side-chains REVERT: A 48 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8530 (mtp) REVERT: A 99 PHE cc_start: 0.7639 (m-10) cc_final: 0.7403 (m-80) REVERT: A 128 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8346 (pm20) REVERT: A 129 LYS cc_start: 0.9148 (mppt) cc_final: 0.8796 (mptt) REVERT: B 270 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: C 184 SER cc_start: 0.8988 (t) cc_final: 0.8774 (t) outliers start: 13 outliers final: 6 residues processed: 109 average time/residue: 1.2198 time to fit residues: 142.4729 Evaluate side-chains 104 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 A residue 507 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 369 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9283 Z= 0.245 Angle : 0.516 6.096 12660 Z= 0.270 Chirality : 0.041 0.137 1419 Planarity : 0.003 0.031 1523 Dihedral : 17.641 176.388 1467 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.61 % Allowed : 12.96 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.26), residues: 1047 helix: 1.81 (0.29), residues: 348 sheet: 0.26 (0.39), residues: 159 loop : -0.11 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 276 HIS 0.003 0.001 HIS B 382 PHE 0.012 0.001 PHE B 18 TYR 0.013 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 117 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.040 Fit side-chains REVERT: A 48 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8485 (mtp) REVERT: A 128 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8184 (pm20) REVERT: A 129 LYS cc_start: 0.9164 (mppt) cc_final: 0.8798 (mptt) REVERT: B 270 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: B 282 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8964 (mmmm) REVERT: C 184 SER cc_start: 0.8979 (t) cc_final: 0.8773 (t) outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 1.1613 time to fit residues: 136.0852 Evaluate side-chains 104 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET 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 A residue 507 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 369 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 104 GLN B 312 GLN B 432 GLN B 440 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1355 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= 0.167 Angle : 0.503 6.799 12660 Z= 0.263 Chirality : 0.040 0.138 1419 Planarity : 0.003 0.030 1523 Dihedral : 17.558 177.259 1467 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.93 % Allowed : 14.03 % Favored : 84.05 % 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: 0.94 (0.26), residues: 1047 helix: 2.02 (0.29), residues: 342 sheet: 0.23 (0.41), residues: 155 loop : -0.10 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 247 HIS 0.002 0.000 HIS B 511 PHE 0.011 0.001 PHE B 59 TYR 0.010 0.001 TYR A 88 ARG 0.006 0.000 ARG B 242 *********************** 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 123 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8419 (mtp) REVERT: A 99 PHE cc_start: 0.7816 (m-80) cc_final: 0.7238 (m-80) REVERT: A 121 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8244 (tp40) REVERT: A 128 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8282 (pm20) REVERT: C 184 SER cc_start: 0.8977 (t) cc_final: 0.8776 (t) outliers start: 18 outliers final: 7 residues processed: 113 average time/residue: 1.2147 time to fit residues: 147.2258 Evaluate side-chains 97 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 369 ASP 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 58 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 432 GLN B 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9283 Z= 0.234 Angle : 0.523 6.300 12660 Z= 0.272 Chirality : 0.040 0.153 1419 Planarity : 0.003 0.030 1523 Dihedral : 17.594 176.774 1467 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.46 % Allowed : 15.42 % Favored : 82.12 % 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: 0.96 (0.26), residues: 1047 helix: 2.00 (0.29), residues: 342 sheet: 0.31 (0.40), residues: 159 loop : -0.09 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 247 HIS 0.003 0.001 HIS A 176 PHE 0.026 0.001 PHE A 216 TYR 0.008 0.001 TYR A 88 ARG 0.007 0.000 ARG B 242 *********************** 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 123 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8465 (mtp) REVERT: A 99 PHE cc_start: 0.7830 (m-80) cc_final: 0.7278 (m-10) REVERT: A 128 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8247 (pm20) REVERT: B 328 GLU cc_start: 0.9456 (OUTLIER) cc_final: 0.9252 (tt0) outliers start: 23 outliers final: 11 residues processed: 111 average time/residue: 1.0455 time to fit residues: 125.3658 Evaluate side-chains 112 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 A residue 507 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 Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 369 ASP 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 92 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.0470 chunk 102 optimal weight: 0.1980 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9283 Z= 0.153 Angle : 0.514 9.304 12660 Z= 0.266 Chirality : 0.039 0.140 1419 Planarity : 0.003 0.035 1523 Dihedral : 17.505 177.736 1467 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.25 % Allowed : 15.74 % 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: 0.96 (0.26), residues: 1047 helix: 2.05 (0.29), residues: 342 sheet: 0.29 (0.41), residues: 155 loop : -0.12 (0.26), residues: 550 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 0.020 0.001 PHE A 211 TYR 0.009 0.001 TYR A 88 ARG 0.008 0.000 ARG B 242 *********************** 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 fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.096 Fit side-chains REVERT: A 48 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8426 (mtp) REVERT: A 99 PHE cc_start: 0.7704 (m-80) cc_final: 0.7132 (m-10) REVERT: A 128 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8141 (pm20) REVERT: A 129 LYS cc_start: 0.9182 (mppt) cc_final: 0.8774 (mptt) REVERT: A 265 LYS cc_start: 0.9096 (ptmm) cc_final: 0.8606 (pptt) REVERT: B 141 ARG cc_start: 0.7907 (tpm170) cc_final: 0.7635 (tpm170) REVERT: B 328 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9220 (tt0) outliers start: 21 outliers final: 9 residues processed: 115 average time/residue: 1.1372 time to fit residues: 140.9446 Evaluate side-chains 108 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 507 THR 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 Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 369 ASP 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 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9283 Z= 0.282 Angle : 0.541 8.959 12660 Z= 0.280 Chirality : 0.041 0.139 1419 Planarity : 0.003 0.031 1523 Dihedral : 17.629 176.334 1467 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.36 % Allowed : 16.27 % Favored : 81.37 % 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: 1.01 (0.26), residues: 1047 helix: 2.14 (0.29), residues: 335 sheet: 0.43 (0.40), residues: 153 loop : -0.13 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 148 HIS 0.005 0.001 HIS A 176 PHE 0.027 0.001 PHE A 216 TYR 0.008 0.001 TYR A 409 ARG 0.007 0.000 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 123 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 1.132 Fit side-chains REVERT: A 48 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8496 (mtp) REVERT: A 99 PHE cc_start: 0.7774 (m-80) cc_final: 0.7256 (m-10) REVERT: A 128 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8308 (pm20) REVERT: A 129 LYS cc_start: 0.9184 (mppt) cc_final: 0.8906 (mptt) REVERT: A 156 ASP cc_start: 0.8845 (m-30) cc_final: 0.8645 (m-30) REVERT: A 265 LYS cc_start: 0.9097 (ptmm) cc_final: 0.8595 (pptt) REVERT: B 141 ARG cc_start: 0.7907 (tpm170) cc_final: 0.7676 (tpm170) REVERT: B 242 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7454 (ttm-80) outliers start: 22 outliers final: 11 residues processed: 112 average time/residue: 1.1205 time to fit residues: 135.4804 Evaluate side-chains 110 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET 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 A residue 507 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 310 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 432 GLN B 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9283 Z= 0.309 Angle : 0.584 11.218 12660 Z= 0.297 Chirality : 0.042 0.150 1419 Planarity : 0.003 0.031 1523 Dihedral : 17.626 175.427 1467 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.14 % Allowed : 17.02 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.26), residues: 1047 helix: 2.07 (0.29), residues: 335 sheet: 0.32 (0.40), residues: 153 loop : -0.14 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 247 HIS 0.004 0.001 HIS B 511 PHE 0.016 0.001 PHE B 59 TYR 0.008 0.001 TYR A 409 ARG 0.007 0.000 ARG B 502 *********************** 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 124 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.112 Fit side-chains REVERT: A 48 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8529 (mtp) REVERT: A 99 PHE cc_start: 0.7733 (m-80) cc_final: 0.7211 (m-10) REVERT: A 128 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8147 (pm20) REVERT: A 129 LYS cc_start: 0.9181 (mppt) cc_final: 0.8794 (mppt) REVERT: A 250 GLU cc_start: 0.8586 (tp30) cc_final: 0.7805 (tp30) REVERT: B 242 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7511 (ttm-80) outliers start: 20 outliers final: 12 residues processed: 111 average time/residue: 1.1791 time to fit residues: 140.8530 Evaluate side-chains 108 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 161 MET 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 507 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 310 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 97 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9283 Z= 0.178 Angle : 0.553 11.110 12660 Z= 0.282 Chirality : 0.040 0.139 1419 Planarity : 0.003 0.030 1523 Dihedral : 17.523 176.779 1467 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.25 % Allowed : 17.45 % Favored : 80.30 % 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: 1.03 (0.26), residues: 1047 helix: 2.15 (0.29), residues: 335 sheet: 0.55 (0.42), residues: 144 loop : -0.14 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.002 0.000 HIS B 511 PHE 0.032 0.001 PHE A 216 TYR 0.009 0.001 TYR A 103 ARG 0.008 0.000 ARG B 502 *********************** 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 126 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8519 (mtp) REVERT: A 99 PHE cc_start: 0.7647 (m-80) cc_final: 0.7131 (m-10) REVERT: A 128 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8121 (pm20) REVERT: A 243 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8705 (mm) REVERT: A 250 GLU cc_start: 0.8588 (tp30) cc_final: 0.7917 (tp30) REVERT: A 265 LYS cc_start: 0.9082 (ptmm) cc_final: 0.8588 (pptt) REVERT: B 238 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8622 (ttmt) REVERT: B 242 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7505 (ttm-80) outliers start: 21 outliers final: 12 residues processed: 113 average time/residue: 1.2474 time to fit residues: 151.9520 Evaluate side-chains 113 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain B residue 18 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 369 ASP Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9283 Z= 0.307 Angle : 0.599 11.499 12660 Z= 0.304 Chirality : 0.042 0.149 1419 Planarity : 0.003 0.033 1523 Dihedral : 17.635 175.805 1467 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.82 % Allowed : 18.20 % Favored : 79.98 % 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: 1.93 (0.29), residues: 342 sheet: 0.37 (0.40), residues: 153 loop : -0.14 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.004 0.001 HIS B 511 PHE 0.018 0.001 PHE B 59 TYR 0.020 0.001 TYR A 103 ARG 0.008 0.000 ARG B 502 ********************** 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 116 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.071 Fit side-chains REVERT: A 48 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8539 (mtp) REVERT: A 99 PHE cc_start: 0.7750 (m-80) cc_final: 0.7219 (m-10) REVERT: A 128 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8082 (pm20) REVERT: A 129 LYS cc_start: 0.9159 (mppt) cc_final: 0.8745 (mptt) REVERT: A 250 GLU cc_start: 0.8650 (tp30) cc_final: 0.7979 (tp30) REVERT: A 265 LYS cc_start: 0.9087 (ptmm) cc_final: 0.8593 (pptt) REVERT: B 242 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7537 (ttm-80) outliers start: 17 outliers final: 11 residues processed: 106 average time/residue: 1.1397 time to fit residues: 130.2193 Evaluate side-chains 109 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET 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 A residue 507 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 310 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** A 293 ASN ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3490 r_free = 0.3490 target = 0.108913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.070015 restraints weight = 15303.988| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.13 r_work: 0.2606 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9283 Z= 0.255 Angle : 0.586 11.541 12660 Z= 0.298 Chirality : 0.041 0.155 1419 Planarity : 0.003 0.034 1523 Dihedral : 17.602 175.779 1467 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.61 % Allowed : 18.74 % Favored : 79.66 % 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: 0.92 (0.26), residues: 1047 helix: 1.97 (0.28), residues: 341 sheet: 0.42 (0.40), residues: 153 loop : -0.15 (0.26), residues: 553 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 0.030 0.001 PHE A 216 TYR 0.014 0.001 TYR A 103 ARG 0.008 0.000 ARG B 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3343.85 seconds wall clock time: 60 minutes 44.48 seconds (3644.48 seconds total)