Starting phenix.real_space_refine on Sat Jul 20 17:28:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/07_2024/8t25_40980.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/07_2024/8t25_40980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/07_2024/8t25_40980.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/07_2024/8t25_40980.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/07_2024/8t25_40980.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/07_2024/8t25_40980.cif" } resolution = 3.62 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= -0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6352 atoms to isotropic. 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 37 5.16 5 C 4096 2.51 5 N 1076 2.21 5 O 1199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6408 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4895 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 30, 'TRANS': 564} Chain breaks: 2 Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1513 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 11, 'TRANS': 180} Chain breaks: 1 Time building chain proxies: 6.59, per 1000 atoms: 1.03 Number of scatterers: 6408 At special positions: 0 Unit cell: (101.01, 101.01, 108.78, 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 37 16.00 O 1199 8.00 N 1076 7.00 C 4096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 543 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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: 2.49 Conformation dependent library (CDL) restraints added in 1.0 seconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 55.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.051A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 109 through 130 removed outlier: 4.277A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.966A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 219 through 252 removed outlier: 4.358A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.964A pdb=" N LEU A 267 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.532A pdb=" N LEU A 278 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Proline residue: A 280 - end of helix No H-bonds generated for 'chain 'A' and resid 275 through 282' Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.555A pdb=" N SER A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.696A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.988A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.789A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.727A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 519 through 534 removed outlier: 3.882A pdb=" N ILE A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.893A pdb=" N GLY A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.598A pdb=" N GLU A 572 " --> pdb=" O THR A 568 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 573 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 596 removed outlier: 3.527A pdb=" N LEU A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.097A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.558A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.337A pdb=" N ALA A 348 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS A 359 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASP A 350 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ARG A 357 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 352 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.786A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 286 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2073 1.35 - 1.47: 1720 1.47 - 1.59: 2738 1.59 - 1.71: 1 1.71 - 1.84: 58 Bond restraints: 6590 Sorted by residual: bond pdb=" CB PRO A 346 " pdb=" CG PRO A 346 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.20e+00 bond pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.57e+00 bond pdb=" CA LYS A 234 " pdb=" C LYS A 234 " ideal model delta sigma weight residual 1.522 1.540 -0.019 1.29e-02 6.01e+03 2.06e+00 bond pdb=" CB LYS A 565 " pdb=" CG LYS A 565 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" C LYS A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.28e+00 ... (remaining 6585 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.02: 134 105.02 - 112.29: 3085 112.29 - 119.56: 2274 119.56 - 126.83: 3324 126.83 - 134.10: 132 Bond angle restraints: 8949 Sorted by residual: angle pdb=" CA PRO A 346 " pdb=" N PRO A 346 " pdb=" CD PRO A 346 " ideal model delta sigma weight residual 112.00 104.58 7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" CB LYS A 565 " pdb=" CG LYS A 565 " pdb=" CD LYS A 565 " ideal model delta sigma weight residual 111.30 119.89 -8.59 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CA PRO A 321 " pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 112.00 107.10 4.90 1.40e+00 5.10e-01 1.22e+01 angle pdb=" CA LYS A 470 " pdb=" CB LYS A 470 " pdb=" CG LYS A 470 " ideal model delta sigma weight residual 114.10 120.28 -6.18 2.00e+00 2.50e-01 9.54e+00 angle pdb=" N LEU A 450 " pdb=" CA LEU A 450 " pdb=" C LEU A 450 " ideal model delta sigma weight residual 109.81 116.62 -6.81 2.21e+00 2.05e-01 9.50e+00 ... (remaining 8944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 3268 17.54 - 35.08: 455 35.08 - 52.62: 146 52.62 - 70.16: 17 70.16 - 87.70: 13 Dihedral angle restraints: 3899 sinusoidal: 1590 harmonic: 2309 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 46.44 46.56 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA CYS B 379 " pdb=" C CYS B 379 " pdb=" N TYR B 380 " pdb=" CA TYR B 380 " ideal model delta harmonic sigma weight residual -180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 127.67 -34.67 1 1.00e+01 1.00e-02 1.70e+01 ... (remaining 3896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 784 0.054 - 0.109: 119 0.109 - 0.163: 20 0.163 - 0.217: 0 0.217 - 0.272: 1 Chirality restraints: 924 Sorted by residual: chirality pdb=" CB VAL A 582 " pdb=" CA VAL A 582 " pdb=" CG1 VAL A 582 " pdb=" CG2 VAL A 582 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR A 371 " pdb=" CA THR A 371 " pdb=" OG1 THR A 371 " pdb=" CG2 THR A 371 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA LYS A 234 " pdb=" N LYS A 234 " pdb=" C LYS A 234 " pdb=" CB LYS A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 921 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 345 " 0.079 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 346 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 90 " -0.065 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO A 91 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " -0.035 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 321 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.029 5.00e-02 4.00e+02 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 527 2.74 - 3.28: 6393 3.28 - 3.82: 10584 3.82 - 4.36: 11280 4.36 - 4.90: 19478 Nonbonded interactions: 48262 Sorted by model distance: nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR A 365 " pdb=" OD1 ASP A 368 " model vdw 2.274 2.440 nonbonded pdb=" OD2 ASP A 435 " pdb=" OH TYR A 541 " model vdw 2.306 2.440 nonbonded pdb=" O SER A 155 " pdb=" NH1 ARG A 161 " model vdw 2.310 2.520 ... (remaining 48257 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: 8.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.450 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 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 0.114 6590 Z= 0.206 Angle : 0.627 8.588 8949 Z= 0.329 Chirality : 0.041 0.272 924 Planarity : 0.006 0.115 1164 Dihedral : 18.086 87.703 2397 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.44 % Allowed : 29.51 % Favored : 70.06 % 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: -0.27 (0.29), residues: 777 helix: 1.20 (0.27), residues: 365 sheet: 0.41 (1.17), residues: 24 loop : -1.64 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 69 HIS 0.006 0.001 HIS A 417 PHE 0.010 0.001 PHE B 338 TYR 0.015 0.001 TYR B 508 ARG 0.002 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.662 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 77 average time/residue: 0.1874 time to fit residues: 19.4891 Evaluate side-chains 74 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.0040 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 0.0980 overall best weight: 0.2550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.0548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6590 Z= 0.159 Angle : 0.541 10.666 8949 Z= 0.270 Chirality : 0.040 0.168 924 Planarity : 0.005 0.067 1164 Dihedral : 3.988 20.206 861 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.63 % Allowed : 26.16 % Favored : 70.20 % 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: -0.09 (0.29), residues: 777 helix: 1.39 (0.27), residues: 364 sheet: -0.68 (1.01), residues: 27 loop : -1.50 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 69 HIS 0.007 0.001 HIS A 417 PHE 0.017 0.001 PHE B 338 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.745 Fit side-chains REVERT: A 512 PHE cc_start: 0.5175 (OUTLIER) cc_final: 0.4852 (t80) outliers start: 25 outliers final: 13 residues processed: 94 average time/residue: 0.1612 time to fit residues: 20.9460 Evaluate side-chains 87 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 490 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.0570 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 56 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6590 Z= 0.167 Angle : 0.547 9.547 8949 Z= 0.273 Chirality : 0.041 0.207 924 Planarity : 0.004 0.059 1164 Dihedral : 3.983 20.708 861 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.94 % Allowed : 25.29 % Favored : 69.77 % 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: 0.03 (0.29), residues: 777 helix: 1.55 (0.28), residues: 359 sheet: -0.54 (1.01), residues: 27 loop : -1.48 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 69 HIS 0.007 0.001 HIS A 417 PHE 0.008 0.001 PHE A 438 TYR 0.015 0.001 TYR A 385 ARG 0.002 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 75 time to evaluate : 0.769 Fit side-chains REVERT: A 169 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6077 (ttm170) REVERT: A 401 HIS cc_start: 0.4962 (OUTLIER) cc_final: 0.4681 (m-70) REVERT: A 438 PHE cc_start: 0.5241 (OUTLIER) cc_final: 0.4785 (t80) REVERT: A 512 PHE cc_start: 0.4865 (OUTLIER) cc_final: 0.4489 (t80) outliers start: 34 outliers final: 16 residues processed: 101 average time/residue: 0.1633 time to fit residues: 22.9192 Evaluate side-chains 93 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6590 Z= 0.200 Angle : 0.584 9.242 8949 Z= 0.294 Chirality : 0.042 0.225 924 Planarity : 0.004 0.053 1164 Dihedral : 4.210 22.055 861 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 6.40 % Allowed : 24.85 % Favored : 68.75 % 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: -0.06 (0.30), residues: 777 helix: 1.53 (0.28), residues: 359 sheet: -1.03 (0.95), residues: 27 loop : -1.55 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.006 0.001 HIS A 417 PHE 0.010 0.001 PHE B 400 TYR 0.020 0.001 TYR A 202 ARG 0.004 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 77 time to evaluate : 0.852 Fit side-chains REVERT: A 169 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.6124 (ttm170) REVERT: A 183 TYR cc_start: 0.5804 (OUTLIER) cc_final: 0.5274 (t80) REVERT: A 203 TRP cc_start: 0.5810 (OUTLIER) cc_final: 0.5106 (m-10) REVERT: A 401 HIS cc_start: 0.5337 (OUTLIER) cc_final: 0.5051 (m-70) REVERT: A 438 PHE cc_start: 0.5390 (OUTLIER) cc_final: 0.4750 (t80) REVERT: A 512 PHE cc_start: 0.5103 (OUTLIER) cc_final: 0.4557 (t80) outliers start: 44 outliers final: 27 residues processed: 111 average time/residue: 0.1743 time to fit residues: 26.6600 Evaluate side-chains 105 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 72 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 0.0670 chunk 19 optimal weight: 0.0020 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6590 Z= 0.163 Angle : 0.553 10.165 8949 Z= 0.277 Chirality : 0.041 0.235 924 Planarity : 0.004 0.049 1164 Dihedral : 4.045 21.136 861 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.52 % Allowed : 26.02 % Favored : 68.46 % 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: -0.07 (0.29), residues: 777 helix: 1.44 (0.27), residues: 365 sheet: -1.04 (0.99), residues: 27 loop : -1.50 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 69 HIS 0.008 0.001 HIS A 417 PHE 0.008 0.001 PHE A 438 TYR 0.015 0.001 TYR A 202 ARG 0.003 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 79 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 169 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.6117 (ttm170) REVERT: A 183 TYR cc_start: 0.5816 (OUTLIER) cc_final: 0.5287 (t80) REVERT: A 438 PHE cc_start: 0.5420 (OUTLIER) cc_final: 0.4980 (t80) REVERT: A 512 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.4430 (t80) outliers start: 38 outliers final: 27 residues processed: 108 average time/residue: 0.1660 time to fit residues: 24.4122 Evaluate side-chains 103 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 72 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.0470 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6590 Z= 0.183 Angle : 0.577 9.957 8949 Z= 0.289 Chirality : 0.041 0.272 924 Planarity : 0.004 0.046 1164 Dihedral : 4.126 21.279 861 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 6.83 % Allowed : 24.56 % Favored : 68.60 % 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: -0.11 (0.29), residues: 777 helix: 1.48 (0.28), residues: 359 sheet: -1.16 (0.99), residues: 27 loop : -1.55 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 69 HIS 0.007 0.001 HIS A 417 PHE 0.008 0.001 PHE B 400 TYR 0.013 0.001 TYR A 385 ARG 0.002 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 76 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 169 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.6116 (ttm170) REVERT: A 183 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.5273 (t80) REVERT: A 203 TRP cc_start: 0.5629 (OUTLIER) cc_final: 0.4968 (m-10) REVERT: A 255 ARG cc_start: 0.4775 (ttt180) cc_final: 0.4561 (tpt170) REVERT: A 401 HIS cc_start: 0.5331 (OUTLIER) cc_final: 0.5065 (m-70) REVERT: A 438 PHE cc_start: 0.5310 (OUTLIER) cc_final: 0.4716 (t80) REVERT: A 512 PHE cc_start: 0.5029 (OUTLIER) cc_final: 0.4454 (t80) outliers start: 47 outliers final: 30 residues processed: 116 average time/residue: 0.1617 time to fit residues: 25.7658 Evaluate side-chains 113 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 77 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6590 Z= 0.186 Angle : 0.584 10.540 8949 Z= 0.293 Chirality : 0.042 0.290 924 Planarity : 0.004 0.045 1164 Dihedral : 4.216 22.241 861 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.96 % Allowed : 25.87 % Favored : 68.17 % 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: -0.14 (0.29), residues: 777 helix: 1.46 (0.28), residues: 359 sheet: -1.27 (1.00), residues: 27 loop : -1.57 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 69 HIS 0.007 0.001 HIS A 417 PHE 0.012 0.001 PHE B 377 TYR 0.013 0.001 TYR A 202 ARG 0.002 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 80 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 169 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6119 (ttm170) REVERT: A 183 TYR cc_start: 0.5884 (OUTLIER) cc_final: 0.5307 (t80) REVERT: A 203 TRP cc_start: 0.5872 (OUTLIER) cc_final: 0.5204 (m-10) REVERT: A 249 MET cc_start: 0.3423 (mmt) cc_final: 0.3137 (mmt) REVERT: A 401 HIS cc_start: 0.5359 (OUTLIER) cc_final: 0.5141 (m-70) REVERT: A 438 PHE cc_start: 0.5206 (OUTLIER) cc_final: 0.4286 (t80) REVERT: A 512 PHE cc_start: 0.5131 (OUTLIER) cc_final: 0.4540 (t80) outliers start: 41 outliers final: 30 residues processed: 114 average time/residue: 0.1735 time to fit residues: 26.9749 Evaluate side-chains 110 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 74 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6590 Z= 0.214 Angle : 0.626 10.179 8949 Z= 0.314 Chirality : 0.043 0.313 924 Planarity : 0.004 0.044 1164 Dihedral : 4.400 24.249 861 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 6.25 % Allowed : 26.45 % Favored : 67.30 % 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: -0.28 (0.29), residues: 777 helix: 1.39 (0.27), residues: 358 sheet: -1.78 (0.87), residues: 32 loop : -1.64 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.006 0.001 HIS A 417 PHE 0.011 0.001 PHE B 377 TYR 0.022 0.001 TYR A 202 ARG 0.004 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 74 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 169 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.6136 (ttm170) REVERT: A 183 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.5459 (t80) REVERT: A 203 TRP cc_start: 0.5948 (OUTLIER) cc_final: 0.5187 (m-10) REVERT: A 401 HIS cc_start: 0.5362 (OUTLIER) cc_final: 0.5096 (m-70) REVERT: A 438 PHE cc_start: 0.5333 (OUTLIER) cc_final: 0.4409 (t80) REVERT: A 512 PHE cc_start: 0.5126 (OUTLIER) cc_final: 0.4482 (t80) outliers start: 43 outliers final: 33 residues processed: 108 average time/residue: 0.1710 time to fit residues: 25.4414 Evaluate side-chains 110 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 71 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6590 Z= 0.237 Angle : 0.651 11.893 8949 Z= 0.328 Chirality : 0.044 0.330 924 Planarity : 0.004 0.044 1164 Dihedral : 4.592 26.177 861 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.25 % Allowed : 26.74 % Favored : 67.01 % 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: -0.45 (0.29), residues: 777 helix: 1.20 (0.27), residues: 362 sheet: -1.72 (0.96), residues: 27 loop : -1.72 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.006 0.001 HIS A 417 PHE 0.012 0.001 PHE B 429 TYR 0.021 0.001 TYR A 202 ARG 0.002 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 72 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 169 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6021 (ttm170) REVERT: A 183 TYR cc_start: 0.5888 (OUTLIER) cc_final: 0.5288 (t80) REVERT: A 203 TRP cc_start: 0.6018 (OUTLIER) cc_final: 0.5227 (m-10) REVERT: A 401 HIS cc_start: 0.5420 (OUTLIER) cc_final: 0.5126 (m-70) REVERT: A 438 PHE cc_start: 0.5383 (OUTLIER) cc_final: 0.4631 (t80) REVERT: A 512 PHE cc_start: 0.5304 (OUTLIER) cc_final: 0.4603 (t80) outliers start: 43 outliers final: 33 residues processed: 108 average time/residue: 0.1763 time to fit residues: 25.7669 Evaluate side-chains 110 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 71 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 0.0670 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6590 Z= 0.186 Angle : 0.615 11.948 8949 Z= 0.307 Chirality : 0.043 0.316 924 Planarity : 0.004 0.044 1164 Dihedral : 4.383 26.183 861 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.23 % Allowed : 27.18 % Favored : 67.59 % 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: -0.32 (0.29), residues: 777 helix: 1.32 (0.27), residues: 358 sheet: -1.58 (1.00), residues: 27 loop : -1.64 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 69 HIS 0.003 0.001 HIS A 373 PHE 0.010 0.001 PHE B 377 TYR 0.023 0.001 TYR A 202 ARG 0.002 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 78 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 169 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6028 (ttm170) REVERT: A 183 TYR cc_start: 0.5938 (OUTLIER) cc_final: 0.5355 (t80) REVERT: A 203 TRP cc_start: 0.5773 (OUTLIER) cc_final: 0.5074 (m-10) REVERT: A 512 PHE cc_start: 0.5058 (OUTLIER) cc_final: 0.4437 (t80) outliers start: 36 outliers final: 31 residues processed: 106 average time/residue: 0.1742 time to fit residues: 25.3954 Evaluate side-chains 112 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 77 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.187973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.170402 restraints weight = 12138.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.172344 restraints weight = 10063.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.173782 restraints weight = 7673.592| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6590 Z= 0.210 Angle : 0.640 11.668 8949 Z= 0.319 Chirality : 0.043 0.315 924 Planarity : 0.004 0.043 1164 Dihedral : 4.444 26.971 861 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.81 % Allowed : 26.60 % Favored : 67.59 % 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: -0.38 (0.29), residues: 777 helix: 1.28 (0.27), residues: 358 sheet: -1.66 (0.99), residues: 27 loop : -1.68 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 69 HIS 0.006 0.001 HIS A 417 PHE 0.010 0.001 PHE B 377 TYR 0.020 0.001 TYR A 202 ARG 0.003 0.000 ARG A 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.87 seconds wall clock time: 34 minutes 31.60 seconds (2071.60 seconds total)