Starting phenix.real_space_refine on Sat Dec 9 23:38:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/12_2023/8t25_40980.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/12_2023/8t25_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_40980/12_2023/8t25_40980.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/12_2023/8t25_40980.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/12_2023/8t25_40980.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t25_40980/12_2023/8t25_40980.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.85, per 1000 atoms: 0.60 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: 2.29 Conformation dependent library (CDL) restraints added in 1.2 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: 0.50 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: 1.50 Time building geometry restraints manager: 2.49 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: 9.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 27.650 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 19.990 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.230 ------------------------------------------------------------------------------- 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 : 0.740 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 77 average time/residue: 0.2002 time to fit residues: 20.6707 Evaluate side-chains 74 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0789 ------------------------------------------------------------------------------- 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 : 0.761 Fit side-chains outliers start: 25 outliers final: 13 residues processed: 94 average time/residue: 0.1696 time to fit residues: 22.4066 Evaluate side-chains 86 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0634 time to fit residues: 2.5385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 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: 0.0470 chunk 56 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.6003 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6590 Z= 0.185 Angle : 0.564 9.627 8949 Z= 0.283 Chirality : 0.041 0.205 924 Planarity : 0.004 0.059 1164 Dihedral : 4.099 21.324 861 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.07 % Allowed : 25.00 % Favored : 70.93 % 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: -0.02 (0.30), residues: 777 helix: 1.53 (0.28), residues: 359 sheet: -0.65 (0.99), residues: 27 loop : -1.53 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.007 0.001 HIS A 417 PHE 0.008 0.001 PHE A 438 TYR 0.013 0.001 TYR A 385 ARG 0.003 0.000 ARG A 583 *********************** 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 105 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 0.739 Fit side-chains outliers start: 28 outliers final: 11 residues processed: 101 average time/residue: 0.1727 time to fit residues: 24.2197 Evaluate side-chains 84 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0689 time to fit residues: 2.3847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0030 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 75 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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: 0.5987 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6590 Z= 0.173 Angle : 0.558 10.628 8949 Z= 0.280 Chirality : 0.041 0.225 924 Planarity : 0.004 0.053 1164 Dihedral : 4.098 21.216 861 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.20 % Allowed : 26.02 % Favored : 70.78 % 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: -0.04 (0.29), residues: 777 helix: 1.46 (0.27), residues: 365 sheet: -0.80 (0.98), residues: 27 loop : -1.52 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 69 HIS 0.006 0.001 HIS A 417 PHE 0.020 0.001 PHE A 438 TYR 0.019 0.001 TYR A 202 ARG 0.002 0.000 ARG A 169 *********************** 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 103 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.710 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 94 average time/residue: 0.1790 time to fit residues: 23.5927 Evaluate side-chains 88 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0740 time to fit residues: 2.8547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.0030 chunk 52 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 0.0010 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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: 0.5948 moved from start: 0.1095 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= 0.160 Angle : 0.545 9.723 8949 Z= 0.273 Chirality : 0.040 0.237 924 Planarity : 0.004 0.048 1164 Dihedral : 4.012 20.495 861 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.45 % Allowed : 27.18 % Favored : 71.37 % 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: -0.03 (0.29), residues: 777 helix: 1.44 (0.27), residues: 365 sheet: -0.76 (0.99), residues: 27 loop : -1.48 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 69 HIS 0.007 0.001 HIS A 417 PHE 0.019 0.001 PHE A 438 TYR 0.014 0.001 TYR A 202 ARG 0.002 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 90 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.737 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 87 average time/residue: 0.1841 time to fit residues: 22.2286 Evaluate side-chains 78 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1456 time to fit residues: 1.8785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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: 0.6060 moved from start: 0.1449 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= 0.211 Angle : 0.600 9.745 8949 Z= 0.303 Chirality : 0.042 0.269 924 Planarity : 0.004 0.046 1164 Dihedral : 4.289 22.016 861 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.18 % Allowed : 28.20 % Favored : 69.62 % 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: -0.19 (0.29), residues: 777 helix: 1.36 (0.28), residues: 365 sheet: -1.03 (0.97), residues: 27 loop : -1.59 (0.29), residues: 385 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 0.017 0.001 PHE A 438 TYR 0.015 0.001 TYR B 351 ARG 0.002 0.000 ARG A 583 *********************** 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 93 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.711 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 86 average time/residue: 0.1702 time to fit residues: 20.6258 Evaluate side-chains 82 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0633 time to fit residues: 1.5895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.0270 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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: 0.6049 moved from start: 0.1555 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= 0.199 Angle : 0.602 11.154 8949 Z= 0.302 Chirality : 0.042 0.282 924 Planarity : 0.004 0.044 1164 Dihedral : 4.365 23.009 861 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.89 % Allowed : 28.78 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.29), residues: 777 helix: 1.26 (0.27), residues: 365 sheet: -1.23 (1.00), residues: 27 loop : -1.63 (0.29), residues: 385 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 0.017 0.001 PHE A 438 TYR 0.012 0.001 TYR A 202 ARG 0.002 0.000 ARG A 255 *********************** 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 94 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.725 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 88 average time/residue: 0.1932 time to fit residues: 23.1625 Evaluate side-chains 80 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.718 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1554 time to fit residues: 2.4074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.0370 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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: 0.6021 moved from start: 0.1584 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= 0.185 Angle : 0.603 11.084 8949 Z= 0.302 Chirality : 0.042 0.297 924 Planarity : 0.004 0.044 1164 Dihedral : 4.273 24.634 861 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.45 % Allowed : 29.65 % Favored : 68.90 % 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: 1.28 (0.27), residues: 365 sheet: -1.69 (0.89), residues: 32 loop : -1.63 (0.29), residues: 380 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 0.016 0.001 PHE A 438 TYR 0.012 0.001 TYR A 202 ARG 0.003 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 87 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.667 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.1788 time to fit residues: 20.1928 Evaluate side-chains 82 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.685 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0665 time to fit residues: 1.7119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0070 chunk 55 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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: 0.6052 moved from start: 0.1726 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= 0.209 Angle : 0.619 11.462 8949 Z= 0.311 Chirality : 0.043 0.312 924 Planarity : 0.004 0.043 1164 Dihedral : 4.383 25.759 861 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.02 % Allowed : 29.94 % Favored : 69.04 % 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: -0.35 (0.29), residues: 777 helix: 1.32 (0.27), residues: 358 sheet: -1.82 (0.88), residues: 32 loop : -1.67 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 69 HIS 0.007 0.001 HIS A 417 PHE 0.016 0.001 PHE A 438 TYR 0.012 0.001 TYR B 351 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 88 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.720 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 84 average time/residue: 0.1697 time to fit residues: 19.9945 Evaluate side-chains 80 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.730 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0627 time to fit residues: 1.3571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0970 chunk 71 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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: 0.5988 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6590 Z= 0.183 Angle : 0.599 11.852 8949 Z= 0.299 Chirality : 0.043 0.314 924 Planarity : 0.004 0.043 1164 Dihedral : 4.214 25.553 861 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.58 % Allowed : 31.10 % Favored : 68.31 % 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: -0.29 (0.29), residues: 777 helix: 1.31 (0.27), residues: 360 sheet: -1.87 (0.89), residues: 32 loop : -1.58 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 69 HIS 0.003 0.001 HIS A 373 PHE 0.016 0.001 PHE A 438 TYR 0.011 0.001 TYR A 202 ARG 0.004 0.000 ARG A 255 ********************** 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 83 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.773 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 80 average time/residue: 0.1820 time to fit residues: 20.2705 Evaluate side-chains 80 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.773 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0616 time to fit residues: 1.2417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.0970 chunk 61 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.0870 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.1756 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.194322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.175544 restraints weight = 11925.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.178231 restraints weight = 8264.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.179753 restraints weight = 6028.642| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6590 Z= 0.163 Angle : 0.565 11.712 8949 Z= 0.281 Chirality : 0.042 0.302 924 Planarity : 0.004 0.043 1164 Dihedral : 3.951 23.966 861 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.58 % Allowed : 30.81 % 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: -0.17 (0.29), residues: 777 helix: 1.40 (0.27), residues: 360 sheet: -1.83 (0.89), residues: 32 loop : -1.49 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 69 HIS 0.002 0.001 HIS A 373 PHE 0.015 0.001 PHE A 438 TYR 0.012 0.001 TYR A 202 ARG 0.005 0.000 ARG A 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.75 seconds wall clock time: 36 minutes 1.81 seconds (2161.81 seconds total)