Starting phenix.real_space_refine on Mon Mar 11 06:54:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/03_2024/8ozc_17304.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/03_2024/8ozc_17304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/03_2024/8ozc_17304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/03_2024/8ozc_17304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/03_2024/8ozc_17304.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozc_17304/03_2024/8ozc_17304.pdb" } resolution = 4.0 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= 0.011 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4840 2.51 5 N 1233 2.21 5 O 1382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7478 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3758 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 12, 'TRANS': 439} Chain: "B" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3720 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 24, 'TRANS': 436} Chain breaks: 1 Time building chain proxies: 4.35, per 1000 atoms: 0.58 Number of scatterers: 7478 At special positions: 0 Unit cell: (76.23, 85.3776, 126.034, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1382 8.00 N 1233 7.00 C 4840 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: 2.92 Conformation dependent library (CDL) restraints added in 1.4 seconds 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 36.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 17 through 28 Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.054A pdb=" N ASN A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 removed outlier: 4.237A pdb=" N LEU A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 124 through 138 removed outlier: 4.184A pdb=" N GLN A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 227 through 232 removed outlier: 4.086A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 281 removed outlier: 3.651A pdb=" N LYS A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 354 through 366 Processing helix chain 'A' and resid 370 through 385 removed outlier: 4.693A pdb=" N LYS A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 429 removed outlier: 3.743A pdb=" N GLU A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 429 " --> pdb=" O GLU A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 429' Processing helix chain 'A' and resid 442 through 448 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 62 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 109 through 124 removed outlier: 3.585A pdb=" N ASP B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 119 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 208 through 213 removed outlier: 4.244A pdb=" N ARG B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 217 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 249 through 263 removed outlier: 3.883A pdb=" N ILE B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 258 " --> pdb=" O TRP B 254 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 350 removed outlier: 4.762A pdb=" N ALA B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 4.603A pdb=" N ALA B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 464 removed outlier: 3.617A pdb=" N LYS B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 482 through 493 removed outlier: 3.844A pdb=" N SER B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 6.745A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 178 removed outlier: 5.608A pdb=" N LYS A 167 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 414 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 408 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TRP A 175 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU A 406 " --> pdb=" O TRP A 175 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 177 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 401 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.562A pdb=" N VAL A 208 " --> pdb=" O CYS A 215 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 214 " --> pdb=" O HIS A 188 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS A 188 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 216 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 186 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA5, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 314 removed outlier: 3.584A pdb=" N ASN A 318 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.671A pdb=" N ILE B 443 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 420 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 143 Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 305 removed outlier: 3.903A pdb=" N LYS B 314 " --> pdb=" O GLN B 302 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 425 through 426 removed outlier: 3.894A pdb=" N VAL B 426 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR B 431 " --> pdb=" O VAL B 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 227 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2353 1.34 - 1.46: 1494 1.46 - 1.58: 3780 1.58 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 7662 Sorted by residual: bond pdb=" C LEU A 227 " pdb=" O LEU A 227 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.72e+00 bond pdb=" C ASN B 322 " pdb=" N PRO B 323 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.25e-02 6.40e+03 1.63e+00 bond pdb=" CA ILE B 248 " pdb=" CB ILE B 248 " ideal model delta sigma weight residual 1.535 1.550 -0.015 1.29e-02 6.01e+03 1.35e+00 bond pdb=" CD GLU A 133 " pdb=" OE1 GLU A 133 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.35e+00 bond pdb=" CA GLU B 348 " pdb=" C GLU B 348 " ideal model delta sigma weight residual 1.522 1.539 -0.016 1.40e-02 5.10e+03 1.35e+00 ... (remaining 7657 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.54: 186 106.54 - 113.41: 4096 113.41 - 120.27: 2777 120.27 - 127.14: 3199 127.14 - 134.00: 93 Bond angle restraints: 10351 Sorted by residual: angle pdb=" CA GLU B 348 " pdb=" C GLU B 348 " pdb=" N GLN B 349 " ideal model delta sigma weight residual 118.14 129.21 -11.07 1.31e+00 5.83e-01 7.14e+01 angle pdb=" CA GLU B 348 " pdb=" C GLU B 348 " pdb=" O GLU B 348 " ideal model delta sigma weight residual 119.38 113.21 6.17 1.23e+00 6.61e-01 2.52e+01 angle pdb=" C LEU A 132 " pdb=" N GLU A 133 " pdb=" CA GLU A 133 " ideal model delta sigma weight residual 120.72 113.42 7.30 1.67e+00 3.59e-01 1.91e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.42 108.67 4.75 1.17e+00 7.31e-01 1.65e+01 angle pdb=" N GLU A 133 " pdb=" CA GLU A 133 " pdb=" CB GLU A 133 " ideal model delta sigma weight residual 110.39 117.12 -6.73 1.66e+00 3.63e-01 1.64e+01 ... (remaining 10346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4135 17.43 - 34.85: 394 34.85 - 52.28: 54 52.28 - 69.70: 8 69.70 - 87.13: 4 Dihedral angle restraints: 4595 sinusoidal: 1907 harmonic: 2688 Sorted by residual: dihedral pdb=" CA LYS B 85 " pdb=" C LYS B 85 " pdb=" N TRP B 86 " pdb=" CA TRP B 86 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA LYS B 324 " pdb=" C LYS B 324 " pdb=" N ASN B 325 " pdb=" CA ASN B 325 " ideal model delta harmonic sigma weight residual -180.00 -159.34 -20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE B 313 " pdb=" C PHE B 313 " pdb=" N LYS B 314 " pdb=" CA LYS B 314 " ideal model delta harmonic sigma weight residual -180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 876 0.048 - 0.095: 181 0.095 - 0.143: 54 0.143 - 0.190: 2 0.190 - 0.238: 1 Chirality restraints: 1114 Sorted by residual: chirality pdb=" CB ILE B 248 " pdb=" CA ILE B 248 " pdb=" CG1 ILE B 248 " pdb=" CG2 ILE B 248 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA GLN B 349 " pdb=" N GLN B 349 " pdb=" C GLN B 349 " pdb=" CB GLN B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA GLU A 133 " pdb=" N GLU A 133 " pdb=" C GLU A 133 " pdb=" CB GLU A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1111 not shown) Planarity restraints: 1311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 86 " -0.019 2.00e-02 2.50e+03 1.63e-02 6.62e+00 pdb=" CG TRP B 86 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 86 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 86 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 86 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 86 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 86 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 86 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 499 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 500 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 500 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 500 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 175 " 0.014 2.00e-02 2.50e+03 1.25e-02 3.90e+00 pdb=" CG TRP A 175 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 175 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 175 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 175 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 175 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 175 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 175 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 175 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 175 " 0.002 2.00e-02 2.50e+03 ... (remaining 1308 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 168 2.68 - 3.23: 7300 3.23 - 3.79: 11796 3.79 - 4.34: 15451 4.34 - 4.90: 24496 Nonbonded interactions: 59211 Sorted by model distance: nonbonded pdb=" O TRP B 269 " pdb=" OH TYR B 467 " model vdw 2.124 2.440 nonbonded pdb=" OH TYR A 416 " pdb=" O THR B 404 " model vdw 2.131 2.440 nonbonded pdb=" OG1 THR B 377 " pdb=" OG1 THR B 381 " model vdw 2.173 2.440 nonbonded pdb=" OE1 GLU A 429 " pdb=" OG1 THR B 431 " model vdw 2.244 2.440 nonbonded pdb=" ND2 ASN B 322 " pdb=" O HIS B 329 " model vdw 2.264 2.520 ... (remaining 59206 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 2.140 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.490 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 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 : 0.002 0.030 7662 Z= 0.154 Angle : 0.618 11.066 10351 Z= 0.342 Chirality : 0.042 0.238 1114 Planarity : 0.004 0.055 1311 Dihedral : 13.399 87.128 2857 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.73 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.97 (0.28), residues: 907 helix: -0.00 (0.34), residues: 262 sheet: -1.09 (0.51), residues: 120 loop : -2.14 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 86 HIS 0.011 0.001 HIS A 358 PHE 0.025 0.001 PHE A 135 TYR 0.025 0.001 TYR A 190 ARG 0.005 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.3722 (tmtt) cc_final: 0.3486 (tptp) REVERT: A 94 ILE cc_start: 0.7719 (pt) cc_final: 0.7335 (pt) REVERT: A 122 MET cc_start: 0.5792 (tpt) cc_final: 0.5465 (tpt) REVERT: A 198 PHE cc_start: 0.7769 (m-80) cc_final: 0.7434 (m-80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2082 time to fit residues: 36.9399 Evaluate side-chains 96 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 82 optimal weight: 0.0060 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7662 Z= 0.168 Angle : 0.592 8.927 10351 Z= 0.307 Chirality : 0.043 0.236 1114 Planarity : 0.004 0.052 1311 Dihedral : 4.117 20.601 983 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.28 % Favored : 92.50 % Rotamer: Outliers : 2.08 % Allowed : 9.05 % Favored : 88.88 % 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: -2.03 (0.27), residues: 907 helix: -0.10 (0.32), residues: 288 sheet: -1.07 (0.51), residues: 114 loop : -2.26 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 86 HIS 0.009 0.001 HIS A 358 PHE 0.029 0.002 PHE A 305 TYR 0.019 0.002 TYR B 65 ARG 0.003 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.3757 (tmtt) cc_final: 0.3551 (tptp) REVERT: A 122 MET cc_start: 0.5779 (tpt) cc_final: 0.5467 (tpt) REVERT: A 198 PHE cc_start: 0.7763 (m-80) cc_final: 0.7362 (m-80) REVERT: B 74 MET cc_start: 0.6163 (ppp) cc_final: 0.5636 (ppp) REVERT: B 344 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7279 (pp30) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 0.2158 time to fit residues: 35.9768 Evaluate side-chains 111 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 234 HIS A 314 GLN A 364 GLN B 341 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 7662 Z= 0.405 Angle : 0.810 13.193 10351 Z= 0.425 Chirality : 0.050 0.376 1114 Planarity : 0.006 0.052 1311 Dihedral : 5.450 20.689 983 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 33.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.14 % Favored : 89.53 % Rotamer: Outliers : 4.89 % Allowed : 13.57 % Favored : 81.54 % 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: -2.73 (0.26), residues: 907 helix: -0.96 (0.29), residues: 282 sheet: -1.20 (0.50), residues: 123 loop : -2.57 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 86 HIS 0.015 0.002 HIS A 358 PHE 0.023 0.003 PHE B 140 TYR 0.024 0.003 TYR B 328 ARG 0.008 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.3723 (tmtt) cc_final: 0.3502 (tptp) REVERT: A 94 ILE cc_start: 0.8632 (pt) cc_final: 0.8289 (pt) REVERT: A 122 MET cc_start: 0.6485 (tpt) cc_final: 0.6041 (tpt) REVERT: A 198 PHE cc_start: 0.7938 (m-80) cc_final: 0.7438 (m-80) REVERT: A 235 LYS cc_start: 0.8348 (tmtt) cc_final: 0.7525 (tppt) REVERT: A 274 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: B 283 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8532 (pp) outliers start: 40 outliers final: 25 residues processed: 149 average time/residue: 0.2323 time to fit residues: 44.7925 Evaluate side-chains 140 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7662 Z= 0.190 Angle : 0.646 11.950 10351 Z= 0.330 Chirality : 0.044 0.172 1114 Planarity : 0.004 0.060 1311 Dihedral : 4.842 18.963 983 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.50 % Favored : 92.17 % Rotamer: Outliers : 3.67 % Allowed : 17.24 % Favored : 79.10 % 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: -2.37 (0.26), residues: 907 helix: -0.45 (0.30), residues: 282 sheet: -1.13 (0.51), residues: 118 loop : -2.44 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 86 HIS 0.007 0.001 HIS A 358 PHE 0.018 0.002 PHE A 305 TYR 0.015 0.001 TYR A 190 ARG 0.006 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8323 (pt) cc_final: 0.7951 (pt) REVERT: A 121 LYS cc_start: 0.7218 (mtpt) cc_final: 0.6760 (mtpt) REVERT: A 122 MET cc_start: 0.6134 (tpt) cc_final: 0.5674 (tpt) REVERT: A 198 PHE cc_start: 0.7835 (m-80) cc_final: 0.7367 (m-80) REVERT: A 235 LYS cc_start: 0.8208 (tmtt) cc_final: 0.7398 (tppt) REVERT: A 430 LEU cc_start: 0.9045 (mt) cc_final: 0.8771 (pp) REVERT: B 74 MET cc_start: 0.6200 (ppp) cc_final: 0.5641 (ppp) REVERT: B 344 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7186 (pp30) outliers start: 30 outliers final: 21 residues processed: 138 average time/residue: 0.2562 time to fit residues: 45.0198 Evaluate side-chains 134 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 75 optimal weight: 0.0070 chunk 60 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7662 Z= 0.217 Angle : 0.657 11.592 10351 Z= 0.336 Chirality : 0.044 0.163 1114 Planarity : 0.005 0.054 1311 Dihedral : 4.763 21.451 983 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.04 % Favored : 90.63 % Rotamer: Outliers : 4.16 % Allowed : 18.83 % Favored : 77.02 % 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: -2.34 (0.26), residues: 907 helix: -0.42 (0.30), residues: 281 sheet: -1.07 (0.51), residues: 119 loop : -2.44 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 86 HIS 0.007 0.001 HIS A 358 PHE 0.014 0.002 PHE B 14 TYR 0.014 0.002 TYR A 190 ARG 0.004 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8476 (pt) cc_final: 0.8045 (pt) REVERT: A 122 MET cc_start: 0.6209 (tpt) cc_final: 0.5735 (tpt) REVERT: A 198 PHE cc_start: 0.7881 (m-80) cc_final: 0.7403 (m-80) REVERT: A 230 THR cc_start: 0.3437 (OUTLIER) cc_final: 0.3217 (p) REVERT: A 235 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7312 (tppt) REVERT: B 74 MET cc_start: 0.6434 (ppp) cc_final: 0.5713 (ppp) REVERT: B 215 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6764 (mt) outliers start: 34 outliers final: 26 residues processed: 142 average time/residue: 0.2410 time to fit residues: 44.3798 Evaluate side-chains 142 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7662 Z= 0.183 Angle : 0.638 11.115 10351 Z= 0.327 Chirality : 0.043 0.167 1114 Planarity : 0.004 0.047 1311 Dihedral : 4.681 24.129 983 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.60 % Favored : 91.18 % Rotamer: Outliers : 4.03 % Allowed : 20.90 % Favored : 75.06 % 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: -2.22 (0.27), residues: 907 helix: -0.29 (0.31), residues: 281 sheet: -1.01 (0.51), residues: 119 loop : -2.38 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 86 HIS 0.007 0.001 HIS A 358 PHE 0.015 0.001 PHE B 14 TYR 0.015 0.001 TYR A 190 ARG 0.006 0.001 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8438 (pt) cc_final: 0.7989 (pt) REVERT: A 122 MET cc_start: 0.6209 (tpt) cc_final: 0.5764 (tpt) REVERT: A 198 PHE cc_start: 0.7936 (m-80) cc_final: 0.7442 (m-80) REVERT: A 230 THR cc_start: 0.3391 (OUTLIER) cc_final: 0.3166 (p) REVERT: A 235 LYS cc_start: 0.8158 (tmtt) cc_final: 0.7293 (tppt) REVERT: A 256 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6800 (tp) REVERT: B 74 MET cc_start: 0.6406 (ppp) cc_final: 0.5725 (ppp) REVERT: B 86 TRP cc_start: 0.6933 (m-10) cc_final: 0.6691 (m-90) outliers start: 33 outliers final: 22 residues processed: 136 average time/residue: 0.2185 time to fit residues: 39.1316 Evaluate side-chains 136 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 64 optimal weight: 0.0010 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7662 Z= 0.209 Angle : 0.662 11.162 10351 Z= 0.335 Chirality : 0.044 0.168 1114 Planarity : 0.004 0.043 1311 Dihedral : 4.717 22.525 983 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.82 % Favored : 90.96 % Rotamer: Outliers : 3.91 % Allowed : 21.88 % Favored : 74.21 % 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: -2.19 (0.27), residues: 907 helix: -0.23 (0.31), residues: 282 sheet: -0.94 (0.52), residues: 119 loop : -2.40 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 86 HIS 0.007 0.001 HIS A 358 PHE 0.037 0.002 PHE B 313 TYR 0.017 0.002 TYR B 506 ARG 0.004 0.001 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.6200 (tpt) cc_final: 0.5717 (tpt) REVERT: A 198 PHE cc_start: 0.7993 (m-80) cc_final: 0.7500 (m-80) REVERT: A 230 THR cc_start: 0.3439 (OUTLIER) cc_final: 0.3233 (p) REVERT: A 235 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7310 (tppt) REVERT: B 74 MET cc_start: 0.6269 (ppp) cc_final: 0.5586 (ppp) outliers start: 32 outliers final: 24 residues processed: 143 average time/residue: 0.2454 time to fit residues: 45.6831 Evaluate side-chains 140 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 7662 Z= 0.262 Angle : 0.710 11.012 10351 Z= 0.368 Chirality : 0.046 0.186 1114 Planarity : 0.004 0.040 1311 Dihedral : 5.014 20.864 983 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 28.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.14 % Favored : 89.64 % Rotamer: Outliers : 4.40 % Allowed : 23.23 % Favored : 72.37 % 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: -2.44 (0.26), residues: 907 helix: -0.49 (0.30), residues: 279 sheet: -1.15 (0.50), residues: 122 loop : -2.49 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 86 HIS 0.008 0.001 HIS A 358 PHE 0.018 0.002 PHE B 419 TYR 0.018 0.002 TYR B 506 ARG 0.004 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8587 (mp) cc_final: 0.7958 (tp) REVERT: A 122 MET cc_start: 0.6179 (tpt) cc_final: 0.5707 (tpt) REVERT: A 198 PHE cc_start: 0.8063 (m-80) cc_final: 0.7569 (m-80) REVERT: A 230 THR cc_start: 0.3632 (OUTLIER) cc_final: 0.3366 (p) REVERT: A 235 LYS cc_start: 0.8200 (tmtt) cc_final: 0.7273 (tppt) REVERT: A 256 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.7050 (tp) REVERT: A 287 MET cc_start: 0.7213 (ppp) cc_final: 0.6019 (ppp) REVERT: A 336 MET cc_start: 0.7295 (mmm) cc_final: 0.6706 (mmm) REVERT: B 74 MET cc_start: 0.6340 (ppp) cc_final: 0.5762 (ppp) REVERT: B 86 TRP cc_start: 0.7194 (m-10) cc_final: 0.6830 (m-90) outliers start: 36 outliers final: 27 residues processed: 139 average time/residue: 0.2329 time to fit residues: 41.9851 Evaluate side-chains 139 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 328 TYR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 495 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 0.0470 chunk 53 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7662 Z= 0.218 Angle : 0.698 11.208 10351 Z= 0.355 Chirality : 0.046 0.222 1114 Planarity : 0.004 0.039 1311 Dihedral : 5.020 26.476 983 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.48 % Favored : 90.30 % Rotamer: Outliers : 3.67 % Allowed : 24.82 % Favored : 71.52 % 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: -2.35 (0.27), residues: 907 helix: -0.50 (0.30), residues: 282 sheet: -1.08 (0.50), residues: 119 loop : -2.40 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 20 HIS 0.007 0.001 HIS A 358 PHE 0.022 0.002 PHE B 245 TYR 0.016 0.002 TYR A 190 ARG 0.003 0.001 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.5805 (mtm110) cc_final: 0.5540 (ptt-90) REVERT: A 87 GLN cc_start: 0.8993 (tp40) cc_final: 0.8741 (pt0) REVERT: A 122 MET cc_start: 0.6036 (tpt) cc_final: 0.5575 (tpt) REVERT: A 198 PHE cc_start: 0.8019 (m-80) cc_final: 0.7529 (m-80) REVERT: A 230 THR cc_start: 0.3496 (OUTLIER) cc_final: 0.3279 (p) REVERT: A 235 LYS cc_start: 0.8221 (tmtt) cc_final: 0.7281 (tppt) REVERT: A 274 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: A 287 MET cc_start: 0.7267 (ppp) cc_final: 0.6151 (ppp) REVERT: A 293 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: A 336 MET cc_start: 0.7213 (mmm) cc_final: 0.6765 (mmm) REVERT: B 74 MET cc_start: 0.6350 (ppp) cc_final: 0.5740 (ppp) REVERT: B 86 TRP cc_start: 0.7234 (m-10) cc_final: 0.6896 (m-90) REVERT: B 344 GLN cc_start: 0.8116 (mm110) cc_final: 0.7848 (mm-40) outliers start: 30 outliers final: 22 residues processed: 130 average time/residue: 0.2397 time to fit residues: 40.8648 Evaluate side-chains 132 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7662 Z= 0.191 Angle : 0.703 10.818 10351 Z= 0.352 Chirality : 0.046 0.230 1114 Planarity : 0.004 0.039 1311 Dihedral : 4.965 31.780 983 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.82 % Favored : 90.96 % Rotamer: Outliers : 2.81 % Allowed : 25.67 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.34 (0.27), residues: 907 helix: -0.54 (0.30), residues: 282 sheet: -1.08 (0.50), residues: 120 loop : -2.36 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 20 HIS 0.007 0.001 HIS A 358 PHE 0.033 0.002 PHE B 313 TYR 0.016 0.002 TYR A 190 ARG 0.003 0.000 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLN cc_start: 0.8992 (tp40) cc_final: 0.8750 (pt0) REVERT: A 122 MET cc_start: 0.6020 (tpt) cc_final: 0.5589 (tpt) REVERT: A 198 PHE cc_start: 0.8001 (m-80) cc_final: 0.7521 (m-80) REVERT: A 235 LYS cc_start: 0.8256 (tmtt) cc_final: 0.7323 (tppt) REVERT: A 287 MET cc_start: 0.7258 (ppp) cc_final: 0.6148 (ppp) REVERT: B 74 MET cc_start: 0.6284 (ppp) cc_final: 0.5725 (ppp) REVERT: B 86 TRP cc_start: 0.7241 (m-10) cc_final: 0.6945 (m-90) outliers start: 23 outliers final: 22 residues processed: 127 average time/residue: 0.2346 time to fit residues: 38.9382 Evaluate side-chains 132 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 0.0040 chunk 74 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.158642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.134337 restraints weight = 26587.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.136559 restraints weight = 20882.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.137901 restraints weight = 17435.744| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7662 Z= 0.177 Angle : 0.702 10.536 10351 Z= 0.348 Chirality : 0.046 0.332 1114 Planarity : 0.004 0.037 1311 Dihedral : 4.785 29.636 983 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.16 % Favored : 91.62 % Rotamer: Outliers : 2.69 % Allowed : 25.79 % Favored : 71.52 % 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: -2.28 (0.27), residues: 907 helix: -0.50 (0.30), residues: 283 sheet: -1.02 (0.49), residues: 121 loop : -2.32 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 20 HIS 0.007 0.001 HIS A 358 PHE 0.027 0.002 PHE B 245 TYR 0.014 0.001 TYR B 403 ARG 0.003 0.000 ARG A 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1780.40 seconds wall clock time: 33 minutes 31.44 seconds (2011.44 seconds total)