Starting phenix.real_space_refine on Fri Aug 2 19:31:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vac_43088/08_2024/8vac_43088.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vac_43088/08_2024/8vac_43088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vac_43088/08_2024/8vac_43088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vac_43088/08_2024/8vac_43088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vac_43088/08_2024/8vac_43088.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vac_43088/08_2024/8vac_43088.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 2950 2.51 5 N 782 2.21 5 O 895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4669 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4623 Classifications: {'peptide': 581} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 556} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'9TP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.17, per 1000 atoms: 1.11 Number of scatterers: 4669 At special positions: 0 Unit cell: (67.354, 89.994, 95.088, 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 42 16.00 O 895 8.00 N 782 7.00 C 2950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 101 " distance=2.02 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 169 " distance=2.04 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 279 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 448 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " 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: 1.95 Conformation dependent library (CDL) restraints added in 847.5 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 15 through 31 Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 65 through 76 removed outlier: 4.073A pdb=" N THR A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 80 removed outlier: 4.339A pdb=" N LEU A 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 80' Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.997A pdb=" N CYS A 90 " --> pdb=" O MET A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.684A pdb=" N GLU A 100 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 130 through 146 removed outlier: 3.577A pdb=" N PHE A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 Processing helix chain 'A' and resid 174 through 207 removed outlier: 3.513A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.771A pdb=" N GLY A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 223 removed outlier: 3.825A pdb=" N PHE A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 247 Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 268 through 271 Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.997A pdb=" N LYS A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 322 through 338 removed outlier: 3.526A pdb=" N PHE A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 361 Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.285A pdb=" N TYR A 370 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 371 " --> pdb=" O HIS A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 376 through 415 removed outlier: 4.112A pdb=" N LEU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.872A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N TYR A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 438 removed outlier: 4.014A pdb=" N GLY A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.989A pdb=" N CYS A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 517 through 536 Processing helix chain 'A' and resid 540 through 558 Processing helix chain 'A' and resid 563 through 582 319 hydrogen bonds defined for protein. 927 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: 1.30 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 815 1.30 - 1.43: 1163 1.43 - 1.56: 2734 1.56 - 1.70: 5 1.70 - 1.83: 49 Bond restraints: 4766 Sorted by residual: bond pdb=" C14 9TP A 601 " pdb=" O15 9TP A 601 " ideal model delta sigma weight residual 1.337 1.640 -0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C14 9TP A 601 " pdb=" C8 9TP A 601 " ideal model delta sigma weight residual 1.505 1.217 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C8 9TP A 601 " pdb=" C9 9TP A 601 " ideal model delta sigma weight residual 1.513 1.800 -0.287 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C16 9TP A 601 " pdb=" C9 9TP A 601 " ideal model delta sigma weight residual 1.519 1.297 0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C4 9TP A 601 " pdb=" C5 9TP A 601 " ideal model delta sigma weight residual 1.393 1.609 -0.216 2.00e-02 2.50e+03 1.17e+02 ... (remaining 4761 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.36: 121 106.36 - 113.27: 2590 113.27 - 120.18: 1803 120.18 - 127.08: 1880 127.08 - 133.99: 43 Bond angle restraints: 6437 Sorted by residual: angle pdb=" C40 9TP A 601 " pdb=" S1 9TP A 601 " pdb=" C42 9TP A 601 " ideal model delta sigma weight residual 91.72 107.24 -15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C ALA A 364 " pdb=" CA ALA A 364 " pdb=" CB ALA A 364 " ideal model delta sigma weight residual 115.79 110.65 5.14 1.19e+00 7.06e-01 1.87e+01 angle pdb=" C LYS A 359 " pdb=" N CYS A 360 " pdb=" CA CYS A 360 " ideal model delta sigma weight residual 122.42 116.20 6.22 1.77e+00 3.19e-01 1.23e+01 angle pdb=" C MET A 123 " pdb=" N CYS A 124 " pdb=" CA CYS A 124 " ideal model delta sigma weight residual 122.06 115.54 6.52 1.86e+00 2.89e-01 1.23e+01 angle pdb=" C ALA A 553 " pdb=" N PHE A 554 " pdb=" CA PHE A 554 " ideal model delta sigma weight residual 120.68 114.75 5.93 1.70e+00 3.46e-01 1.22e+01 ... (remaining 6432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 2648 17.43 - 34.86: 323 34.86 - 52.28: 61 52.28 - 69.71: 12 69.71 - 87.14: 12 Dihedral angle restraints: 3056 sinusoidal: 1318 harmonic: 1738 Sorted by residual: dihedral pdb=" CB CYS A 360 " pdb=" SG CYS A 360 " pdb=" SG CYS A 369 " pdb=" CB CYS A 369 " ideal model delta sinusoidal sigma weight residual 93.00 175.67 -82.67 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CA CYS A 168 " pdb=" C CYS A 168 " pdb=" N CYS A 169 " pdb=" CA CYS A 169 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual -86.00 -41.68 -44.32 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 3053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 579 0.051 - 0.102: 110 0.102 - 0.153: 19 0.153 - 0.204: 3 0.204 - 0.254: 5 Chirality restraints: 716 Sorted by residual: chirality pdb=" C7 9TP A 601 " pdb=" C17 9TP A 601 " pdb=" C4 9TP A 601 " pdb=" C8 9TP A 601 " both_signs ideal model delta sigma weight residual False 2.52 2.78 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C8 9TP A 601 " pdb=" C14 9TP A 601 " pdb=" C7 9TP A 601 " pdb=" C9 9TP A 601 " both_signs ideal model delta sigma weight residual False 2.40 2.15 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C38 9TP A 601 " pdb=" C40 9TP A 601 " pdb=" O37 9TP A 601 " pdb=" O39 9TP A 601 " both_signs ideal model delta sigma weight residual False 2.26 2.51 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 713 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 485 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 486 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 486 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 486 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 117 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C ARG A 117 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG A 117 " 0.009 2.00e-02 2.50e+03 pdb=" N PRO A 118 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 95 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 96 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " 0.017 5.00e-02 4.00e+02 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 874 2.77 - 3.30: 4771 3.30 - 3.83: 7977 3.83 - 4.37: 8909 4.37 - 4.90: 15393 Nonbonded interactions: 37924 Sorted by model distance: nonbonded pdb=" OG SER A 312 " pdb=" OD1 ASP A 314 " model vdw 2.232 3.040 nonbonded pdb=" O PRO A 113 " pdb=" NH2 ARG A 145 " model vdw 2.296 3.120 nonbonded pdb=" OD1 ASP A 121 " pdb=" NZ LYS A 174 " model vdw 2.322 3.120 nonbonded pdb=" OD1 ASP A 471 " pdb=" N ARG A 472 " model vdw 2.338 3.120 nonbonded pdb=" NH2 ARG A 348 " pdb=" OE2 GLU A 450 " model vdw 2.355 3.120 ... (remaining 37919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 19.880 Find NCS groups from input model: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.012 0.303 4766 Z= 0.810 Angle : 0.786 15.524 6437 Z= 0.375 Chirality : 0.046 0.254 716 Planarity : 0.004 0.041 832 Dihedral : 15.868 87.141 1865 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.36), residues: 579 helix: 1.21 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.16 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 PHE 0.023 0.002 PHE A 502 TYR 0.014 0.002 TYR A 150 ARG 0.008 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.560 Fit side-chains REVERT: A 408 LEU cc_start: 0.9162 (tp) cc_final: 0.8938 (tt) REVERT: A 520 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7772 (mt-10) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1446 time to fit residues: 10.8912 Evaluate side-chains 42 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 405 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4766 Z= 0.232 Angle : 0.617 7.622 6437 Z= 0.311 Chirality : 0.041 0.171 716 Planarity : 0.004 0.036 832 Dihedral : 6.319 52.334 699 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.98 % Allowed : 8.86 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.36), residues: 579 helix: 1.44 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.13 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 146 PHE 0.014 0.002 PHE A 554 TYR 0.017 0.002 TYR A 452 ARG 0.005 0.001 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.526 Fit side-chains REVERT: A 520 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7884 (mm-30) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.1217 time to fit residues: 8.5111 Evaluate side-chains 45 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 474 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 405 ASN A 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4766 Z= 0.219 Angle : 0.571 7.098 6437 Z= 0.292 Chirality : 0.041 0.174 716 Planarity : 0.004 0.033 832 Dihedral : 5.598 43.556 699 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.97 % Allowed : 13.58 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.37), residues: 579 helix: 1.65 (0.26), residues: 410 sheet: None (None), residues: 0 loop : 0.06 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.016 0.002 TYR A 150 ARG 0.005 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.500 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.1109 time to fit residues: 9.5724 Evaluate side-chains 46 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 554 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4766 Z= 0.291 Angle : 0.608 7.835 6437 Z= 0.313 Chirality : 0.042 0.184 716 Planarity : 0.004 0.032 832 Dihedral : 5.102 30.984 699 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.56 % Allowed : 15.55 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.37), residues: 579 helix: 1.52 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -0.06 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.006 0.001 HIS A 146 PHE 0.013 0.002 PHE A 554 TYR 0.020 0.002 TYR A 161 ARG 0.005 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.573 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 0.1134 time to fit residues: 9.0103 Evaluate side-chains 47 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 554 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4766 Z= 0.199 Angle : 0.559 10.508 6437 Z= 0.285 Chirality : 0.040 0.154 716 Planarity : 0.004 0.031 832 Dihedral : 4.608 22.132 699 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.56 % Allowed : 17.72 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.37), residues: 579 helix: 1.67 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.06 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.016 0.002 TYR A 161 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7652 (pm20) outliers start: 13 outliers final: 10 residues processed: 60 average time/residue: 0.1078 time to fit residues: 9.6404 Evaluate side-chains 53 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.0030 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4766 Z= 0.236 Angle : 0.581 9.430 6437 Z= 0.296 Chirality : 0.040 0.157 716 Planarity : 0.004 0.033 832 Dihedral : 4.555 22.283 699 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.56 % Allowed : 19.29 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.37), residues: 579 helix: 1.57 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.07 (0.55), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.016 0.002 TYR A 161 ARG 0.004 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7681 (pm20) outliers start: 13 outliers final: 11 residues processed: 56 average time/residue: 0.1102 time to fit residues: 9.2459 Evaluate side-chains 55 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4766 Z= 0.224 Angle : 0.570 8.708 6437 Z= 0.290 Chirality : 0.040 0.170 716 Planarity : 0.004 0.033 832 Dihedral : 4.471 27.036 699 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.54 % Allowed : 18.31 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.37), residues: 579 helix: 1.57 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.10 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.015 0.001 TYR A 161 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7207 (pm20) cc_final: 0.6983 (mp0) REVERT: A 245 CYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8416 (t) REVERT: A 397 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7728 (pm20) REVERT: A 551 PHE cc_start: 0.8411 (m-80) cc_final: 0.7808 (t80) outliers start: 18 outliers final: 13 residues processed: 63 average time/residue: 0.1220 time to fit residues: 10.9908 Evaluate side-chains 56 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 440 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4766 Z= 0.208 Angle : 0.577 8.653 6437 Z= 0.294 Chirality : 0.040 0.179 716 Planarity : 0.003 0.032 832 Dihedral : 4.464 27.196 699 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.95 % Allowed : 19.09 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.37), residues: 579 helix: 1.58 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.03 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.015 0.001 TYR A 161 ARG 0.004 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 245 CYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8415 (t) REVERT: A 397 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7708 (pm20) outliers start: 15 outliers final: 13 residues processed: 58 average time/residue: 0.1146 time to fit residues: 9.6038 Evaluate side-chains 58 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4766 Z= 0.212 Angle : 0.583 9.048 6437 Z= 0.300 Chirality : 0.040 0.186 716 Planarity : 0.004 0.032 832 Dihedral : 4.458 26.975 699 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.15 % Allowed : 19.29 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.37), residues: 579 helix: 1.57 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.01 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.014 0.002 TYR A 161 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7246 (pm20) cc_final: 0.7010 (pm20) REVERT: A 245 CYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8399 (t) REVERT: A 397 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: A 551 PHE cc_start: 0.8383 (m-80) cc_final: 0.7752 (t80) outliers start: 16 outliers final: 14 residues processed: 56 average time/residue: 0.1204 time to fit residues: 9.8814 Evaluate side-chains 58 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.0040 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4766 Z= 0.197 Angle : 0.574 8.034 6437 Z= 0.294 Chirality : 0.040 0.165 716 Planarity : 0.003 0.032 832 Dihedral : 4.404 26.432 699 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.35 % Allowed : 19.29 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.37), residues: 579 helix: 1.60 (0.26), residues: 415 sheet: None (None), residues: 0 loop : 0.05 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.014 0.002 TYR A 161 ARG 0.003 0.000 ARG A 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7211 (pm20) cc_final: 0.6979 (pm20) REVERT: A 245 CYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8378 (t) REVERT: A 397 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: A 551 PHE cc_start: 0.8351 (m-80) cc_final: 0.7789 (t80) outliers start: 17 outliers final: 15 residues processed: 56 average time/residue: 0.1197 time to fit residues: 9.7481 Evaluate side-chains 57 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 40 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.0000 chunk 40 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.099918 restraints weight = 7900.196| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.75 r_work: 0.3172 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4766 Z= 0.169 Angle : 0.559 7.669 6437 Z= 0.286 Chirality : 0.039 0.163 716 Planarity : 0.003 0.033 832 Dihedral : 4.286 25.106 699 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.56 % Allowed : 19.88 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.37), residues: 579 helix: 1.66 (0.26), residues: 418 sheet: None (None), residues: 0 loop : 0.12 (0.55), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.014 0.001 PHE A 554 TYR 0.014 0.001 TYR A 140 ARG 0.003 0.000 ARG A 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1400.90 seconds wall clock time: 25 minutes 41.13 seconds (1541.13 seconds total)